@misc{9747, abstract = {Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.}, author = {Lagator, Mato and Morgan, Andrew and Neve, Paul and Colegrave, Nick}, publisher = {Dryad}, title = {{Data from: Role of sex and migration in adaptation to sink environments}}, doi = {10.5061/dryad.s42n1}, year = {2014}, } @article{977, abstract = {We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems.}, author = {Maksym Serbyn and Knap, Michael J and Gopalakrishnan, Sarang and Papić, Zlatko and Yao, Norman Y and Laumann, Chris R and Abanin, Dmitry A and Lukin, Mikhail D and Demler, Eugene A}, journal = {Physical Review Letters}, number = {14}, publisher = {American Physical Society}, title = {{Interferometric probes of many-body localization}}, doi = {10.1103/PhysRevLett.113.147204}, volume = {113}, year = {2014}, } @article{980, abstract = {Many-body localized (MBL) systems are characterized by the absence of transport and thermalization and, therefore, cannot be described by conventional statistical mechanics. In this paper, using analytic arguments and numerical simulations, we study the behavior of local observables in an isolated MBL system following a quantum quench. For the case of a global quench, we find that the local observables reach stationary, highly nonthermal values at long times as a result of slow dephasing characteristic of the MBL phase. These stationary values retain the local memory of the initial state due to the existence of local integrals of motion in the MBL phase. The temporal fluctuations around stationary values exhibit universal power-law decay in time, with an exponent set by the localization length and the diagonal entropy of the initial state. Such a power-law decay holds for any local observable and is related to the logarithmic in time growth of entanglement in the MBL phase. This behavior distinguishes the MBL phase from both the Anderson insulator (where no stationary state is reached) and from the ergodic phase (where relaxation is expected to be exponential). For the case of a local quench, we also find a power-law approach of local observables to their stationary values when the system is prepared in a mixed state. Quench protocols considered in this paper can be naturally implemented in systems of ultracold atoms in disordered optical lattices, and the behavior of local observables provides a direct experimental signature of many-body localization.}, author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {17}, publisher = {American Physical Society}, title = {{Quantum quenches in the many-body localized phase}}, doi = {10.1103/PhysRevB.90.174302}, volume = {90}, year = {2014}, } @article{98, abstract = {Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.}, author = {Higginbotham, Andrew P and Larsen, Thorvald and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles and Kuemmeth, Ferdinand}, journal = {Nano Letters}, number = {6}, pages = {3582 -- 3586}, publisher = {American Chemical Society}, title = {{Hole spin coherence in a Ge/Si heterostructure nanowire}}, doi = {10.1021/nl501242b}, volume = {14}, year = {2014}, } @article{2086, abstract = {Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen - Nosema ceranae (Microsporidia) - on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed.}, author = {Wolf, Stephan and Mcmahon, Dino and Lim, Ka and Pull, Christopher and Clark, Suzanne and Paxton, Robert and Osborne, Juliet}, journal = {PLoS One}, number = {8}, publisher = {Public Library of Science}, title = {{So near and yet so far: Harmonic radar reveals reduced homing ability of Nosema infected honeybees}}, doi = {10.1371/journal.pone.0103989}, volume = {9}, year = {2014}, } @misc{9888, abstract = {Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results.}, author = {Wolf, Stephan and Mcmahon, Dino and Lim, Ka and Pull, Christopher and Clark, Suzanne and Paxton, Robert and Osborne, Juliet}, publisher = {Public Library of Science}, title = {{Supporting information}}, doi = {10.1371/journal.pone.0103989.s003}, year = {2014}, } @article{845, abstract = {Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.}, author = {Seplyarskiy, Vladimir B and Logacheva, Maria D and Penin, Aleksey A and Baranová, Maria A and Leushkin, Evgeny V and Demidenko, Natalia V and Klepikova, Anna V and Fyodor Kondrashov and Kondrashov, Alexey S and James, Timothy Y}, journal = {Molecular Biology and Evolution}, number = {11}, pages = {3016 -- 3025}, publisher = {Oxford University Press}, title = {{Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity}}, doi = {10.1093/molbev/msu242}, volume = {31}, year = {2014}, } @article{892, abstract = {The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution.}, author = {Ivankov, Dmitry N and Finkelstein, Alexei V and Fyodor Kondrashov}, journal = {Current Opinion in Structural Biology}, number = {1}, pages = {104 -- 112}, publisher = {Elsevier}, title = {{A structural perspective of compensatory evolution}}, doi = {10.1016/j.sbi.2014.05.004}, volume = {26}, year = {2014}, } @article{9050, abstract = {Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter.}, author = {Takagi, Daisuke and Palacci, Jérémie A and Braunschweig, Adam B. and Shelley, Michael J. and Zhang, Jun}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {General Chemistry, Condensed Matter Physics}, number = {11}, publisher = {Royal Society of Chemistry }, title = {{Hydrodynamic capture of microswimmers into sphere-bound orbits}}, doi = {10.1039/c3sm52815d}, volume = {10}, year = {2014}, } @article{9166, abstract = {Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles.}, author = {Palacci, Jérémie A and Sacanna, S. and Kim, S.-H. and Yi, G.-R. and Pine, D. J. and Chaikin, P. M.}, issn = {1471-2962}, journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, keywords = {General Engineering, General Physics and Astronomy, General Mathematics}, number = {2029}, publisher = {The Royal Society}, title = {{Light-activated self-propelled colloids}}, doi = {10.1098/rsta.2013.0372}, volume = {372}, year = {2014}, } @article{926, abstract = {The regulation of cell growth in animal tissues is a question of critical importance: most tissues contain different types of cells in interconversion and the fraction of each type has to be controlled in a precise way, by mechanisms that remain unclear. Here, we provide a theoretical framework for the homeostasis of stem-cell-containing epithelial tissues using mechanical equations, which describe the size of the tissue and kinetic equations, which describe the interconversions of the cell populations. We show that several features, such as the evolution of stem cell fractions during intestinal development, the shape of a developing intestinal wall, as well as the increase in the proliferative compartment in cancer initiation, can be studied and understood from generic modelling which does not rely on a particular regulatory mechanism. Finally, inspired by recent experiments, we propose a model where cell division rates are regulated by the mechanical stresses in the epithelial sheet. We show that pressure-controlled growth can, in addition to the previous features, also explain with few parameters the formation of stem cell compartments as well as the morphologies observed when a colonic crypt becomes cancerous. We also discuss optimal strategies of wound healing, in connection with experiments on the cornea.}, author = {Hannezo, Edouard B and Prost, Jacques and Joanny, Jean}, journal = {Journal of the Royal Society Interface}, number = {93}, publisher = {Royal Society of London}, title = {{Growth homeostatic regulation and stem cell dynamics in tissues}}, doi = {10.1098/rsif.2013.0895}, volume = {11}, year = {2014}, } @article{9458, abstract = {Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.}, author = {Huff, Jason T. and Zilberman, Daniel}, issn = {1097-4172}, journal = {Cell}, number = {6}, pages = {1286--1297}, publisher = {Elsevier}, title = {{Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes}}, doi = {10.1016/j.cell.2014.01.029}, volume = {156}, year = {2014}, } @article{9479, abstract = {Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.}, author = {Mérai, Zsuzsanna and Chumak, Nina and García-Aguilar, Marcelina and Hsieh, Tzung-Fu and Nishimura, Toshiro and Schoft, Vera K. and Bindics, János and Ślusarz, Lucyna and Arnoux, Stéphanie and Opravil, Susanne and Mechtler, Karl and Zilberman, Daniel and Fischer, Robert L. and Tamaru, Hisashi}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {45}, pages = {16166--16171}, publisher = {National Academy of Sciences}, title = {{The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes}}, doi = {10.1073/pnas.1418564111}, volume = {111}, year = {2014}, } @article{9662, abstract = {Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.}, author = {Cheng, Bingqing and Ceriotti, Michele}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, number = {24}, publisher = {AIP Publishing}, title = {{Direct path integral estimators for isotope fractionation ratios}}, doi = {10.1063/1.4904293}, volume = {141}, year = {2014}, } @article{97, abstract = {The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).}, author = {Higginbotham, Andrew P and Kuemmeth, Ferdinand and Larsen, Thorvald and Fitzpatrick, Mattias and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles}, journal = {APS Physics, Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Antilocalization of coulomb blockade in a Ge/Si nanowire}}, doi = {10.1103/PhysRevLett.112.216806}, volume = {112}, year = {2014}, } @article{2004, abstract = {We have assembled a network of cell-fate determining transcription factors that play a key role in the specification of the ventral neuronal subtypes of the spinal cord on the basis of published transcriptional interactions. Asynchronous Boolean modelling of the network was used to compare simulation results with reported experimental observations. Such comparison highlighted the need to include additional regulatory connections in order to obtain the fixed point attractors of the model associated with the five known progenitor cell types located in the ventral spinal cord. The revised gene regulatory network reproduced previously observed cell state switches between progenitor cells observed in knock-out animal models or in experiments where the transcription factors were overexpressed. Furthermore the network predicted the inhibition of Irx3 by Nkx2.2 and this prediction was tested experimentally. Our results provide evidence for the existence of an as yet undescribed inhibitory connection which could potentially have significance beyond the ventral spinal cord. The work presented in this paper demonstrates the strength of Boolean modelling for identifying gene regulatory networks.}, author = {Lovrics, Anna and Gao, Yu and Juhász, Bianka and Bock, István and Byrne, Helen and Dinnyés, András and Kovács, Krisztián}, journal = {PLoS One}, number = {11}, publisher = {Public Library of Science}, title = {{Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord}}, doi = {10.1371/journal.pone.0111430}, volume = {9}, year = {2014}, } @misc{9722, author = {Lovrics, Anna and Gao, Yu and Juhász, Bianka and Bock, István and Byrne, Helen M. and Dinnyés, András and Kovács, Krisztián}, publisher = {Public Library of Science}, title = {{Transition probability between TF expression states when Dbx2 inhibits Nkx2.2}}, doi = {10.1371/journal.pone.0111430.s006}, year = {2014}, } @article{2039, abstract = {A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time.}, author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Adlam, Ben and Nowak, Martin}, journal = {PLoS Computational Biology}, number = {9}, publisher = {Public Library of Science}, title = {{The time scale of evolutionary innovation}}, doi = {10.1371/journal.pcbi.1003818}, volume = {10}, year = {2014}, } @article{2161, abstract = {Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.}, author = {Westhus, Claudia and Ugelvig, Line V and Tourdot, Edouard and Heinze, Jürgen and Doums, Claudie and Cremer, Sylvia}, issn = {0340-5443}, journal = {Behavioral Ecology and Sociobiology}, number = {10}, pages = {1701 -- 1710}, publisher = {Springer}, title = {{Increased grooming after repeated brood care provides sanitary benefits in a clonal ant}}, doi = {10.1007/s00265-014-1778-8}, volume = {68}, year = {2014}, } @article{2036, abstract = { In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. }, author = {Lagator, Mato and Colegrave, Nick and Neve, Paul}, journal = {Proceedings of the Royal Society of London Series B Biological Sciences}, number = {1794}, publisher = {Royal Society, The}, title = {{Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses}}, doi = {10.1098/rspb.2014.1679}, volume = {281}, year = {2014}, } @misc{9740, abstract = {The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.}, author = {Konrad, Matthias and Grasse, Anna V and Tragust, Simon and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host}}, doi = {10.5061/dryad.vm0vc}, year = {2014}, } @misc{9741, abstract = {In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.}, author = {Lagator, Mato and Colegrave, Nick and Neve, Paul}, publisher = {Dryad}, title = {{Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses}}, doi = {10.5061/dryad.85dn7}, year = {2014}, } @misc{9739, author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Adlam, Ben and Novak, Martin}, publisher = {Public Library of Science}, title = {{Detailed proofs for “The time scale of evolutionary innovation”}}, doi = {10.1371/journal.pcbi.1003818.s001}, year = {2014}, } @article{2170, abstract = { Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate between recent, nonequilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning the Western Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.}, author = {Hearn, Jack and Stone, Graham and Bunnefeld, Lynsey and Nicholls, James and Barton, Nicholas H and Lohse, Konrad}, journal = {Molecular Ecology}, number = {1}, pages = {198 -- 211}, publisher = {Wiley-Blackwell}, title = {{Likelihood-based inference of population history from low-coverage de novo genome assemblies}}, doi = {10.1111/mec.12578}, volume = {23}, year = {2014}, } @misc{9753, abstract = {Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.}, author = {Tragust, Simon and Ugelvig, Line V and Chapuisat, Michel and Heinze, Jürgen and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies}}, doi = {10.5061/dryad.nc0gc}, year = {2014}, } @misc{9752, abstract = {Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.}, author = {Simmons, Kristina and Prentice, Jason and Tkačik, Gašper and Homann, Jan and Yee, Heather and Palmer, Stephanie and Nelson, Philip and Balasubramanian, Vijay}, publisher = {Dryad}, title = {{Data from: Transformation of stimulus correlations by the retina}}, doi = {10.5061/dryad.246qg}, year = {2014}, } @article{978, abstract = {The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications.}, author = {Zeljkovic, Ilija and Okada, Yoshinori and Huang, Chengyi and Sankar, Raman and Walkup, Daniel and Zhou, Wenwen and Maksym Serbyn and Chou, Fangcheng and Tsai, Wei-Feng and Lin, Hsin and Bansil, Arun and Fu, Liang and Hasan, Md Z and Madhavan, Vidya}, journal = {Nature Physics}, number = {8}, pages = {572 -- 577}, publisher = {Nature Publishing Group}, title = {{Mapping the unconventional orbital texture in topological crystalline insulators}}, doi = {10.1038/nphys3012}, volume = {10}, year = {2014}, } @article{979, abstract = {In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators.}, author = {Maksym Serbyn and Fu, Liang}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {3}, publisher = {American Physical Society}, title = {{Symmetry breaking and Landau quantization in topological crystalline insulators}}, doi = {10.1103/PhysRevB.90.035402}, volume = {90}, year = {2014}, } @article{9931, abstract = {Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.}, author = {Dhar, Riddhiman and Bergmiller, Tobias and Wagner, Andreas}, issn = {1558-5646}, journal = {Evolution}, number = {6}, pages = {1775--1791}, publisher = {Wiley}, title = {{Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes}}, doi = {10.1111/evo.12373}, volume = {68}, year = {2014}, } @misc{9932, abstract = {Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region.}, author = {Dhar, Riddhiman and Bergmiller, Tobias and Wagner, Andreas}, publisher = {Dryad}, title = {{Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes}}, doi = {10.5061/dryad.jc402}, year = {2014}, } @article{12637, abstract = {The performance of glaciohydrological models which simulate catchment response to climate variability depends to a large degree on the data used to force the models. The forcing data become increasingly important in high-elevation, glacierized catchments where the interplay between extreme topography, climate, and the cryosphere is complex. It is challenging to generate a reliable forcing data set that captures this spatial heterogeneity. In this paper, we analyze the results of a 1 year field campaign focusing on air temperature and precipitation observations in the Langtang valley in the Nepalese Himalayas. We use the observed time series to characterize both temperature lapse rates (LRs) and precipitation gradients (PGs). We study their spatial and temporal variability, and we attempt to identify possible controlling factors. We show that very clear LRs exist in the valley and that there are strong seasonal differences related to the water vapor content in the atmosphere. Results also show that the LRs are generally shallower than the commonly used environmental lapse rates. The analysis of the precipitation observations reveals that there is great variability in precipitation over short horizontal distances. A uniform valley wide PG cannot be established, and several scale-dependent mechanisms may explain our observations. We complete our analysis by showing the impact of the observed LRs and PGs on the outputs of the TOPKAPI-ETH glaciohydrological model. We conclude that LRs and PGs have a very large impact on the water balance composition and that short-term monitoring campaigns have the potential to improve model quality considerably.}, author = {Immerzeel, W. W. and Petersen, L. and Ragettli, S. and Pellicciotti, Francesca}, issn = {1944-7973}, journal = {Water Resources Research}, keywords = {Water Science and Technology}, number = {3}, pages = {2212--2226}, publisher = {American Geophysical Union}, title = {{The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas}}, doi = {10.1002/2013wr014506}, volume = {50}, year = {2014}, } @article{12636, abstract = {Himalayan glacier tongues are commonly debris covered and they are an important source of melt water. However, they remain relatively unstudied because of the inaccessibility of the terrain and the difficulties in field work caused by the thick debris mantles. Observations of debris-covered glaciers are therefore scarce and airborne remote sensing may bridge the gap between scarce field observations and coarse resolution space-borne remote sensing. In this study we deploy an Unmanned Aerial Vehicle (UAV) before and after the melt and monsoon season (May and October 2013) over the debris-covered tongue of the Lirung Glacier in Nepal. Based on stereo-imaging and the structure for motion algorithm we derive highly detailed ortho-mosaics and digital elevation models (DEMs), which we geometrically correct using differential GPS observations collected in the field. Based on DEM differencing and manual feature tracking we derive the mass loss and the surface velocity of the glacier at a high spatial accuracy. On average, mass loss is limited and the surface velocity is very small. However, the spatial variability of melt rates is very high, and ice cliffs and supra-glacial ponds show mass losses that can be an order of magnitude higher than the average. We suggest that future research should focus on the interaction between supra-glacial ponds, ice cliffs and englacial hydrology to further understand the dynamics of debris-covered glaciers. Finally, we conclude that UAV deployment has large potential in glaciology and it may revolutionize methods currently applied in studying glacier surface features.}, author = {Immerzeel, W.W. and Kraaijenbrink, P.D.A. and Shea, J.M. and Shrestha, A.B. and Pellicciotti, Francesca and Bierkens, M.F.P. and de Jong, S.M.}, issn = {0034-4257}, journal = {Remote Sensing of Environment}, keywords = {Computers in Earth Sciences, Geology, Soil Science}, number = {7}, pages = {93--103}, publisher = {Elsevier}, title = {{High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles}}, doi = {10.1016/j.rse.2014.04.025}, volume = {150}, year = {2014}, } @article{12635, abstract = {Switzerland is one of the countries with some of the longest and best glaciological data sets. Its glaciers and their changes in response to climate have been extensively investigated, and the number and quality of related studies are notable. However, a comprehensive review of glacier changes and their impact on the hydrology of glacierised catchments for Switzerland is missing and we use the opportunity provided by the EU-FP7 ACQWA project to review the current state of knowledge about past changes and future projections. We examine the type of models that have been applied to infer glacier evolution and identify knowledge gaps that should be addressed in future research in addition to those indicated in previous publications. Common characteristics in long-term series of projected future glacier runoff are an initial peak followed by a decline, associated with shifts in seasonality, earlier melt onset and reduced summer runoff. However, the quantitative predictions are difficult to compare, as studies differ in terms of model structure, calibration strategies, input data, temporal and spatial resolution as well as future scenarios used for impact studies. We identify two sources of uncertainties among those emerging from recent research, and use simulations over four glaciers to: i) quantify the importance of the correct extrapolation of air temperature, and ii) point at the key role played by debris cover in modulating glacier response.}, author = {Pellicciotti, Francesca and Carenzo, M. and Bordoy, R. and Stoffel, M.}, issn = {0048-9697}, journal = {Science of The Total Environment}, keywords = {Pollution, Waste Management and Disposal, Environmental Chemistry, Environmental Engineering}, pages = {1152--1170}, publisher = {Elsevier}, title = {{Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research}}, doi = {10.1016/j.scitotenv.2014.04.022}, volume = {493}, year = {2014}, } @article{12632, abstract = {We investigate the performance of five glacier melt models over a multi-decadal period in order to assess their ability to model future glacier response. The models range from a simple degree-day model, based solely on air temperature, to more-sophisticated models, including the full shortwave radiation balance. In addition to the empirical models, the performance of a physically based energy-balance (EB) model is examined. The melt models are coupled to an accumulation and a surface evolution model and applied in a distributed manner to Rhonegletscher, Switzerland, over the period 1929–2012 at hourly resolution. For calibration, seasonal mass-balance measurements (2006–12) are used. Decadal ice volume changes for six periods in the years 1929–2012 serve for model validation. Over the period 2006–12, there are almost no differences in performance between the models, except for EB, which is less consistent with observations, likely due to lack of meteorological in situ data. However, simulations over the long term (1929–2012) reveal that models which include a separate term for shortwave radiation agree best with the observed ice volume changes, indicating that their melt relationships are robust in time and thus suitable for long-term modelling, in contrast to more empirical approaches that are oversensitive to temperature fluctuations.}, author = {Gabbi, Jeannette and Carenzo, Marco and Pellicciotti, Francesca and Bauder, Andreas and Funk, Martin}, issn = {1727-5652}, journal = {Journal of Glaciology}, keywords = {Earth-Surface Processes}, number = {224}, pages = {1140--1154}, publisher = {International Glaciological Society}, title = {{A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response}}, doi = {10.3189/2014jog14j011}, volume = {60}, year = {2014}, } @article{12634, abstract = {Glaciers in the Andes of Chile seem to be shrinking and possibly loosing mass, but the number and types of studies conducted, constrained mainly by data availability, are not sufficient to provide a synopsis of glacier changes for the past or future or explain in an explicit way causes of the observed changes. In this paper, we provide a systematic review of changes in glaciers for the entire country, followed by a discussion of the studies that have provided evidence of such changes. We identify a missing type of work in distributed, physically-oriented modelling studies that are needed to bridge the gap between the numerous remote sensing studies and the specific, point scale works focused on process understanding. We use an advanced mass balance model applied to one of the best monitored glaciers in the region to investigate four main research issues that should be addressed in modelling studies for a sound assessment of glacier changes: 1) the use of physically-based models of glacier ablation (energy balance models) versus more empirical models (enhanced temperature index approaches); 2) the importance of the correct extrapolation of air temperature forcing on glaciers and in high elevation areas and the large uncertainty in model outputs associated with it; 3) the role played by snow gravitational redistribution; and 4) the uncertainty associated with future climate scenarios. We quantify differences in model outputs associated with each of these choices, and conclude with suggestions for future work directions.}, author = {Pellicciotti, Francesca and Ragettli, S. and Carenzo, M. and McPhee, J.}, issn = {0048-9697}, journal = {Science of The Total Environment}, keywords = {Pollution, Waste Management and Disposal, Environmental Chemistry, Environmental Engineering}, pages = {1197--1210}, publisher = {Elsevier}, title = {{Changes of glaciers in the Andes of Chile and priorities for future work}}, doi = {10.1016/j.scitotenv.2013.10.055}, volume = {493}, year = {2014}, } @article{13399, abstract = {Nature has long inspired scientists with its seemingly unlimited ability to harness solar energy and to utilize it to drive various physiological processes. With the help of man-made molecular photoswitches, we now have the potential to outperform natural systems in many ways, with the ultimate goal of fabricating multifunctional materials that operate at different light wavelengths. An important challenge in developing light-controlled artificial molecular machines lies in attaining a detailed understanding of the photoisomerization-coupled conformational changes that occur in macromolecules and molecular assemblies. In this issue of ACS Nano, Bléger, Rabe, and co-workers use force microscopy to provide interesting insights into the behavior of individual photoresponsive molecules and to identify contraction, extension, and crawling events accompanying light-induced isomerization.}, author = {Kundu, Pintu K. and Klajn, Rafal}, issn = {1936-086X}, journal = {ACS Nano}, keywords = {General Physics and Astronomy, General Engineering, General Materials Science}, number = {12}, pages = {11913--11916}, publisher = {American Chemical Society}, title = {{Watching single molecules move in response to light}}, doi = {10.1021/nn506656r}, volume = {8}, year = {2014}, } @article{13402, abstract = {Nanoporous frameworks are polymeric materials built from rigid molecules, which give rise to their nanoporous structures with applications in gas sorption and storage, catalysis and others. Conceptually new applications could emerge, should these beneficial properties be manipulated by external stimuli in a reversible manner. One approach to render nanoporous frameworks responsive to external signals would be to immobilize molecular switches within their nanopores. Although the majority of molecular switches require conformational freedom to isomerize, and switching in the solid state is prohibited, the nanopores may provide enough room for the switches to efficiently isomerize. Here we describe two families of nanoporous materials incorporating the spiropyran molecular switch. These materials exhibit a variety of interesting properties, including reversible photochromism and acidochromism under solvent-free conditions, light-controlled capture and release of metal ions, as well reversible chromism induced by solvation/desolvation.}, author = {Kundu, Pintu K. and Olsen, Gregory L. and Kiss, Vladimir and Klajn, Rafal}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary}, publisher = {Springer Nature}, title = {{Nanoporous frameworks exhibiting multiple stimuli responsiveness}}, doi = {10.1038/ncomms4588}, volume = {5}, year = {2014}, } @article{13400, abstract = {Organizing inorganic nanocrystals into complex architectures is challenging and typically relies on preexisting templates, such as properly folded DNA or polypeptide chains. We found that under carefully controlled conditions, cubic nanocrystals of magnetite self-assemble into arrays of helical superstructures in a template-free manner with >99% yield. Computer simulations revealed that the formation of helices is determined by the interplay of van der Waals and magnetic dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed to spontaneous formation of chiral nanocube clusters. Neighboring helices within their densely packed ensembles tended to adopt the same handedness in order to maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality amplification.}, author = {Singh, Gurvinder and Chan, Henry and Baskin, Artem and Gelman, Elijah and Repnin, Nikita and Král, Petr and Klajn, Rafal}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6201}, pages = {1149--1153}, publisher = {American Association for the Advancement of Science}, title = {{Self-assembly of magnetite nanocubes into helical superstructures}}, doi = {10.1126/science.1254132}, volume = {345}, year = {2014}, } @article{13404, abstract = {In the past few years, spiropyran has emerged as the molecule-of-choice for the construction of novel dynamic materials. This unique molecular switch undergoes structural isomerisation in response to a variety of orthogonal stimuli, e.g. light, temperature, metal ions, redox potential, and mechanical stress. Incorporation of this switch onto macromolecular supports or inorganic scaffolds allows for the creation of robust dynamic materials. This review discusses the synthesis, switching conditions, and use of dynamic materials in which spiropyran has been attached to the surfaces of polymers, biomacromolecules, inorganic nanoparticles, as well as solid surfaces. The resulting materials show fascinating properties whereby the state of the switch intimately affects a multitude of useful properties of the support. The utility of the spiropyran switch will undoubtedly endow these materials with far-reaching applications in the near future.}, author = {Klajn, Rafal}, issn = {1460-4744}, journal = {Chemical Society Reviews}, keywords = {General Chemistry}, number = {1}, pages = {148--184}, publisher = {Royal Society of Chemistry}, title = {{Spiropyran-based dynamic materials}}, doi = {10.1039/c3cs60181a}, volume = {43}, year = {2014}, } @article{13401, abstract = {A compound combining the features of a molecular rotor and a photoswitch was synthesized and was shown to exist as three diastereomers, which interconvert via a reversible cyclic reaction scheme. Each of the three diastereomers was isolated, and by following the equilibration kinetics, activation barriers for all reactions were calculated. The results indicate that the properties of molecular switches depend heavily on their immediate chemical environment. The conclusions are important in the context of designing new switchable molecules and materials.}, author = {Kundu, Pintu K. and Lerner, Avishai and Kučanda, Kristina and Leitus, Gregory and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {32}, pages = {11276--11279}, publisher = {American Chemical Society}, title = {{Cyclic kinetics during thermal equilibration of an axially chiral bis-spiropyran}}, doi = {10.1021/ja505948q}, volume = {136}, year = {2014}, } @article{13403, abstract = {We show that bimolecular reactions between species confined to the surfaces of nanoparticles can be manipulated by the nature of the linker, as well as by the curvature of the underlying particles.}, author = {Zdobinsky, Tino and Sankar Maiti, Pradipta and Klajn, Rafal}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {7}, pages = {2711--2714}, publisher = {American Chemical Society}, title = {{Support curvature and conformational freedom control chemical reactivity of immobilized species}}, doi = {10.1021/ja411573a}, volume = {136}, year = {2014}, } @article{14018, abstract = {The sensitivities of high-harmonic generation (HHG) and strong-field ionization (SFI) to coupled electronic and nuclear dynamics are studied, using the nitric oxide (NO) molecule as an example. A coherent superposition of electronic and rotational states of NO is prepared by impulsive stimulated Raman scattering and probed by simultaneous detection of HHG and SFI yields. We observe a fourfold higher sensitivity of high-harmonic generation to electronic dynamics and attribute it to the presence of inelastic quantum paths connecting coherently related electronic states [Kraus et al., Phys. Rev. Lett.111, 243005 (2013)]. Whereas different harmonic orders display very different sensitivities to rotational or electronic dynamics, strong-field ionization is found to be most sensitive to electronic motion. We introduce a general theoretical formalism for high-harmonic generation from coupled nuclear-electronic wave packets. We show that the unequal sensitivities of different harmonic orders to electronic or rotational dynamics result from the angle dependence of the photorecombination matrix elements which encode several autoionizing and shape resonances in the photoionization continuum of NO. We further study the dependence of rotational and electronic coherences on the intensity of the excitation pulse and support the observations with calculations.}, author = {Baykusheva, Denitsa Rangelova and Kraus, Peter M. and Zhang, Song Bin and Rohringer, Nina and Wörner, Hans Jakob}, issn = {1364-5498}, journal = {Faraday Discussions}, keywords = {Physical and Theoretical Chemistry}, pages = {113--132}, publisher = {Royal Society of Chemistry}, title = {{The sensitivities of high-harmonic generation and strong-field ionization to coupled electronic and nuclear dynamics}}, doi = {10.1039/c4fd00018h}, volume = {171}, year = {2014}, } @article{14019, abstract = {The cyclopropene radical cation (c-C3H₄⁺) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X⁺ (2)B2 ground electronic state of c-C3H₄⁺ at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C(2v)-symmetric R0 structure for the ground electronic state of c-C3H₄⁺. Two vibrational modes of c-C3H₄⁺ are found to have vibrational wave numbers below 300 cm(-1), which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm(-1) in c-C3H₄⁺) to the CH2 torsional mode (ν₈⁺, A2 symmetry) and of the second-lowest-frequency mode (≈210 cm(-1) in c-C3H₄⁺) to a mode combining a CH out-of-plane with a CH2 rocking motion (ν₁₅⁺, B2 symmetry). The potential energy along the CH2 torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.}, author = {Vasilatou, K. and Michaud, J. M. and Baykusheva, Denitsa Rangelova and Grassi, G. and Merkt, F.}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {6}, publisher = {AIP Publishing}, title = {{The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra}}, doi = {10.1063/1.4890744}, volume = {141}, year = {2014}, } @article{14021, abstract = {We present the detailed analysis of a new two-pulse orientation scheme that achieves macroscopic field-free orientation at the high particle densities required for attosecond and high-harmonic spectroscopies (Kraus et al 2013 arXiv:1311.3923). Carbon monoxide molecules are oriented by combining one-colour and delayed two-colour non-resonant femtosecond laser pulses. High-harmonic generation is used to probe the oriented wave-packet dynamics and reveals that a very high degree of orientation (Nup/Ntotal = 0.73–0.82) is achieved. We further extend this approach to orienting carbonyl sulphide molecules. We show that the present two-pulse scheme selectively enhances orientation created by the hyperpolarizability interaction whereas the ionization-depletion mechanism plays no role. We further control and optimize orientation through the delay between the one- and two-colour pump pulses. Finally, we demonstrate a complementary encoding of electronic-structure features, such as shape resonances, in the even- and odd-harmonic spectrum. The achieved progress makes two-pulse field-free orientation an attractive tool for a broad class of time-resolved measurements.}, author = {Kraus, P M and Baykusheva, Denitsa Rangelova and Wörner, H J}, issn = {1361-6455}, journal = {Journal of Physics B: Atomic, Molecular and Optical Physics}, keywords = {Condensed Matter Physics, Atomic and Molecular Physics, and Optics}, number = {12}, publisher = {IOP Publishing}, title = {{Two-pulse orientation dynamics and high-harmonic spectroscopy of strongly-oriented molecules}}, doi = {10.1088/0953-4075/47/12/124030}, volume = {47}, year = {2014}, } @article{14020, abstract = {We report the observation of macroscopic field-free orientation, i.e., more than 73% of CO molecules pointing in the same direction. This is achieved through an all-optical scheme operating at high particle densities (>10(17)  cm(-3)) that combines one-color (ω) and two-color (ω+2ω) nonresonant femtosecond laser pulses. We show that the achieved orientation solely relies on the hyperpolarizability interaction as opposed to an ionization-depletion mechanism, thus, opening a wide range of applications. The achieved strong orientation enables us to reveal the molecular-frame anisotropies of the photorecombination amplitudes and phases caused by a shape resonance. The resonance appears as a local maximum in the even-harmonic emission around 28 eV. In contrast, the odd-harmonic emission is suppressed in this spectral region through the combined effects of an asymmetric photorecombination phase and a subcycle Stark effect, generic for polar molecules, that we experimentally identify.}, author = {Kraus, P. M. and Baykusheva, Denitsa Rangelova and Wörner, H. J.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {2}, publisher = {American Physical Society}, title = {{Two-pulse field-free orientation reveals anisotropy of molecular shape resonance}}, doi = {10.1103/physrevlett.113.023001}, volume = {113}, year = {2014}, } @article{535, abstract = {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. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms 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 worst-case instances on which 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 the graph structure does not necessarily help.}, author = {Chatterjee, Krishnendu and Henzinger, Monika H and Krinninger, Sebastian and Nanongkai, Danupon}, journal = {Algorithmica}, number = {3}, pages = {457 -- 492}, publisher = {Springer}, title = {{Polynomial-time algorithms for energy games with special weight structures}}, doi = {10.1007/s00453-013-9843-7}, volume = {70}, year = {2014}, } @inproceedings{10886, abstract = {We propose a method for visualizing two-dimensional symmetric positive definite tensor fields using the Heat Kernel Signature (HKS). The HKS is derived from the heat kernel and was originally introduced as an isometry invariant shape signature. Each positive definite tensor field defines a Riemannian manifold by considering the tensor field as a Riemannian metric. On this Riemmanian manifold we can apply the definition of the HKS. The resulting scalar quantity is used for the visualization of tensor fields. The HKS is closely related to the Gaussian curvature of the Riemannian manifold and the time parameter of the heat kernel allows a multiscale analysis in a natural way. In this way, the HKS represents field related scale space properties, enabling a level of detail analysis of tensor fields. This makes the HKS an interesting new scalar quantity for tensor fields, which differs significantly from usual tensor invariants like the trace or the determinant. A method for visualization and a numerical realization of the HKS for tensor fields is proposed in this chapter. To validate the approach we apply it to some illustrating simple examples as isolated critical points and to a medical diffusion tensor data set.}, author = {Zobel, Valentin and Reininghaus, Jan and Hotz, Ingrid}, booktitle = {Topological Methods in Data Analysis and Visualization III }, isbn = {9783319040981}, issn = {2197-666X}, pages = {249--262}, publisher = {Springer}, title = {{Visualization of two-dimensional symmetric positive definite tensor fields using the heat kernel signature}}, doi = {10.1007/978-3-319-04099-8_16}, year = {2014}, } @inbook{6178, abstract = {Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo.}, author = {Smutny, Michael and Behrndt, Martin and Campinho, Pedro and Ruprecht, Verena and Heisenberg, Carl-Philipp J}, booktitle = {Tissue Morphogenesis}, editor = {Nelson, Celeste}, isbn = {9781493911639}, issn = {1940-6029}, pages = {219--235}, publisher = {Springer}, title = {{UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo}}, doi = {10.1007/978-1-4939-1164-6_15}, volume = {1189}, year = {2014}, } @article{10814, abstract = {We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field.}, author = {Seiringer, Robert}, issn = {1869-7135}, journal = {Jahresbericht der Deutschen Mathematiker-Vereinigung}, keywords = {General Medicine}, pages = {21--41}, publisher = {Springer Nature}, title = {{The excitation spectrum for Bose fluids with weak interactions}}, doi = {10.1365/s13291-014-0083-9}, volume = {116}, year = {2014}, } @inbook{10817, abstract = {The Morse-Smale complex can be either explicitly or implicitly represented. Depending on the type of representation, the simplification of the Morse-Smale complex works differently. In the explicit representation, the Morse-Smale complex is directly simplified by explicitly reconnecting the critical points during the simplification. In the implicit representation, on the other hand, the Morse-Smale complex is given by a combinatorial gradient field. In this setting, the simplification changes the combinatorial flow, which yields an indirect simplification of the Morse-Smale complex. The topological complexity of the Morse-Smale complex is reduced in both representations. However, the simplifications generally yield different results. In this chapter, we emphasize properties of the two representations that cause these differences. We also provide a complexity analysis of the two schemes with respect to running time and memory consumption.}, author = {Günther, David and Reininghaus, Jan and Seidel, Hans-Peter and Weinkauf, Tino}, booktitle = {Topological Methods in Data Analysis and Visualization III.}, editor = {Bremer, Peer-Timo and Hotz, Ingrid and Pascucci, Valerio and Peikert, Ronald}, isbn = {9783319040981}, issn = {2197-666X}, pages = {135--150}, publisher = {Springer Nature}, title = {{Notes on the simplification of the Morse-Smale complex}}, doi = {10.1007/978-3-319-04099-8_9}, year = {2014}, } @phdthesis{1395, abstract = {In this thesis I studied various individual and social immune defences employed by the invasive garden ant Lasius neglectus mostly against entomopathogenic fungi. The first two chapters of this thesis address the phenomenon of 'social immunisation'. Social immunisation, that is the immunological protection of group members due to social contact to a pathogen-exposed nestmate, has been described in various social insect species against different types of pathogens. However, in the case of entomopathogenic fungi it has, so far, only been demonstrated that social immunisation exists at all. Its underlying mechanisms r any other properties were, however, unknown. In the first chapter of this thesis I identified the mechanistic basis of social immunisation in L. neglectus against the entomopathogenous fungus Metarhizium. I could show that nestmates of a pathogen-exposed individual contract low-level infections due to social interactions. These low-level infections are, however, non-lethal and cause an active stimulation of the immune system, which protects the nestmates upon subsequent pathogen encounters. In the second chapter of this thesis I investigated the specificity and colony level effects of social immunisation. I demonstrated that the protection conferred by social immunisation is highly specific, protecting ants only against the same pathogen strain. In addition, depending on the respective context, social immunisation may even cause fitness costs. I further showed that social immunisation crucially affects sanitary behaviour and disease dynamics within ant groups. In the third chapter of this thesis I studied the effects of the ectosymbiotic fungus Laboulbenia formicarum on its host L. neglectus. Although Laboulbeniales are the largest order of insect-parasitic fungi, research concerning host fitness consequence is sparse. I showed that highly Laboulbenia-infected ants sustain fitness costs under resource limitation, however, gain fitness benefits when exposed to an entomopathogenus fungus. These effects are probably cause by a prophylactic upregulation of behavioural as well as physiological immune defences in highly infected ants.}, author = {Konrad, Matthias}, issn = {2663-337X}, pages = {131}, publisher = {Institute of Science and Technology Austria}, title = {{Immune defences in ants: Effects of social immunisation and a fungal ectosymbiont in the ant Lasius neglectus}}, year = {2014}, } @phdthesis{1402, abstract = {Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.}, author = {Marhavá, Petra}, issn = {2663-337X}, pages = {90}, publisher = {Institute of Science and Technology Austria}, title = {{Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana}}, year = {2014}, } @article{2255, abstract = {Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm.}, author = {Edelsbrunner, Herbert and Pausinger, Florian}, issn = {09249907}, journal = {Journal of Mathematical Imaging and Vision}, number = {1}, pages = {164 -- 177}, publisher = {Springer}, title = {{Stable length estimates of tube-like shapes}}, doi = {10.1007/s10851-013-0468-x}, volume = {50}, year = {2014}, } @inproceedings{2159, abstract = {Motivated by topological Tverberg-type problems, we consider multiple (double, triple, and higher multiplicity) selfintersection points of maps from finite simplicial complexes (compact polyhedra) into ℝd and study conditions under which such multiple points can be eliminated. The most classical case is that of embeddings (i.e., maps without double points) of a κ-dimensional complex K into ℝ2κ. For this problem, the work of van Kampen, Shapiro, and Wu provides an efficiently testable necessary condition for embeddability (namely, vanishing of the van Kampen ob-struction). For κ ≥ 3, the condition is also sufficient, and yields a polynomial-time algorithm for deciding embeddability: One starts with an arbitrary map f : K→ℝ2κ, which generically has finitely many double points; if k ≥ 3 and if the obstruction vanishes then one can successively remove these double points by local modifications of the map f. One of the main tools is the famous Whitney trick that permits eliminating pairs of double points of opposite intersection sign. We are interested in generalizing this approach to intersection points of higher multiplicity. We call a point y 2 ℝd an r-fold Tverberg point of a map f : Kκ →ℝd if y lies in the intersection f(σ1)∩. ∩f(σr) of the images of r pairwise disjoint simplices of K. The analogue of (non-)embeddability that we study is the problem Tverbergκ r→d: Given a κ-dimensional complex K, does it satisfy a Tverberg-type theorem with parameters r and d, i.e., does every map f : K κ → ℝd have an r-fold Tverberg point? Here, we show that for fixed r, κ and d of the form d = rm and k = (r-1)m, m ≥ 3, there is a polynomial-time algorithm for deciding this (based on the vanishing of a cohomological obstruction, as in the case of embeddings). Our main tool is an r-fold analogue of the Whitney trick: Given r pairwise disjoint simplices of K such that the intersection of their images contains two r-fold Tverberg points y+ and y- of opposite intersection sign, we can eliminate y+ and y- by a local isotopy of f. In a subsequent paper, we plan to develop this further and present a generalization of the classical Haeiger-Weber Theorem (which yields a necessary and sufficient condition for embeddability of κ-complexes into ℝd for a wider range of dimensions) to intersection points of higher multiplicity.}, author = {Mabillard, Isaac and Wagner, Uli}, booktitle = {Proceedings of the Annual Symposium on Computational Geometry}, location = {Kyoto, Japan}, pages = {171 -- 180}, publisher = {ACM}, title = {{Eliminating Tverberg points, I. An analogue of the Whitney trick}}, doi = {10.1145/2582112.2582134}, year = {2014}, } @article{2023, abstract = {Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution.}, author = {Novak, Sebastian}, journal = {Ecology and Evolution}, number = {24}, pages = {4589 -- 4597}, publisher = {Wiley-Blackwell}, title = {{Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution}}, doi = {10.1002/ece3.1289}, volume = {4}, year = {2014}, } @inproceedings{2218, abstract = {While fixing concurrency bugs, program repair algorithms may introduce new concurrency bugs. We present an algorithm that avoids such regressions. The solution space is given by a set of program transformations we consider in the repair process. These include reordering of instructions within a thread and inserting atomic sections. The new algorithm learns a constraint on the space of candidate solutions, from both positive examples (error-free traces) and counterexamples (error traces). From each counterexample, the algorithm learns a constraint necessary to remove the errors. From each positive examples, it learns a constraint that is necessary in order to prevent the repair from turning the trace into an error trace. We implemented the algorithm and evaluated it on simplified Linux device drivers with known bugs.}, author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun and Ryzhyk, Leonid and Tarrach, Thorsten}, isbn = {978-331908866-2}, location = {Vienna, Austria}, pages = {568 -- 584}, publisher = {Springer}, title = {{Regression-free synthesis for concurrency}}, doi = {10.1007/978-3-319-08867-9_38}, volume = {8559}, year = {2014}, } @inproceedings{2167, abstract = {Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing. In this paper, we study compositional properties of the ioco-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the ioco conformance relation, the resulting methodology can be applied to a broader class of systems.}, author = {Daca, Przemyslaw and Henzinger, Thomas A and Krenn, Willibald and Nickovic, Dejan}, booktitle = {IEEE 7th International Conference on Software Testing, Verification and Validation}, isbn = {978-1-4799-2255-0}, issn = {2159-4848}, location = {Cleveland, USA}, publisher = {IEEE}, title = {{Compositional specifications for IOCO testing}}, doi = {10.1109/ICST.2014.50}, year = {2014}, } @inproceedings{2063, abstract = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements.}, author = {Chatterjee, Krishnendu and Chmelik, Martin and Daca, Przemyslaw}, location = {Vienna, Austria}, pages = {473 -- 490}, publisher = {Springer}, title = {{CEGAR for qualitative analysis of probabilistic systems}}, doi = {10.1007/978-3-319-08867-9_31}, volume = {8559}, year = {2014}, } @article{2001, abstract = {Antibiotics affect bacterial cell physiology at many levels. Rather than just compensating for the direct cellular defects caused by the drug, bacteria respond to antibiotics by changing their morphology, macromolecular composition, metabolism, gene expression and possibly even their mutation rate. Inevitably, these processes affect each other, resulting in a complex response with changes in the expression of numerous genes. Genome‐wide approaches can thus help in gaining a comprehensive understanding of bacterial responses to antibiotics. In addition, a combination of experimental and theoretical approaches is needed for identifying general principles that underlie these responses. Here, we review recent progress in our understanding of bacterial responses to antibiotics and their combinations, focusing on effects at the levels of growth rate and gene expression. We concentrate on studies performed in controlled laboratory conditions, which combine promising experimental techniques with quantitative data analysis and mathematical modeling. While these basic research approaches are not immediately applicable in the clinic, uncovering the principles and mechanisms underlying bacterial responses to antibiotics may, in the long term, contribute to the development of new treatment strategies to cope with and prevent the rise of resistant pathogenic bacteria.}, author = {Mitosch, Karin and Bollenbach, Tobias}, journal = {Environmental Microbiology Reports}, number = {6}, pages = {545 -- 557}, publisher = {Wiley}, title = {{Bacterial responses to antibiotics and their combinations}}, doi = {10.1111/1758-2229.12190}, volume = {6}, year = {2014}, } @inproceedings{2082, abstract = {NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). Security proofs and attacks for NMAC can typically be lifted to HMAC. NMAC was introduced by Bellare, Canetti and Krawczyk [Crypto'96], who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, assuming that (1) f is a PRF and (2) the function we get when cascading f is weakly collision-resistant. Unfortunately, HMAC is typically instantiated with cryptographic hash functions like MD5 or SHA-1 for which (2) has been found to be wrong. To restore the provable guarantees for NMAC, Bellare [Crypto'06] showed its security based solely on the assumption that f is a PRF, albeit via a non-uniform reduction. - Our first contribution is a simpler and uniform proof for this fact: If f is an ε-secure PRF (against q queries) and a δ-non-adaptively secure PRF (against q queries), then NMAC f is an (ε+ℓqδ)-secure PRF against q queries of length at most ℓ blocks each. - We then show that this ε+ℓqδ bound is basically tight. For the most interesting case where ℓqδ ≥ ε we prove this by constructing an f for which an attack with advantage ℓqδ exists. This also violates the bound O(ℓε) on the PRF-security of NMAC recently claimed by Koblitz and Menezes. - Finally, we analyze the PRF-security of a modification of NMAC called NI [An and Bellare, Crypto'99] that differs mainly by using a compression function with an additional keying input. This avoids the constant rekeying on multi-block messages in NMAC and allows for a security proof starting by the standard switch from a PRF to a random function, followed by an information-theoretic analysis. We carry out such an analysis, obtaining a tight ℓq2/2 c bound for this step, improving over the trivial bound of ℓ2q2/2c. The proof borrows combinatorial techniques originally developed for proving the security of CBC-MAC [Bellare et al., Crypto'05].}, author = {Gazi, Peter and Pietrzak, Krzysztof Z and Rybar, Michal}, editor = {Garay, Juan and Gennaro, Rosario}, location = {Santa Barbara, USA}, number = {1}, pages = {113 -- 130}, publisher = {Springer}, title = {{The exact PRF-security of NMAC and HMAC}}, doi = {10.1007/978-3-662-44371-2_7}, volume = {8616}, year = {2014}, } @article{1912, abstract = {Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function.}, author = {Compagnon, Julien and Barone, Vanessa and Rajshekar, Srivarsha and Kottmeier, Rita and Pranjic-Ferscha, Kornelija and Behrndt, Martin and Heisenberg, Carl-Philipp J}, journal = {Developmental Cell}, number = {6}, pages = {774 -- 783}, publisher = {Cell Press}, title = {{The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ}}, doi = {10.1016/j.devcel.2014.11.003}, volume = {31}, year = {2014}, } @article{2084, abstract = {Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour.}, author = {Grusch, Michael and Schelch, Karin and Riedler, Robert and Gschaider-Reichhart, Eva and Differ, Christopher and Berger, Walter and Inglés Prieto, Álvaro and Janovjak, Harald L}, journal = {EMBO Journal}, number = {15}, pages = {1713 -- 1726}, publisher = {Wiley-Blackwell}, title = {{Spatio-temporally precise activation of engineered receptor tyrosine kinases by light}}, doi = {10.15252/embj.201387695}, volume = {33}, year = {2014}, } @inproceedings{2157, abstract = {We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, i.e., an essential curve in the boundary of X bounding a disk in S3 nX with length bounded by a computable function of the number of tetrahedra of X.}, author = {Matoušek, Jiří and Sedgwick, Eric and Tancer, Martin and Wagner, Uli}, booktitle = {Proceedings of the Annual Symposium on Computational Geometry}, location = {Kyoto, Japan}, pages = {78 -- 84}, publisher = {ACM}, title = {{Embeddability in the 3 sphere is decidable}}, doi = {10.1145/2582112.2582137}, year = {2014}, } @inproceedings{10894, abstract = {PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations.}, author = {Bauer, Ulrich and Kerber, Michael and Reininghaus, Jan and Wagner, Hubert}, booktitle = {ICMS 2014: International Congress on Mathematical Software}, isbn = {9783662441985}, issn = {1611-3349}, location = {Seoul, South Korea}, pages = {137--143}, publisher = {Springer Berlin Heidelberg}, title = {{PHAT – Persistent Homology Algorithms Toolbox}}, doi = {10.1007/978-3-662-44199-2_24}, volume = {8592}, year = {2014}, } @misc{5428, abstract = {Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms. In this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan and Velner, Yaron}, issn = {2664-1690}, pages = {26}, publisher = {IST Austria}, title = {{Quantitative fair simulation games}}, doi = {10.15479/AT:IST-2014-315-v1-1}, year = {2014}, } @article{1887, author = {Cremer, Sylvia}, journal = {Zoologie}, pages = {23 -- 30}, publisher = {Deutsche Zoologische Gesellschaft}, title = {{Gemeinsame Krankheitsabwehr in Ameisengesellschaften}}, year = {2014}, } @article{2175, abstract = {The cerebral cortex, the seat of our cognitive abilities, is composed of an intricate network of billions of excitatory projection and inhibitory interneurons. Postmitotic cortical neurons are generated by a diverse set of neural stem cell progenitors within dedicated zones and defined periods of neurogenesis during embryonic development. Disruptions in neurogenesis can lead to alterations in the neuronal cytoarchitecture, which is thought to represent a major underlying cause for several neurological disorders, including microcephaly, autism and epilepsy. Although a number of signaling pathways regulating neurogenesis have been described, the precise cellular and molecular mechanisms regulating the functional neural stem cell properties in cortical neurogenesis remain unclear. Here, we discuss the most up-to-date strategies to monitor the fundamental mechanistic parameters of neuronal progenitor proliferation, and recent advances deciphering the logic and dynamics of neurogenesis.}, author = {Postiglione, Maria P and Hippenmeyer, Simon}, issn = {1748-6971}, journal = {Future Neurology}, number = {3}, pages = {323 -- 340}, publisher = {Future Science Group}, title = {{Monitoring neurogenesis in the cerebral cortex: an update}}, doi = {10.2217/fnl.14.18}, volume = {9}, year = {2014}, } @article{1913, abstract = {Deposits of phosphorylated tau protein and convergence of pathology in the hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed to evaluate whether regional and cellular vulnerability patterns in the hippocampus distinguish tauopathies or are influenced by their concomitant presence. Methods: We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal subregions/layers in individuals with Alzheimer's disease (AD)-related neurofibrillary degeneration (n = 40), Pick's disease (n = 8), progressive supranuclear palsy (n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n = 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly (n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis. Results: Our study reveals disease-specific hot spots and regional selective vulnerability for these disorders. The pattern of hippocampal AD-related tau pathology is strongly influenced by concomitant AGD. Mathematical analysis reveals that hippocampal involvement in primary tauopathies is distinguishable from early-stage AD-related neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies, which primarily do not affect the hippocampus. These hot spots can be shifted to other regions by the co-occurrence of tauopathies like AGD. Our observations support the notion that globular glial tauopathies and tau-astrogliopathy of the elderly are distinct entities.}, author = {Milenković, Ivan and Petrov, Tatjana and Kovács, Gábor}, issn = {1420-8008}, journal = {Dementia and Geriatric Cognitive Disorders}, number = {5-6}, pages = {375 -- 388}, publisher = {Karger Publishers}, title = {{Patterns of hippocampal tau pathology differentiate neurodegenerative dementias}}, doi = {10.1159/000365548}, volume = {38}, year = {2014}, } @inproceedings{1507, abstract = {The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large real and complex Hermitian matrices with independent, identically distributed entries are universal in a sense that they depend only on the symmetry class of the matrix and otherwise are independent of the details of the distribution. We present the recent solution to this half-century old conjecture. We explain how stochastic tools, such as the Dyson Brownian motion, and PDE ideas, such as De Giorgi-Nash-Moser regularity theory, were combined in the solution. We also show related results for log-gases that represent a universal model for strongly correlated systems. Finally, in the spirit of Wigner’s original vision, we discuss the extensions of these universality results to more realistic physical systems such as random band matrices.}, author = {Erdös, László}, booktitle = {Proceedings of the International Congress of Mathematicians}, location = {Seoul, Korea}, pages = {214 -- 236}, publisher = {International Congress of Mathematicians}, title = {{Random matrices, log-gases and Hölder regularity}}, volume = {3}, year = {2014}, } @inproceedings{8044, abstract = {Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.}, author = {Seiringer, Robert}, booktitle = {Proceeding of the International Congress of Mathematicans}, isbn = {9788961058063}, location = {Seoul, South Korea}, pages = {1175--1194}, publisher = {International Congress of Mathematicians}, title = {{Structure of the excitation spectrum for many-body quantum systems}}, volume = {3}, year = {2014}, } @inproceedings{2160, abstract = {Transfer learning has received a lot of attention in the machine learning community over the last years, and several effective algorithms have been developed. However, relatively little is known about their theoretical properties, especially in the setting of lifelong learning, where the goal is to transfer information to tasks for which no data have been observed so far. In this work we study lifelong learning from a theoretical perspective. Our main result is a PAC-Bayesian generalization bound that offers a unified view on existing paradigms for transfer learning, such as the transfer of parameters or the transfer of low-dimensional representations. We also use the bound to derive two principled lifelong learning algorithms, and we show that these yield results comparable with existing methods.}, author = {Pentina, Anastasia and Lampert, Christoph}, location = {Beijing, China}, pages = {991 -- 999}, publisher = {ML Research Press}, title = {{A PAC-Bayesian bound for Lifelong Learning}}, volume = {32}, year = {2014}, } @phdthesis{1403, abstract = {A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis.}, author = {Behrndt, Martin}, pages = {91}, publisher = {IST Austria}, title = {{Forces driving epithelial spreading in zebrafish epiboly}}, year = {2014}, } @inbook{1888, abstract = {Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig? Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen ergänzt werden.}, author = {Cremer, Sylvia}, booktitle = {Soziale Insekten in einer sich wandelnden Welt}, issn = {2366-2875}, pages = {65 -- 72}, publisher = {Verlag Dr. Friedrich Pfeil}, title = {{Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt Bayerische Akademie der Wissenschaften}}, volume = {43}, year = {2014}, } @unpublished{2012, abstract = {The classical sphere packing problem asks for the best (infinite) arrangement of non-overlapping unit balls which cover as much space as possible. We define a generalized version of the problem, where we allow each ball a limited amount of overlap with other balls. We study two natural choices of overlap measures and obtain the optimal lattice packings in a parameterized family of lattices which contains the FCC, BCC, and integer lattice.}, author = {Iglesias Ham, Mabel and Kerber, Michael and Uhler, Caroline}, booktitle = {arXiv}, title = {{Sphere packing with limited overlap}}, doi = {10.48550/arXiv.1401.0468}, year = {2014}, } @article{14301, abstract = {DNA has become a prime material for assembling complex three-dimensional objects that promise utility in various areas of application. However, achieving user-defined goals with DNA objects has been hampered by the difficulty to prepare them at arbitrary concentrations and in user-defined solution conditions. Here, we describe a method that solves this problem. The method is based on poly(ethylene glycol)-induced depletion of species with high molecular weight. We demonstrate that our method is applicable to a wide spectrum of DNA shapes and that it achieves excellent recovery yields of target objects up to 97 %, while providing efficient separation from non-integrated DNA strands. DNA objects may be prepared at concentrations up to the limit of solubility, including the possibility for bringing DNA objects into a solid phase. Due to the fidelity and simplicity of our method we anticipate that it will help to catalyze the development of new types of applications that use self-assembled DNA objects.}, author = {Stahl, Evi and Martin, Thomas and Praetorius, Florian M and Dietz, Hendrik}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, number = {47}, pages = {12949--12954}, publisher = {Wiley}, title = {{Facile and scalable preparation of pure and dense DNA origami solutions}}, doi = {10.1002/ange.201405991}, volume = {126}, year = {2014}, } @article{7699, author = {Sweeney, Lora Beatrice Jaeger and Kelley, Darcy B}, issn = {0959-4388}, journal = {Current Opinion in Neurobiology}, number = {10}, pages = {34--41}, publisher = {Elsevier}, title = {{Harnessing vocal patterns for social communication}}, doi = {10.1016/j.conb.2014.06.006}, volume = {28}, year = {2014}, } @article{2281, abstract = {We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential.}, author = {Guo, Yujin and Seiringer, Robert}, journal = {Letters in Mathematical Physics}, number = {2}, pages = {141 -- 156}, publisher = {Springer}, title = {{On the mass concentration for Bose-Einstein condensates with attractive interactions}}, doi = {10.1007/s11005-013-0667-9}, volume = {104}, year = {2014}, } @article{2257, abstract = {Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction.}, author = {Tkacik, Gasper and Marre, Olivier and Amodei, Dario and Schneidman, Elad and Bialek, William and Berry, Michael}, issn = {1553734X}, journal = {PLoS Computational Biology}, number = {1}, publisher = {Public Library of Science}, title = {{Searching for collective behavior in a large network of sensory neurons}}, doi = {10.1371/journal.pcbi.1003408}, volume = {10}, year = {2014}, } @article{15161, abstract = {The copper-catalyzed diboration of ketones followed by an acid-catalyzed elimination leads to the formation of 1,1-disubstituted and trisubstituted vinyl boronate esters with moderate to good yields and selectivity. Addition of tosic acid to the crude diboration products provides the corresponding vinyl boronate esters upon elimination. The trisubstituted vinyl boronate esters are formed as the (Z)-olefin isomer, which was established by subjecting the products to a Suzuki–Miyaura coupling reaction to obtain alkenes of known geometry.}, author = {Guan, Weiye and Michael, Alicia Kathleen and McIntosh, Melissa L. and Koren-Selfridge, Liza and Scott, John P. and Clark, Timothy B.}, issn = {1520-6904}, journal = {The Journal of Organic Chemistry}, keywords = {Organic Chemistry}, number = {15}, pages = {7199--7204}, publisher = {American Chemical Society}, title = {{Stereoselective formation of trisubstituted vinyl boronate esters by the acid-mediated elimination of α-hydroxyboronate esters}}, doi = {10.1021/jo500773t}, volume = {79}, year = {2014}, } @article{1999, abstract = {Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses.}, author = {Stroeymeyt, Nathalie and Casillas Perez, Barbara E and Cremer, Sylvia}, journal = {Current Opinion in Insect Science}, number = {1}, pages = {1 -- 15}, publisher = {Elsevier}, title = {{Organisational immunity in social insects}}, doi = {10.1016/j.cois.2014.09.001}, volume = {5}, year = {2014}, } @article{10384, abstract = {Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.}, author = {Mognetti, B. M. and Šarić, Anđela and Angioletti-Uberti, S. and Cacciuto, A. and Valeriani, C. and Frenkel, D.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {24}, publisher = {American Physical Society}, title = {{Living clusters and crystals from low-density suspensions of active colloids}}, doi = {10.1103/physrevlett.111.245702}, volume = {111}, year = {2013}, } @article{10386, abstract = {In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {29}, publisher = {Royal Society of Chemistry}, title = {{Self-assembly of nanoparticles adsorbed on fluid and elastic membranes}}, doi = {10.1039/c3sm50188d}, volume = {9}, year = {2013}, } @article{10385, abstract = {We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials.}, author = {Napoli, Joseph A. and Šarić, Anđela and Cacciuto, Angelo}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {37}, pages = {8881--8886}, publisher = {Royal Society of Chemistry}, title = {{Collapsing nanoparticle-laden nanotubes}}, doi = {10.1039/c3sm51495a}, volume = {9}, year = {2013}, } @article{10396, abstract = {Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable.}, author = {Schlögl, Alois and Jonas, Peter M and Schmidt-Hieber, C. and Guzman, S. J.}, issn = {1862-278X}, journal = {Biomedical Engineering / Biomedizinische Technik}, keywords = {biomedical engineering, data analysis, free software}, location = {Graz, Austria}, number = {SI-1-Track-G}, publisher = {De Gruyter}, title = {{Stimfit: A fast visualization and analysis environment for cellular neurophysiology}}, doi = {10.1515/bmt-2013-4181}, volume = {58}, year = {2013}, } @inproceedings{10749, abstract = {Fluxoid quantization provides a direct means to study phase coherence. In cuprate superconductors, there have been observations which suggest that phase coherent superconducting fluctuations may persist at temperatures significantly above Tc. The focus of this work is to study the vortex states in mesoscopic cuprate superconducting samples to directly probe phase coherence over a wide range of temperatures. We present cantilever torque susceptometry measurements of micron and sub-micron size Bi2212 rings and disks. The high sensitivity of this technique allowed observation of transitions between different fluxoid states of a single ring, and the discrete vortex states of micron size disks. The dependence of magnetic susceptibility on diameter and wall thickness of the ring was investigated. Measurements were made at different values of the in-plane magnetic field, and over a wide range of temperatures.}, author = {Polshyn, Hryhoriy and Budakian, Raffi and Gu, Genda}, booktitle = {APS March Meeting 2013}, issn = {0003-0503}, location = {Baltimore, MD, United States}, number = {1}, publisher = {American Physical Society}, title = {{Cantilever micro-susceptometry of mesoscopic Bi2212 samples}}, volume = {58}, year = {2013}, } @article{10895, abstract = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. }, author = {Vanneste, Steffen and Friml, Jiří}, issn = {2223-7747}, journal = {Plants}, keywords = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics}, number = {4}, pages = {650--675}, publisher = {MDPI}, title = {{Calcium: The missing link in auxin action}}, doi = {10.3390/plants2040650}, volume = {2}, year = {2013}, } @inproceedings{10898, abstract = {A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered.}, author = {Haas, Andreas and Lippautz, Michael and Henzinger, Thomas A and Payer, Hannes and Sokolova, Ana and Kirsch, Christoph M. and Sezgin, Ali}, booktitle = {Proceedings of the ACM International Conference on Computing Frontiers - CF '13}, isbn = {978-145032053-5}, location = {Ischia, Italy}, number = {5}, publisher = {ACM Press}, title = {{Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation}}, doi = {10.1145/2482767.2482789}, year = {2013}, } @inbook{10899, author = {Barton, Nicholas H}, booktitle = {Encyclopedia of Biodiversity}, isbn = {978-0-12-384720-1}, keywords = {Adaptive landscape, Cline, Coalescent process, Gene flow, Hybrid zone, Local adaptation, Natural selection, Neutral theory, Population structure, Speciation}, pages = {508--515}, publisher = {Elsevier}, title = {{Differentiation}}, doi = {10.1016/b978-0-12-384719-5.00031-9}, year = {2013}, } @article{11086, abstract = {Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs.}, author = {Liang, Yun and Franks, Tobias M. and Marchetto, Maria C. and Gage, Fred H. and HETZER, Martin W}, issn = {1553-7404}, journal = {PLoS Genetics}, keywords = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics}, number = {2}, publisher = {Public Library of Science}, title = {{Dynamic association of NUP98 with the human genome}}, doi = {10.1371/journal.pgen.1003308}, volume = {9}, year = {2013}, } @article{11087, abstract = {Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process.}, author = {Toyama, Brandon H. and Savas, Jeffrey N. and Park, Sung Kyu and Harris, Michael S. and Ingolia, Nicholas T. and Yates, John R. and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {5}, pages = {971--982}, publisher = {Elsevier}, title = {{Identification of long-lived proteins reveals exceptional stability of essential cellular structures}}, doi = {10.1016/j.cell.2013.07.037}, volume = {154}, year = {2013}, } @article{11085, abstract = {During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy.}, author = {Hatch, Emily M. and Fischer, Andrew H. and Deerinck, Thomas J. and HETZER, Martin W}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {1}, pages = {47--60}, publisher = {Elsevier}, title = {{Catastrophic nuclear envelope collapse in cancer cell micronuclei}}, doi = {10.1016/j.cell.2013.06.007}, volume = {154}, year = {2013}, } @article{11088, abstract = {The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM.}, author = {Regner, Benjamin M. and Vučinić, Dejan and Domnisoru, Cristina and Bartol, Thomas M. and HETZER, Martin W and Tartakovsky, Daniel M. and Sejnowski, Terrence J.}, issn = {0006-3495}, journal = {Biophysical Journal}, keywords = {Biophysics}, number = {8}, pages = {1652--1660}, publisher = {Elsevier}, title = {{Anomalous diffusion of single particles in cytoplasm}}, doi = {10.1016/j.bpj.2013.01.049}, volume = {104}, year = {2013}, } @article{11083, abstract = {Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML.}, author = {Franks, Tobias M. and HETZER, Martin W}, issn = {0962-8924}, journal = {Trends in Cell Biology}, keywords = {Cell Biology}, number = {3}, pages = {112--117}, publisher = {Elsevier}, title = {{The role of Nup98 in transcription regulation in healthy and diseased cells}}, doi = {10.1016/j.tcb.2012.10.013}, volume = {23}, year = {2013}, } @article{11084, abstract = {Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing.}, author = {Toyama, Brandon H. and HETZER, Martin W}, issn = {1471-0072}, journal = {Nature Reviews Molecular Cell Biology}, keywords = {Cell Biology, Molecular Biology}, pages = {55--61}, publisher = {Springer Nature}, title = {{Protein homeostasis: Live long, won't prosper}}, doi = {10.1038/nrm3496}, volume = {14}, year = {2013}, } @article{115, abstract = {We present the design and performance characterization of a new experimental technique for measuring individual particle charges in large ensembles of macroscopic grains. The measurement principle is qualitatively similar to that used in determining the elementary charge by Millikan in that it follows individual particle trajectories. However, by taking advantage of new technology we are able to work with macroscopic grains and achieve several orders of magnitude better resolution in charge to mass ratios. By observing freely falling grains accelerated in a horizontal electric field with a co-falling, high-speed video camera, we dramatically increase particle tracking time and measurement precision. Keeping the granular medium under vacuum, we eliminate air drag, leaving the electrostatic force as the primary source of particle accelerations in the co-moving frame. Because the technique is based on direct imaging, we can distinguish between different particle types during the experiment, opening up the possibility of studying charge transfer processes between different particle species. For the ∼300 μm diameter grains reported here, we achieve an average acceleration resolution of ∼0.008 m/s2, a force resolution of ∼500 pN, and a median charge resolution ∼6× 104 elementary charges per grain (corresponding to surface charge densities ∼1 elementary charges per μm2). The primary source of error is indeterminacy in the grain mass, but with higher resolution cameras and better optics this can be further improved. The high degree of resolution and the ability to visually identify particles of different species or sizes with direct imaging make this a powerful new tool to characterize charging processes in granular media.}, author = {Waitukaitis, Scott R and Jaeger, Heinrich}, journal = {Review of Scientific Instruments}, number = {2}, publisher = {AIP}, title = {{In situ granular charge measurement by free-fall videography}}, doi = {10.1063/1.4789496}, volume = {84}, year = {2013}, } @article{11520, abstract = {We present the spatially resolved Hα dynamics of 16 star-forming galaxies at z ∼ 0.81 using the new KMOS multi-object integral field spectrograph on the ESO Very Large Telescope. These galaxies, selected using 1.18 μm narrowband imaging from the 10 deg2 CFHT-HiZELS survey of the SA 22 hr field, are found in a ∼4 Mpc overdensity of Hα emitters and likely reside in a group/intermediate environment, but not a cluster. We confirm and identify a rich group of star-forming galaxies at z = 0.813 ± 0.003, with 13 galaxies within 1000 km s−1 of each other, and seven within a diameter of 3 Mpc. All of our galaxies are “typical” star-forming galaxies at their redshift, 0.8 ± 0.4 SFR$^*_{z = 0.8}$, spanning a range of specific star formation rates (sSFRs) of 0.2–1.1 Gyr−1 and have a median metallicity very close to solar of 12 + log(O/H) = 8.62 ± 0.06. We measure the spatially resolved Hα dynamics of the galaxies in our sample and show that 13 out of 16 galaxies can be described by rotating disks and use the data to derive inclination corrected rotation speeds of 50–275 km s−1. The fraction of disks within our sample is 75% ± 8%, consistent with previous results based on Hubble Space Telescope morphologies of Hα-selected galaxies at z ∼ 1 and confirming that disks dominate the SFR density at z ∼ 1. Our Hα galaxies are well fitted by the z ∼ 1–2 Tully–Fisher (TF) relation, confirming the evolution seen in the zero point. Apart from having, on average, higher stellar masses and lower sSFRs, our group galaxies at z = 0.81 present the same mass–metallicity and TF relation as z ∼ 1 field galaxies and are all disk galaxies.}, author = {Sobral, D. and Swinbank, A. M. and Stott, J. P. and Matthee, Jorryt J and Bower, R. G. and Smail, Ian and Best, P. and Geach, J. E. and Sharples, R. M.}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution – galaxies, high-redshift – galaxies, starburst}, number = {2}, publisher = {IOP Publishing}, title = {{The dynamics of z=0.8 H-alpha-selected star-forming galaxies from KMOS/CF-HiZELS}}, doi = {10.1088/0004-637x/779/2/139}, volume = {779}, year = {2013}, } @article{116, abstract = {We describe a model experiment for dynamic jamming: a two-dimensional collection of initially unjammed disks that are forced into the jammed state by uniaxial compression via a rake. This leads to a stable densification front that travels ahead of the rake, leaving regions behind it jammed. Using disk conservation in conjunction with an upper limit to the packing fraction at jamming onset, we predict the front speed as a function of packing fraction and rake speed. However, we find that the jamming front has a finite width, a feature that cannot be explained by disk conservation alone. This width appears to diverge on approach to jamming, which suggests that it may be related to growing lengthscales encountered in other jamming studies.}, author = {Waitukaitis, Scott R and Roth, Leah and Vitelli, Vincenzo and Jaeger, Heinrich}, journal = {EPL}, number = {4}, publisher = {Elsevier}, title = {{Dynamic jamming fronts}}, doi = {10.1209/0295-5075/102/44001}, volume = {102}, year = {2013}, } @article{11671, abstract = {Given only the URL of a Web page, can we identify its language? In this article we examine this question. URL-based language classification is useful when the content of the Web page is not available or downloading the content is a waste of bandwidth and time. We built URL-based language classifiers for English, German, French, Spanish, and Italian by applying a variety of algorithms and features. As algorithms we used machine learning algorithms which are widely applied for text classification and state-of-art algorithms for language identification of text. As features we used words, various sized n-grams, and custom-made features (our novel feature set). We compared our approaches with two baseline methods, namely classification by country code top-level domains and classification by IP addresses of the hosting Web servers. We trained and tested our classifiers in a 10-fold cross-validation setup on a dataset obtained from the Open Directory Project and from querying a commercial search engine. We obtained the lowest F1-measure for English (94) and the highest F1-measure for German (98) with the best performing classifiers. We also evaluated the performance of our methods: (i) on a set of Web pages written in Adobe Flash and (ii) as part of a language-focused crawler. In the first case, the content of the Web page is hard to extract and in the second page downloading pages of the “wrong” language constitutes a waste of bandwidth. In both settings the best classifiers have a high accuracy with an F1-measure between 95 (for English) and 98 (for Italian) for the Adobe Flash pages and a precision between 90 (for Italian) and 97 (for French) for the language-focused crawler.}, author = {Baykan, Eda and Weber, Ingmar and Henzinger, Monika H}, issn = {1559-114X}, journal = {ACM Transactions on the Web}, keywords = {Computer Networks and Communications}, number = {1}, publisher = {Association for Computing Machinery}, title = {{A comprehensive study of techniques for URL-based web page language classification}}, doi = {10.1145/2435215.2435218}, volume = {7}, year = {2013}, } @inproceedings{117, abstract = {The packing arrangement of individual particles inside a granular material and the resulting response to applied stresses depend critically on particle-particle interactions. One aspect that recently received attention are nanoscale surface features of particles, which play an important role in determining the strength of cohesive van der Waals and capillary interactions and also affect tribo-charging of grains. We describe experiments on freely falling granular streams that can detect the contributions from all three of these forces. We show that it is possible to measure the charge of individual grains and build up distributions that are detailed enough to provide stringent tests of tribo-charging models currently available. A second aspect concerns particle shape. In this case steric interactions become important and new types of aggregate behavior can be expected when non-convex particle shapes are considered that can interlock or entangle. However, a general connection between the mechanical response of a granular material and the constituents\' shape remains unknown. This has made it infeasible to tackle the "inverse packing problem", namely to start from a given, desired behavior for the aggregate as a whole and then find the particle shape the produces it. We discuss a new approach, using concepts rooted in artificial evolution that provides a way to solve this inverse problem. This approach facilitates exploring the role of arbitrary particle geometry in jammed systems and invites the discovery and design of granular matter with optimized properties.}, author = {Jaeger, Heinrich and Miskin, Marc and Waitukaitis, Scott R}, booktitle = { AIP Conference Proceedings}, location = {Sydney, Australia}, pages = {3 -- 6}, publisher = {AIP}, title = {{From nanoscale cohesion to macroscale entanglement: opportunities for designing granular aggregate behaviour by tailoring grain shape and interactions}}, doi = {10.1063/1.4811858}, volume = {1542}, year = {2013}, } @article{11759, abstract = {Matching markets play a prominent role in economic theory. A prime example of such a market is the sponsored search market. Here, as in other markets of that kind, market equilibria correspond to feasible, envy free, and bidder optimal outcomes. For settings without budgets such an outcome always exists and can be computed in polynomial-time by the so-called Hungarian Method. Moreover, every mechanism that computes such an outcome is incentive compatible. We show that the Hungarian Method can be modified so that it finds a feasible, envy free, and bidder optimal outcome for settings with budgets. We also show that in settings with budgets no mechanism that computes such an outcome can be incentive compatible for all inputs. For inputs in general position, however, the presented mechanism—as any other mechanism that computes such an outcome for settings with budgets—is incentive compatible.}, author = {Dütting, Paul and Henzinger, Monika H and Weber, Ingmar}, issn = {0020-0190}, journal = {Information Processing Letters}, number = {3}, pages = {67--73}, publisher = {Elsevier}, title = {{Sponsored search, market equilibria, and the Hungarian Method}}, doi = {10.1016/j.ipl.2012.11.006}, volume = {113}, year = {2013}, }