TY - JOUR AB - Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km. AU - Ugelvig, Line V AU - Andersen, Anne AU - Boomsma, Jacobus AU - Nash, David ID - 3156 IS - 13 JF - Molecular Ecology TI - Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion VL - 21 ER - TY - JOUR AB - We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment. AU - Schachtner, Hannah AU - Li, Ang AU - Stevenson, David AU - Calaminus, Simon AU - Thomas, Steven AU - Watson, Steve AU - Sixt, Michael K AU - Wedlich Söldner, Roland AU - Strathdee, Douglas AU - Machesky, Laura ID - 3158 IS - 11-12 JF - European Journal of Cell Biology TI - Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo VL - 91 ER - TY - JOUR AB - We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz. AU - Lampert, Christoph AU - Peters, Jan ID - 3248 IS - 1 JF - Journal of Real-Time Image Processing SN - 1861-8200 TI - Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components VL - 7 ER - TY - JOUR AB - The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species. AU - Vilaça, Sibelle AU - Fernandes Redondo, Rodrigo A AU - Lins, Lívia AU - Santos, Fabrício ID - 3247 IS - 1 JF - Conservation Genetics TI - Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus) VL - 13 ER - TY - JOUR AB - How cells orchestrate their behavior during collective migration is a long-standing question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated mechanosensitive response that promotes cell polarization and movement persistence during the collective mesendoderm migration in gastrulation. AU - Behrndt, Martin AU - Heisenberg, Carl-Philipp J ID - 3245 IS - 1 JF - Developmental Cell TI - Spurred by resistance mechanosensation in collective migration VL - 22 ER - TY - JOUR AB - Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point. AU - Tkacik, Gasper AU - Walczak, Aleksandra AU - Bialek, William ID - 3262 IS - 4 JF - Physical Review E statistical nonlinear and soft matter physics TI - Optimizing information flow in small genetic networks. III. A self-interacting gene VL - 85 ER - TY - JOUR AB - Consider a convex relaxation f̂ of a pseudo-Boolean function f. We say that the relaxation is totally half-integral if f̂(x) is a polyhedral function with half-integral extreme points x, and this property is preserved after adding an arbitrary combination of constraints of the form x i=x j, x i=1-x j, and x i=γ where γ∈{0,1,1/2} is a constant. A well-known example is the roof duality relaxation for quadratic pseudo-Boolean functions f. We argue that total half-integrality is a natural requirement for generalizations of roof duality to arbitrary pseudo-Boolean functions. Our contributions are as follows. First, we provide a complete characterization of totally half-integral relaxations f̂ by establishing a one-to-one correspondence with bisubmodular functions. Second, we give a new characterization of bisubmodular functions. Finally, we show some relationships between general totally half-integral relaxations and relaxations based on the roof duality. On the conceptual level, our results show that bisubmodular functions provide a natural generalization of the roof duality approach to higher-order terms. This can be viewed as a non-submodular analogue of the fact that submodular functions generalize the s-t minimum cut problem with non-negative weights to higher-order terms. AU - Kolmogorov, Vladimir ID - 3257 IS - 4-5 JF - Discrete Applied Mathematics TI - Generalized roof duality and bisubmodular functions VL - 160 ER - TY - CHAP AB - The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons. AU - de Vladar, Harold AU - Chela Flores, Julian ID - 3277 T2 - Life on Earth and other planetary bodies TI - Can the evolution of multicellularity be anticipated in the exploration of the solar system? VL - 24 ER - TY - CONF AB - We show a hardness-preserving construction of a PRF from any length doubling PRG which improves upon known constructions whenever we can put a non-trivial upper bound q on the number of queries to the PRF. Our construction requires only O(logq) invocations to the underlying PRG with each query. In comparison, the number of invocations by the best previous hardness-preserving construction (GGM using Levin's trick) is logarithmic in the hardness of the PRG. For example, starting from an exponentially secure PRG {0,1} n → {0,1} 2n, we get a PRF which is exponentially secure if queried at most q = exp(√n)times and where each invocation of the PRF requires Θ(√n) queries to the underlying PRG. This is much less than the Θ(n) required by known constructions. AU - Jain, Abhishek AU - Pietrzak, Krzysztof Z AU - Tentes, Aris ID - 3279 TI - Hardness preserving constructions of pseudorandom functions VL - 7194 ER - TY - JOUR AB - A boundary element model of a tunnel running through horizontally layered soil with anisotropic material properties is presented. Since there is no analytical fundamental solution for wave propagation inside a layered orthotropic medium in 3D, the fundamental displacements and stresses have to be calculated numerically. In our model this is done in the Fourier domain with respect to space and time. The assumption of a straight tunnel with infinite extension in the x direction makes it possible to decouple the system for every wave number kx, leading to a 2.5D-problem, which is suited for parallel computation. The special form of the fundamental solution, resulting from our Fourier ansatz, and the fact, that the calculation of the boundary integral equation is performed in the Fourier domain, enhances the stability and efficiency of the numerical calculations. AU - Rieckh, Georg AU - Kreuzer, Wolfgang AU - Waubke, Holger AU - Balazs, Peter ID - 3274 IS - 6 JF - Engineering Analysis with Boundary Elements TI - A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil VL - 36 ER - TY - JOUR AB - Viral manipulation of transduction pathways associated with key cellular functions such as survival, response to microbial infection, and cytoskeleton reorganization can provide the supportive milieu for a productive infection. Here, we demonstrate that vaccinia virus (VACV) infection leads to activation of the stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK) 4/7 (MKK4/7)-c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the stimulation of this pathway requires postpenetration, prereplicative events in the viral replication cycle. Although the formation of intracellular mature virus (IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an accentuated deregulation of microtubule and actin network organization in infected JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery and enhanced enveloped particle release. Furthermore, VACV infection induced alterations in the cell contractility and morphology, and cell migration was reduced in the JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell contractility and cell migration, such as microtubule-associated protein 1B and paxillin, respectively, was not detected in the VACV-infected KO cells. In sum, our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in cytoskeleton reorganization during VACV infection. AU - Pereira, Anna AU - Leite, Flávia AU - Brasil, Bruno AU - Soares Martins, Jamaria AU - Torres, Alice AU - Pimenta, Paulo AU - Souto Padrón, Thais AU - Tranktman, Paula AU - Ferreira, Paulo AU - Kroon, Erna AU - Bonjardim, Cláudio ID - 3289 IS - 1 JF - Journal of Virology TI - A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization VL - 86 ER - TY - JOUR AB - The theory of persistent homology opens up the possibility to reason about topological features of a space or a function quantitatively and in combinatorial terms. We refer to this new angle at a classical subject within algebraic topology as a point calculus, which we present for the family of interlevel sets of a real-valued function. Our account of the subject is expository, devoid of proofs, and written for non-experts in algebraic topology. AU - Bendich, Paul AU - Cabello, Sergio AU - Edelsbrunner, Herbert ID - 3310 IS - 11 JF - Pattern Recognition Letters TI - A point calculus for interlevel set homology VL - 33 ER - TY - JOUR AB - The ample chemical and structural freedom of quaternary compounds permits engineering materials that fulfill the requirements of a wide variety of applications. In this work, the mechanisms to achieve unprecedented size, shape, and composition control in quaternary nanocrystals are detailed. The described procedure allows obtaining tetrahedral and penta-tetrahedral quaternary nanocrystals with tuned size distributions and controlled compositions from a plethora of I 2-II-IV-VI 4 semiconductors. AU - Ibáñez, Maria AU - Zamani, Reza AU - Li, Wenhua AU - Shavel, Alexey AU - Arbiol, Jordi AU - Morante, Joan AU - Cabot, Andreu ID - 338 IS - 3 JF - Crystal Growth and Design TI - Extending the nanocrystal synthesis control to quaternary compositions VL - 12 ER - TY - JOUR AB - A high-yield and upscalable colloidal synthesis route for the production of quaternary I 2-II-IV-VI 4 nanocrystals, particularly stannite Cu 2+xCd 1-xSnSe 4, with narrow size distribution and precisely controlled composition is presented. It is also shown here how the diversity of valences in the constituent elements allows an effective control of their electrical conductivity through the adjustment of the cation ratios. At the same time, while the crystallographic complexity of quaternary chalcogenides is associated with intrinsically low thermal conductivities, the reduction of the lattice dimensions to the nanoscale further reduces the materials thermal conductivity. In the specific case of the stannite crystal structure, a convenient slab distribution of the valence band maximum states permits a partial decoupling of the p-type electrical conductivity from both the Seebeck coefficient and the thermal conductivity. Combining these features, we demonstrate how an initial optimization of the nanocrystals Cd/Cu ratio allowed us to obtain low-temperature solution-processed materials with ZT values up to 0.71 at 685 K. AU - Ibáñez, Maria AU - Cadavid, Doris AU - Zamani, Reza AU - García Castelló, Nuria AU - Izquierdo Roca, Victora AU - Li, Wenhua AU - Fairbrother, Andrew AU - Prades, Joan AU - Shavel, Alexey AU - Arbiol, Jordi AU - Pérez Rodríguez, Alejandro AU - Morante, Joan AU - Cabot, Andreu ID - 339 IS - 3 JF - Chemistry of Materials TI - Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4 VL - 24 ER - TY - JOUR AB - A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. AU - Shavel, Alexey AU - Cadavid, Doris AU - Ibáñez, Maria AU - Carrete, Alex AU - Cabot, Andreu ID - 340 IS - 3 JF - Journal of the American Chemical Society TI - Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor VL - 134 ER - TY - JOUR AB - Nanocomposites are highly promising materials to enhance the efficiency of current thermoelectric devices. A straightforward and at the same time highly versatile and controllable approach to produce nanocomposites is the assembly of solution-processed nanocrystal building blocks. The convenience of this bottom-up approach to produce nanocomposites with homogeneous phase distributions and adjustable composition is demonstrated here by blending Ag2Te and PbTe colloidal nanocrystals to form Ag2Te–PbTe bulk nanocomposites. The thermoelectric properties of these nanocomposites are analyzed in the temperature range from 300 to 700 K. The evolution of their electrical conductivity and Seebeck coefficient is discussed in terms of the blend composition and the characteristics of the constituent materials. AU - Cadavid, Doris AU - Ibáñez, Maria AU - Gorsse, Stéphane AU - López, Antonio AU - Cirera, Albert AU - Morante, Joan AU - Cabot, Andreu ID - 345 IS - 12 JF - Journal of Nanoparticle Research TI - Bottom-up processing of thermoelectric nanocomposites from colloidal nanocrystal building blocks: The case of Ag2Te–PbTe VL - 14 ER - TY - JOUR AB - A synthetic route for producing Cu 2ZnGeSe 4 nanocrystals with narrow size distributions and controlled composition is presented. These nanocrystals were used to produce densely packed nanomaterials by hot-pressing. From the characterization of the thermoelectric properties of these nanomaterials, Cu 2ZnGeSe 4 is demonstrated to show excellent thermoelectric properties. A very preliminary adjustment of the nanocrystal composition has already resulted in a figure of merit of up to 0.55 at 450°C. AU - Ibáñez, Maria AU - Zamani, Reza AU - Lalonde, Aaron AU - Cadavid, Doris AU - Li, Wenhua AU - Shavel, Alexey AU - Arbiol, Jordi AU - Morante, Joan AU - Gorsse, Stéphane AU - Snyder, G Jeffrey AU - Cabot, Andreu ID - 347 IS - 9 JF - Journal of the American Chemical Society TI - Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties VL - 134 ER - TY - JOUR AB - Hierarchical Timing Language (HTL) is a coordination language for distributed, hard real-time applications. HTL is a hierarchical extension of Giotto and, like its predecessor, based on the logical execution time (LET) paradigm of real-time programming. Giotto is compiled into code for a virtual machine, called the EmbeddedMachine (or E machine). If HTL is targeted to the E machine, then the hierarchicalprogram structure needs to be flattened; the flattening makes separatecompilation difficult, and may result in E machinecode of exponential size. In this paper, we propose a generalization of the E machine, which supports a hierarchicalprogram structure at runtime through real-time trigger mechanisms that are arranged in a tree. We present the generalized E machine, and a modular compiler for HTL that generates code of linear size. The compiler may generate code for any part of a given HTL program separately in any order. AU - Ghosal, Arkadeb AU - Iercan, Daniel AU - Kirsch, Christoph AU - Henzinger, Thomas A AU - Sangiovanni Vincentelli, Alberto ID - 3836 IS - 2 JF - Science of Computer Programming TI - Separate compilation of hierarchical real-time programs into linear-bounded embedded machine code VL - 77 ER - TY - JOUR AB - Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objectives. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is logspace-equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games. AU - Chatterjee, Krishnendu AU - Doyen, Laurent ID - 2972 JF - Theoretical Computer Science TI - Energy parity games VL - 458 ER - TY - JOUR AB - For programs whose data variables range over Boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this article, we consider algorithmic verification of programs that use Boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over an unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) PSPACE-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly nested loops. The second result establishes connections to automata and logics defining languages over data words. AU - Alur, Rajeev AU - Cerny, Pavol AU - Weinstein, Scott ID - 2967 IS - 3 JF - ACM Transactions on Computational Logic (TOCL) TI - Algorithmic analysis of array-accessing programs VL - 13 ER -