@article{3158, abstract = {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.}, author = {Schachtner, Hannah and Li, Ang and Stevenson, David and Calaminus, Simon and Thomas, Steven and Watson, Steve and Sixt, Michael K and Wedlich Söldner, Roland and Strathdee, Douglas and Machesky, Laura}, journal = {European Journal of Cell Biology}, number = {11-12}, pages = {923 -- 929}, publisher = {Elsevier}, title = {{Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo}}, doi = {10.1016/j.ejcb.2012.04.002}, volume = {91}, year = {2012}, } @article{3248, abstract = {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.}, author = {Lampert, Christoph and Peters, Jan}, issn = {1861-8219}, journal = {Journal of Real-Time Image Processing}, number = {1}, pages = {31 -- 41}, publisher = {Springer}, title = {{Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components}}, doi = {10.1007/s11554-010-0168-3}, volume = {7}, year = {2012}, } @article{3247, abstract = {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.}, author = {Vilaça, Sibelle and Fernandes Redondo, Rodrigo A and Lins, Lívia and Santos, Fabrício}, journal = {Conservation Genetics}, number = {1}, pages = {293 -- 298}, publisher = {Springer}, title = {{Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)}}, doi = {10.1007/s10592-011-0262-5}, volume = {13}, year = {2012}, } @article{3245, abstract = {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.}, author = {Behrndt, Martin and Heisenberg, Carl-Philipp J}, journal = {Developmental Cell}, number = {1}, pages = {3 -- 4}, publisher = {Cell Press}, title = {{Spurred by resistance mechanosensation in collective migration}}, doi = {10.1016/j.devcel.2011.12.018}, volume = {22}, year = {2012}, } @article{3262, abstract = {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.}, author = {Tkacik, Gasper and Walczak, Aleksandra and Bialek, William}, journal = { Physical Review E statistical nonlinear and soft matter physics }, number = {4}, publisher = {American Institute of Physics}, title = {{Optimizing information flow in small genetic networks. III. A self-interacting gene}}, doi = {10.1103/PhysRevE.85.041903}, volume = {85}, year = {2012}, } @article{3257, abstract = {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.}, author = {Kolmogorov, Vladimir}, journal = {Discrete Applied Mathematics}, number = {4-5}, pages = {416 -- 426}, publisher = {Elsevier}, title = {{Generalized roof duality and bisubmodular functions}}, doi = {10.1016/j.dam.2011.10.026}, volume = {160}, year = {2012}, } @inbook{3277, abstract = {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.}, author = {de Vladar, Harold and Chela Flores, Julian}, booktitle = {Life on Earth and other planetary bodies}, pages = {387 -- 405}, publisher = {Springer}, title = {{Can the evolution of multicellularity be anticipated in the exploration of the solar system?}}, doi = {10.1007/978-94-007-4966-5_22}, volume = {24}, year = {2012}, } @inproceedings{3279, abstract = {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. }, author = {Jain, Abhishek and Pietrzak, Krzysztof Z and Tentes, Aris}, location = {Taormina, Sicily, Italy}, pages = {369 -- 382}, publisher = {Springer}, title = {{Hardness preserving constructions of pseudorandom functions}}, doi = {10.1007/978-3-642-28914-9_21}, volume = {7194}, year = {2012}, } @article{3274, abstract = {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.}, author = {Rieckh, Georg and Kreuzer, Wolfgang and Waubke, Holger and Balazs, Peter}, journal = { Engineering Analysis with Boundary Elements}, number = {6}, pages = {960 -- 967}, publisher = {Elsevier}, title = {{A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil}}, doi = {10.1016/j.enganabound.2011.12.014}, volume = {36}, year = {2012}, } @article{3289, abstract = {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. }, author = {Pereira, Anna and Leite, Flávia and Brasil, Bruno and Soares Martins, Jamaria and Torres, Alice and Pimenta, Paulo and Souto Padrón, Thais and Tranktman, Paula and Ferreira, Paulo and Kroon, Erna and Bonjardim, Cláudio}, journal = {Journal of Virology}, number = {1}, pages = {172 -- 184}, publisher = {ASM}, title = {{A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization}}, doi = {10.1128/JVI.05638-11}, volume = {86}, year = {2012}, }