@article{1546,
abstract = {Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (<30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This "perimeter release model" provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course.},
author = {Nakamura, Yukihiro and Harada, Harumi and Kamasawa, Naomi and Matsui, Ko and Rothman, Jason and Shigemoto, Ryuichi and Silver, R Angus and Digregorio, David and Takahashi, Tomoyuki},
journal = {Neuron},
number = {1},
pages = {145 -- 158},
publisher = {Elsevier},
title = {{Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development}},
doi = {10.1016/j.neuron.2014.11.019},
volume = {85},
year = {2015},
}
@article{1558,
abstract = {CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation.},
author = {Ivanchenko, Maria and Zhu, Jinsheng and Wang, Bangjun and Medvecka, Eva and Du, Yunlong and Azzarello, Elisa and Mancuso, Stefano and Megraw, Molly and Filichkin, Sergei and Dubrovsky, Joseph and Friml, Jirí and Geisler, Markus},
journal = {Development},
number = {4},
pages = {712 -- 721},
publisher = {Company of Biologists},
title = {{The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation}},
doi = {10.1242/dev.113225},
volume = {142},
year = {2015},
}
@article{1560,
abstract = {Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function.},
author = {Hons, Miroslav and Sixt, Michael K},
journal = {Nature Immunology},
number = {4},
pages = {338 -- 340},
publisher = {Nature Publishing Group},
title = {{The lymph node filter revealed}},
doi = {10.1038/ni.3126},
volume = {16},
year = {2015},
}
@article{1565,
abstract = {Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release.},
author = {Gavello, Daniela and Vandael, David H and Gosso, Sara and Carbone, Emilio and Carabelli, Valentina},
journal = {Journal of Physiology},
number = {22},
pages = {4835 -- 4853},
publisher = {Wiley-Blackwell},
title = {{Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells}},
doi = {10.1113/JP271078},
volume = {593},
year = {2015},
}
@article{1584,
abstract = {We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.},
author = {Biedl, Therese and Held, Martin and Huber, Stefan and Kaaser, Dominik and Palfrader, Peter},
journal = {Computational Geometry: Theory and Applications},
number = {5},
pages = {429 -- 442},
publisher = {Elsevier},
title = {{Reprint of: Weighted straight skeletons in the plane}},
doi = {10.1016/j.comgeo.2015.01.004},
volume = {48},
year = {2015},
}
@article{1589,
abstract = {We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices.},
author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system}},
doi = {10.1038/srep18589},
volume = {5},
year = {2015},
}
@article{1572,
abstract = {We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.
},
author = {Correggi, Michele and Giuliani, Alessandro and Seiringer, Robert},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {279 -- 307},
publisher = {Springer},
title = {{Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet}},
doi = {10.1007/s00220-015-2402-0},
volume = {339},
year = {2015},
}
@inproceedings{1596,
abstract = {Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon.},
author = {Fulek, Radoslav and Radoičić, Radoš},
location = {Los Angeles, CA, United States},
pages = {373 -- 379},
publisher = {Springer},
title = {{Vertical visibility among parallel polygons in three dimensions}},
doi = {10.1007/978-3-319-27261-0_31},
volume = {9411},
year = {2015},
}
@article{1577,
abstract = {Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.},
author = {Carvalho, Antonio and Vicoso, Beatriz and Russo, Claudia and Swenor, Bonnielin and Clark, Andrew},
journal = {PNAS},
number = {40},
pages = {12450 -- 12455},
publisher = {National Academy of Sciences},
title = {{Birth of a new gene on the Y chromosome of Drosophila melanogaster}},
doi = {10.1073/pnas.1516543112},
volume = {112},
year = {2015},
}
@article{1623,
abstract = {Background
Photosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.
Results
We present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.
Conclusions
The workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.
},
author = {Hammar, Petter and Angermayr, Andreas and Sjostrom, Staffan and Van Der Meer, Josefin and Hellingwerf, Klaas and Hudson, Elton and Joensson, Hakaan},
journal = {Biotechnology for Biofuels},
number = {1},
publisher = {BioMed Central},
title = {{Single-cell screening of photosynthetic growth and lactate production by cyanobacteria}},
doi = {10.1186/s13068-015-0380-2},
volume = {8},
year = {2015},
}
@inproceedings{1628,
abstract = {We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications.},
author = {Schumacher, Christian and Bickel, Bernd and Rys, Jan and Marschner, Steve and Daraio, Chiara and Gross, Markus},
location = {Los Angeles, CA, USA},
number = {4},
publisher = {ACM},
title = {{Microstructures to control elasticity in 3D printing}},
doi = {10.1145/2766926},
volume = {34},
year = {2015},
}
@article{1611,
abstract = {Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue.},
author = {Whitfield, Jason and Zhang, William and Herde, Michel and Clifton, Ben and Radziejewski, Johanna and Janovjak, Harald L and Henneberger, Christian and Jackson, Colin},
journal = {Protein Science},
number = {9},
pages = {1412 -- 1422},
publisher = {Wiley},
title = {{Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction}},
doi = {10.1002/pro.2721},
volume = {24},
year = {2015},
}
@article{1635,
abstract = {We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.},
author = {Erbar, Matthias and Maas, Jan and Tetali, Prasad},
journal = {Annales de la faculté des sciences de Toulouse},
number = {4},
pages = {781 -- 800},
publisher = {Univ. Paul Sabatier},
title = {{Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models}},
doi = {10.5802/afst.1464},
volume = {24},
year = {2015},
}
@article{1666,
abstract = {Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics.},
author = {Tugrul, Murat and Paixao, Tiago and Barton, Nicholas H and Tkacik, Gasper},
journal = {PLoS Genetics},
number = {11},
publisher = {Public Library of Science},
title = {{Dynamics of transcription factor binding site evolution}},
doi = {10.1371/journal.pgen.1005639},
volume = {11},
year = {2015},
}
@inproceedings{1685,
abstract = {Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.
Our techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest.},
author = {Cohen Addad, Vincent and De Mesmay, Arnaud N},
location = {Patras, Greece},
pages = {386 -- 398},
publisher = {Springer},
title = {{A fixed parameter tractable approximation scheme for the optimal cut graph of a surface}},
doi = {10.1007/978-3-662-48350-3_33},
volume = {9294},
year = {2015},
}
@inproceedings{1647,
abstract = {Round-optimal blind signatures are notoriously hard to construct in the standard model, especially in the malicious-signer model, where blindness must hold under adversarially chosen keys. This is substantiated by several impossibility results. The only construction that can be termed theoretically efficient, by Garg and Gupta (Eurocrypt’14), requires complexity leveraging, inducing an exponential security loss. We present a construction of practically efficient round-optimal blind signatures in the standard model. It is conceptually simple and builds on the recent structure-preserving signatures on equivalence classes (SPSEQ) from Asiacrypt’14. While the traditional notion of blindness follows from standard assumptions, we prove blindness under adversarially chosen keys under an interactive variant of DDH. However, we neither require non-uniform assumptions nor complexity leveraging. We then show how to extend our construction to partially blind signatures and to blind signatures on message vectors, which yield a construction of one-show anonymous credentials à la “anonymous credentials light” (CCS’13) in the standard model. Furthermore, we give the first SPS-EQ construction under noninteractive assumptions and show how SPS-EQ schemes imply conventional structure-preserving signatures, which allows us to apply optimality results for the latter to SPS-EQ.},
author = {Fuchsbauer, Georg and Hanser, Christian and Slamanig, Daniel},
location = {Santa Barbara, CA, United States},
pages = {233 -- 253},
publisher = {Springer},
title = {{Practical round-optimal blind signatures in the standard model}},
doi = {10.1007/978-3-662-48000-7_12},
volume = {9216},
year = {2015},
}
@inproceedings{1654,
abstract = {HMAC and its variant NMAC are the most popular approaches to deriving a MAC (and more generally, a PRF) from a cryptographic hash function. Despite nearly two decades of research, their exact security still remains far from understood in many different contexts. Indeed, recent works have re-surfaced interest for {\em generic} attacks, i.e., attacks that treat the compression function of the underlying hash function as a black box.
Generic security can be proved in a model where the underlying compression function is modeled as a random function -- yet, to date, the question of proving tight, non-trivial bounds on the generic security of HMAC/NMAC even as a PRF remains a challenging open question.
In this paper, we ask the question of whether a small modification to HMAC and NMAC can allow us to exactly characterize the security of the resulting constructions, while only incurring little penalty with respect to efficiency. To this end, we present simple variants of NMAC and HMAC, for which we prove tight bounds on the generic PRF security, expressed in terms of numbers of construction and compression function queries necessary to break the construction. All of our constructions are obtained via a (near) {\em black-box} modification of NMAC and HMAC, which can be interpreted as an initial step of key-dependent message pre-processing.
While our focus is on PRF security, a further attractive feature of our new constructions is that they clearly defeat all recent generic attacks against properties such as state recovery and universal forgery. These exploit properties of the so-called ``functional graph'' which are not directly accessible in our new constructions. },
author = {Gazi, Peter and Pietrzak, Krzysztof Z and Tessaro, Stefano},
location = {Auckland, New Zealand},
pages = {85 -- 109},
publisher = {Springer},
title = {{Generic security of NMAC and HMAC with input whitening}},
doi = {10.1007/978-3-662-48800-3_4},
volume = {9453},
year = {2015},
}
@article{1642,
abstract = {The Hanani-Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this result to clustered graphs with two disjoint clusters, and show that a straightforward extension to flat clustered graphs with three or more disjoint clusters is not possible. For general clustered graphs we show a variant of the Hanani-Tutte theorem in the case when each cluster induces a connected subgraph. Di Battista and Frati proved that clustered planarity of embedded clustered graphs whose every face is incident to at most five vertices can be tested in polynomial time. We give a new and short proof of this result, using the matroid intersection algorithm.},
author = {Fulek, Radoslav and Kynčl, Jan and Malinovič, Igor and Pálvölgyi, Dömötör},
journal = {Electronic Journal of Combinatorics},
number = {4},
publisher = {Electronic Journal of Combinatorics},
title = {{Clustered planarity testing revisited}},
volume = {22},
year = {2015},
}
@article{1700,
abstract = {We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.},
author = {Van Loon, Erik and Katsnelson, Mikhail and Lemeshko, Mikhail},
journal = {Physical Review B},
number = {8},
publisher = {American Physical Society},
title = {{Ultralong-range order in the Fermi-Hubbard model with long-range interactions}},
doi = {10.1103/PhysRevB.92.081106},
volume = {92},
year = {2015},
}
@article{1712,
abstract = {The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses.},
author = {Ratheesh, Aparna and Belyaeva, Vera and Siekhaus, Daria E},
journal = {Current Opinion in Cell Biology},
number = {10},
pages = {71 -- 79},
publisher = {Elsevier},
title = {{Drosophila immune cell migration and adhesion during embryonic development and larval immune responses}},
doi = {10.1016/j.ceb.2015.07.003},
volume = {36},
year = {2015},
}
@article{1813,
abstract = {We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.},
author = {Schmidt, Richard and Lemeshko, Mikhail},
journal = {Physical Review Letters},
number = {20},
publisher = {American Physical Society},
title = {{Rotation of quantum impurities in the presence of a many-body environment}},
doi = {10.1103/PhysRevLett.114.203001},
volume = {114},
year = {2015},
}
@article{1818,
abstract = {Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.},
author = {Polechova, Jitka and Barton, Nicholas H},
journal = {PNAS},
number = {20},
pages = {6401 -- 6406},
publisher = {National Academy of Sciences},
title = {{Limits to adaptation along environmental gradients}},
doi = {10.1073/pnas.1421515112},
volume = {112},
year = {2015},
}
@article{1837,
abstract = {Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed.},
author = {Kühnen, Jakob and Braunshier, P and Schwegel, M and Kuhlmann, Hendrik and Hof, Björn},
journal = {Journal of Fluid Mechanics},
number = {5},
publisher = {Cambridge University Press},
title = {{Subcritical versus supercritical transition to turbulence in curved pipes}},
doi = {10.1017/jfm.2015.184},
volume = {770},
year = {2015},
}
@article{1793,
abstract = {We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.},
author = {Symonova, Olga and Topp, Christopher and Edelsbrunner, Herbert},
journal = {PLoS One},
number = {6},
publisher = {Public Library of Science},
title = {{DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots}},
doi = {10.1371/journal.pone.0127657},
volume = {10},
year = {2015},
}
@article{1868,
abstract = {We investigate high-dimensional nonlinear dynamical systems exhibiting multiple resonances under adiabatic parameter variations. Our motivations come from experimental considerations where time-dependent sweeping of parameters is a practical approach to probing and characterizing the bifurcations of the system. The question is whether bifurcations so detected are faithful representations of the bifurcations intrinsic to the original stationary system. Utilizing a harmonically forced, closed fluid flow system that possesses multiple resonances and solving the Navier-Stokes equation under proper boundary conditions, we uncover the phenomenon of the early effect. Specifically, as a control parameter, e.g., the driving frequency, is adiabatically increased from an initial value, resonances emerge at frequency values that are lower than those in the corresponding stationary system. The phenomenon is established by numerical characterization of physical quantities through the resonances, which include the kinetic energy and the vorticity field, and a heuristic analysis based on the concept of instantaneous frequency. A simple formula is obtained which relates the resonance points in the time-dependent and time-independent systems. Our findings suggest that, in general, any true bifurcation of a nonlinear dynamical system can be unequivocally uncovered through adiabatic parameter sweeping, in spite of a shift in the bifurcation point, which is of value to experimental studies of nonlinear dynamical systems.},
author = {Park, Youngyong and Do, Younghae and Altmeyer, Sebastian and Lai, Yingcheng and Lee, Gyuwon},
issn = {1539-3755},
journal = {Physical Review E},
number = {2},
publisher = {American Physical Society},
title = {{Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances}},
doi = {10.1103/PhysRevE.91.022906},
volume = {91},
year = {2015},
}
@article{1940,
abstract = {We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.},
author = {Sokolowski, Thomas R and Tkacik, Gasper},
journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics},
number = {6},
publisher = {American Institute of Physics},
title = {{Optimizing information flow in small genetic networks. IV. Spatial coupling}},
doi = {10.1103/PhysRevE.91.062710},
volume = {91},
year = {2015},
}
@article{1938,
abstract = {We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2.},
author = {Pausinger, Florian and Steinerberger, Stefan},
journal = {Physics Letters, Section A},
number = {6},
pages = {535 -- 541},
publisher = {Elsevier},
title = {{On the distribution of local extrema in quantum chaos}},
doi = {10.1016/j.physleta.2014.12.010},
volume = {379},
year = {2015},
}
@article{1849,
abstract = {Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.},
author = {Himschoot, Ellie and Beeckman, Tom and Friml, Jiřĺ and Vanneste, Steffen},
journal = {Biochimica et Biophysica Acta - Molecular Cell Research},
number = {9},
pages = {2168 -- 2172},
publisher = {Elsevier},
title = {{Calcium is an organizer of cell polarity in plants}},
doi = {10.1016/j.bbamcr.2015.02.017},
volume = {1853},
year = {2015},
}
@article{1851,
abstract = {We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them.},
author = {Priklopil, Tadeas and Kisdi, Eva and Gyllenberg, Mats},
journal = {Evolution},
number = {4},
pages = {1015 -- 1026},
publisher = {Wiley-Blackwell},
title = {{Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating}},
doi = {10.1111/evo.12618},
volume = {69},
year = {2015},
}
@article{2025,
abstract = {Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.},
author = {Kawada, Daiki and Kobayashi, Hiromu and Tomita, Tsuyoshi and Nakata, Eisuke and Nagano, Makoto and Siekhaus, Daria E and Toshima, Junko and Toshimaa, Jiro},
journal = {Biochimica et Biophysica Acta - Molecular Cell Research},
number = {1},
pages = {144 -- 156},
publisher = {Elsevier},
title = {{The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins}},
doi = {10.1016/j.bbamcr.2014.10.009},
volume = {1853},
year = {2015},
}
@phdthesis{1399,
abstract = {This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold.},
author = {Pausinger, Florian},
pages = {144},
publisher = {IST Austria},
title = {{On the approximation of intrinsic volumes}},
year = {2015},
}
@article{3585,
abstract = {We prove that the dual of the digital Voronoi diagram constructed by flooding the plane from the data points gives a geometrically and topologically correct dual triangulation. This provides the proof of correctness for
recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional
Delaunay triangulations.},
author = {Cao, Thanh and Edelsbrunner, Herbert and Tan, Tiow},
journal = {Computational Geometry: Theory and Applications},
number = {7},
pages = {507 -- 519},
publisher = {Elsevier},
title = {{Proof of correctness of the digital Delaunay triangulation algorithm}},
doi = {10.1016/j.comgeo.2015.04.001},
volume = {48},
year = {2015},
}
@article{477,
abstract = {Dendritic cells are potent antigen-presenting cells endowed with the unique ability to initiate adaptive immune responses upon inflammation. Inflammatory processes are often associated with an increased production of serotonin, which operates by activating specific receptors. However, the functional role of serotonin receptors in regulation of dendritic cell functions is poorly understood. Here, we demonstrate that expression of serotonin receptor 5-HT7 (5-HT7TR) as well as its downstream effector Cdc42 is upregulated in dendritic cells upon maturation. Although dendritic cell maturation was independent of 5-HT7TR, receptor stimulation affected dendritic cell morphology through Cdc42-mediated signaling. In addition, basal activity of 5-HT7TR was required for the proper expression of the chemokine receptor CCR7, which is a key factor that controls dendritic cell migration. Consistent with this, we observed that 5-HT7TR enhances chemotactic motility of dendritic cells in vitro by modulating their directionality and migration velocity. Accordingly, migration of dendritic cells in murine colon explants was abolished after pharmacological receptor inhibition. Our results indicate that there is a crucial role for 5-HT7TR-Cdc42-mediated signaling in the regulation of dendritic cell morphology and motility, suggesting that 5-HT7TR could be a new target for treatment of a variety of inflammatory and immune disorders.},
author = {Holst, Katrin and Guseva, Daria and Schindler, Susann and Sixt, Michael K and Braun, Armin and Chopra, Himpriya and Pabst, Oliver and Ponimaskin, Evgeni},
journal = {Journal of Cell Science},
number = {15},
pages = {2866 -- 2880},
publisher = {Company of Biologists},
title = {{The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells}},
doi = {10.1242/jcs.167999},
volume = {128},
year = {2015},
}
@article{802,
abstract = {Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis.},
author = {Engel, Jakob and Schmalhorst, Philipp S and Kruger, Anke and Muller, Christina and Buettner, Falk and Routier, Françoise},
journal = {Glycobiology},
number = {12},
pages = {1423 -- 1430},
publisher = {Oxford University Press},
title = {{Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis}},
doi = {10.1093/glycob/cwv059},
volume = {25},
year = {2015},
}
@article{1591,
abstract = {Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well.},
author = {Adamowski, Maciek and Friml, Jirí},
journal = {Plant Cell},
number = {1},
pages = {20 -- 32},
publisher = {American Society of Plant Biologists},
title = {{PIN-dependent auxin transport: Action, regulation, and evolution}},
doi = {10.1105/tpc.114.134874},
volume = {27},
year = {2015},
}
@inproceedings{1510,
abstract = {The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. },
author = {Franek, Peter and Krcál, Marek},
location = {Eindhoven, Netherlands},
pages = {842 -- 856},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{On computability and triviality of well groups}},
doi = {10.4230/LIPIcs.SOCG.2015.842},
volume = {34},
year = {2015},
}
@misc{5430,
abstract = {We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean- payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m = O ( n ) ) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a mul- tiplicative factor of ∊ in time O ( n · log( n/∊ )) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O ( n · log( | a · b · n | )) = O ( n · log( n · W )) , when the output is a b , as compared to the previously best known algorithm with running time O ( n 2 · log( n · W )) . Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O ( n 2 · m ) time and the associated decision problem can be solved in O ( n · m ) time, improving the previous known O ( n 3 · m · log( n · W )) and O ( n 2 · m ) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O ( n · log n ) time, improving the previous known O ( n 4 · log( n · W )) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
issn = {2664-1690},
pages = {31},
publisher = {IST Austria},
title = {{Faster algorithms for quantitative verification in constant treewidth graphs}},
doi = {10.15479/AT:IST-2015-319-v1-1},
year = {2015},
}
@inproceedings{1541,
abstract = {We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision.},
author = {Ray, Rajarshi and Gurung, Amit and Das, Binayak and Bartocci, Ezio and Bogomolov, Sergiy and Grosu, Radu},
location = {Haifa, Israel},
pages = {3 -- 18},
publisher = {Springer},
title = {{XSpeed: Accelerating reachability analysis on multi-core processors}},
doi = {10.1007/978-3-319-26287-1_1},
volume = {9434},
year = {2015},
}
@article{1553,
abstract = {Cell movement has essential functions in development, immunity, and cancer. Various cell migration patterns have been reported, but no general rule has emerged so far. Here, we show on the basis of experimental data in vitro and in vivo that cell persistence, which quantifies the straightness of trajectories, is robustly coupled to cell migration speed. We suggest that this universal coupling constitutes a generic law of cell migration, which originates in the advection of polarity cues by an actin cytoskeleton undergoing flows at the cellular scale. Our analysis relies on a theoretical model that we validate by measuring the persistence of cells upon modulation of actin flow speeds and upon optogenetic manipulation of the binding of an actin regulator to actin filaments. Beyond the quantitative prediction of the coupling, the model yields a generic phase diagram of cellular trajectories, which recapitulates the full range of observed migration patterns.},
author = {Maiuri, Paolo and Rupprecht, Jean and Wieser, Stefan and Ruprecht, Verena and Bénichou, Olivier and Carpi, Nicolas and Coppey, Mathieu and De Beco, Simon and Gov, Nir and Heisenberg, Carl-Philipp J and Lage Crespo, Carolina and Lautenschlaeger, Franziska and Le Berre, Maël and Lennon Duménil, Ana and Raab, Matthew and Thiam, Hawa and Piel, Matthieu and Sixt, Michael K and Voituriez, Raphaël},
journal = {Cell},
number = {2},
pages = {374 -- 386},
publisher = {Cell Press},
title = {{Actin flows mediate a universal coupling between cell speed and cell persistence}},
doi = {10.1016/j.cell.2015.01.056},
volume = {161},
year = {2015},
}
@article{1539,
abstract = {Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. },
author = {Ruess, Jakob},
journal = {Journal of Chemical Physics},
number = {24},
publisher = {American Institute of Physics},
title = {{Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space}},
doi = {10.1063/1.4937937},
volume = {143},
year = {2015},
}
@inproceedings{1609,
abstract = {The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Vardi, Moshe},
location = {Kyoto, Japan},
pages = {108 -- 120},
publisher = {Springer},
title = {{The complexity of synthesis from probabilistic components}},
doi = {10.1007/978-3-662-47666-6_9},
volume = {9135},
year = {2015},
}
@inproceedings{1692,
abstract = {Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples.},
author = {Frehse, Goran and Bogomolov, Sergiy and Greitschus, Marius and Strump, Thomas and Podelski, Andreas},
booktitle = {Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control},
isbn = {978-1-4503-3433-4},
location = {Seattle, WA, United States},
pages = {149 -- 158},
publisher = {ACM},
title = {{Eliminating spurious transitions in reachability with support functions}},
doi = {10.1145/2728606.2728622},
year = {2015},
}
@article{1697,
abstract = {Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.},
author = {Marre, Olivier and Botella Soler, Vicente and Simmons, Kristina and Mora, Thierry and Tkacik, Gasper and Berry, Michael},
journal = {PLoS Computational Biology},
number = {7},
publisher = {Public Library of Science},
title = {{High accuracy decoding of dynamical motion from a large retinal population}},
doi = {10.1371/journal.pcbi.1004304},
volume = {11},
year = {2015},
}
@article{1673,
abstract = {When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement-that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two. },
author = {Adlam, Ben and Chatterjee, Krishnendu and Nowak, Martin},
journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
number = {2181},
publisher = {Royal Society of London},
title = {{Amplifiers of selection}},
doi = {10.1098/rspa.2015.0114},
volume = {471},
year = {2015},
}
@inproceedings{1630,
abstract = {We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction.},
author = {Guerrero, Paul and Jeschke, Stefan and Wimmer, Michael and Wonka, Peter},
location = {Los Angeles, CA, United States},
number = {4},
publisher = {ACM},
title = {{Learning shape placements by example}},
doi = {10.1145/2766933},
volume = {34},
year = {2015},
}
@article{1678,
abstract = {High-throughput live-cell screens are intricate elements of systems biology studies and drug discovery pipelines. Here, we demonstrate an optogenetics-assisted method that avoids the need for chemical activators and reporters, reduces the number of operational steps and increases information content in a cell-based small-molecule screen against human protein kinases, including an orphan receptor tyrosine kinase. This blueprint for all-optical screening can be adapted to many drug targets and cellular processes.},
author = {Inglés Prieto, Álvaro and Gschaider-Reichhart, Eva and Muellner, Markus and Nowak, Matthias and Nijman, Sebastian and Grusch, Michael and Janovjak, Harald L},
journal = {Nature Chemical Biology},
number = {12},
pages = {952 -- 954},
publisher = {Nature Publishing Group},
title = {{Light-assisted small-molecule screening against protein kinases}},
doi = {10.1038/nchembio.1933},
volume = {11},
year = {2015},
}
@article{1680,
abstract = {We consider the satisfiability problem for modal logic over first-order definable classes of frames.We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is eitherNP-complete or PSPACE-complete, and global satisfiability is NP-complete, PSPACE-complete, or ExpTime-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability.},
author = {Michaliszyn, Jakub and Otop, Jan and Kieroňski, Emanuel},
journal = {ACM Transactions on Computational Logic},
number = {1},
publisher = {ACM},
title = {{On the decidability of elementary modal logics}},
doi = {10.1145/2817825},
volume = {17},
year = {2015},
}
@inproceedings{1659,
abstract = {The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata.},
author = {Boker, Udi and Henzinger, Thomas A and Otop, Jan},
booktitle = {LICS},
issn = {1043-6871 },
location = {Kyoto, Japan},
pages = {750 -- 761},
publisher = {IEEE},
title = {{The target discounted-sum problem}},
doi = {10.1109/LICS.2015.74},
year = {2015},
}
@article{1856,
abstract = {The traditional synthesis question given a specification asks for the automatic construction of a system that satisfies the specification, whereas often there exists a preference order among the different systems that satisfy the given specification. Under a probabilistic assumption about the possible inputs, such a preference order is naturally expressed by a weighted automaton, which assigns to each word a value, such that a system is preferred if it generates a higher expected value. We solve the following optimal synthesis problem: given an omega-regular specification, a Markov chain that describes the distribution of inputs, and a weighted automaton that measures how well a system satisfies the given specification under the input assumption, synthesize a system that optimizes the measured value. For safety specifications and quantitative measures that are defined by mean-payoff automata, the optimal synthesis problem reduces to finding a strategy in a Markov decision process (MDP) that is optimal for a long-run average reward objective, which can be achieved in polynomial time. For general omega-regular specifications along with mean-payoff automata, the solution rests on a new, polynomial-time algorithm for computing optimal strategies in MDPs with mean-payoff parity objectives. Our algorithm constructs optimal strategies that consist of two memoryless strategies and a counter. The counter is in general not bounded. To obtain a finite-state system, we show how to construct an ε-optimal strategy with a bounded counter, for all ε > 0. Furthermore, we show how to decide in polynomial time if it is possible to construct an optimal finite-state system (i.e., a system without a counter) for a given specification. We have implemented our approach and the underlying algorithms in a tool that takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. We present some experimental results showing optimal systems that were automatically generated in this way.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara and Singh, Rohit},
journal = {Journal of the ACM},
number = {1},
publisher = {ACM},
title = {{Measuring and synthesizing systems in probabilistic environments}},
doi = {10.1145/2699430},
volume = {62},
year = {2015},
}
@inproceedings{1882,
abstract = {We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations.},
author = {Fahrenberg, Uli and Kretinsky, Jan and Legay, Axel and Traonouez, Louis},
location = {Bertinoro, Italy},
pages = {306 -- 324},
publisher = {Springer},
title = {{Compositionality for quantitative specifications}},
doi = {10.1007/978-3-319-15317-9_19},
volume = {8997},
year = {2015},
}