@article{1564,
author = {Gilson, Matthieu and Savin, Cristina and Zenke, Friedemann},
journal = {Frontiers in Computational Neuroscience},
number = {11},
publisher = {Frontiers Research Foundation},
title = {{Editorial: Emergent neural computation from the interaction of different forms of plasticity}},
doi = {10.3389/fncom.2015.00145},
volume = {9},
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{1566,
abstract = {Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease.},
author = {Gómez Sicilia, Àngel and Sikora, Mateusz K and Cieplak, Marek and Carrión Vázquez, Mariano},
journal = {PLoS Computational Biology},
number = {10},
publisher = {Public Library of Science},
title = {{An exploration of the universe of polyglutamine structures}},
doi = {10.1371/journal.pcbi.1004541},
volume = {11},
year = {2015},
}
@article{1569,
abstract = {Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.},
author = {Doyle, Siamsa and Haegera, Ash and Vain, Thomas and Rigala, Adeline and Viotti, Corrado and Łangowskaa, Małgorzata and Maa, Qian and Friml, Jirí and Raikhel, Natasha and Hickse, Glenn and Robert, Stéphanie},
journal = {PNAS},
number = {7},
pages = {E806 -- E815},
publisher = {National Academy of Sciences},
title = {{An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana}},
doi = {10.1073/pnas.1424856112},
volume = {112},
year = {2015},
}
@article{1570,
abstract = {Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.},
author = {Der, Ralf and Martius, Georg S},
journal = {PNAS},
number = {45},
pages = {E6224 -- E6232},
publisher = {National Academy of Sciences},
title = {{Novel plasticity rule can explain the development of sensorimotor intelligence}},
doi = {10.1073/pnas.1508400112},
volume = {112},
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},
}
@article{1573,
abstract = {We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau.},
author = {Chen, Thomas and Hainzl, Christian and Pavlović, Nataša and Seiringer, Robert},
journal = {Communications on Pure and Applied Mathematics},
number = {10},
pages = {1845 -- 1884},
publisher = {Wiley},
title = {{Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti}},
doi = {10.1002/cpa.21552},
volume = {68},
year = {2015},
}
@article{1574,
abstract = {Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.},
author = {Chen, Qian and Liu, Yang and Maere, Steven and Lee, Eunkyoung and Van Isterdael, Gert and Xie, Zidian and Xuan, Wei and Lucas, Jessica and Vassileva, Valya and Kitakura, Saeko and Marhavy, Peter and Wabnik, Krzysztof T and Geldner, Niko and Benková, Eva and Le, Jie and Fukaki, Hidehiro and Grotewold, Erich and Li, Chuanyou and Friml, Jirí and Sack, Fred and Beeckman, Tom and Vanneste, Steffen},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development}},
doi = {10.1038/ncomms9821},
volume = {6},
year = {2015},
}
@article{1575,
abstract = {The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space.},
author = {Chabaud, Mélanie and Heuzé, Mélina and Bretou, Marine and Vargas, Pablo and Maiuri, Paolo and Solanes, Paola and Maurin, Mathieu and Terriac, Emmanuel and Le Berre, Maël and Lankar, Danielle and Piolot, Tristan and Adelstein, Robert and Zhang, Yingfan and Sixt, Michael K and Jacobelli, Jordan and Bénichou, Olivier and Voituriez, Raphaël and Piel, Matthieu and Lennon Duménil, Ana},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells}},
doi = {10.1038/ncomms8526},
volume = {6},
year = {2015},
}
@article{1576,
abstract = {Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state.},
author = {Cepeda Humerez, Sarah A and Rieckh, Georg and Tkacik, Gasper},
journal = {Physical Review Letters},
number = {24},
publisher = {American Physical Society},
title = {{Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation}},
doi = {10.1103/PhysRevLett.115.248101},
volume = {115},
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{1579,
abstract = {We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality.},
author = {Brooks, Christopher and Martin Del Campo Sanchez, Abraham and Sottile, Frank},
journal = {Transactions of the American Mathematical Society},
number = {6},
pages = {4183 -- 4206},
publisher = {American Mathematical Society},
title = {{Galois groups of Schubert problems of lines are at least alternating}},
doi = {10.1090/S0002-9947-2014-06192-8},
volume = {367},
year = {2015},
}
@article{1580,
abstract = {Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs.},
author = {Brenes, Oscar and Vandael, David H and Carbone, Emilio and Montarolo, Pier and Ghirardi, Mirella},
journal = {Neuroscience},
pages = {430 -- 443},
publisher = {Elsevier},
title = {{Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons}},
doi = {10.1016/j.neuroscience.2015.10.046},
volume = {311},
year = {2015},
}
@article{1582,
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 = {2},
pages = {120 -- 133},
publisher = {Elsevier},
title = {{Weighted straight skeletons in the plane}},
doi = {10.1016/j.comgeo.2014.08.006},
volume = {48},
year = {2015},
}
@article{1583,
abstract = {We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon.},
author = {Biedl, Therese and Held, Martin and Huber, Stefan and Kaaser, Dominik and Palfrader, Peter},
journal = {Information Processing Letters},
number = {2},
pages = {243 -- 247},
publisher = {Elsevier},
title = {{A simple algorithm for computing positively weighted straight skeletons of monotone polygons}},
doi = {10.1016/j.ipl.2014.09.021},
volume = {115},
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{1587,
abstract = {We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.},
author = {Amaro, Pedro and Fratini, Filippo and Safari, Laleh and Antognini, Aldo and Indelicato, Paul and Pohl, Randolf and Santos, José},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {6},
publisher = {American Physical Society},
title = {{Quantum interference shifts in laser spectroscopy with elliptical polarization}},
doi = {10.1103/PhysRevA.92.062506},
volume = {92},
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},
}
@inbook{1590,
abstract = {The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed.},
author = {Aichholzer, Oswin and Biedl, Therese and Hackl, Thomas and Held, Martin and Huber, Stefan and Palfrader, Peter and Vogtenhuber, Birgit},
booktitle = {Graph Drawing and Network Visualization},
location = {Los Angeles, CA, United States},
pages = {335 -- 347},
publisher = {Springer},
title = {{Representing directed trees as straight skeletons}},
doi = {10.1007/978-3-319-27261-0_28},
volume = {9411},
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},
}
@article{1593,
abstract = {Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.},
author = {Žádníková, Petra and Smet, Dajo and Zhu, Qiang and Van Der Straeten, Dominique and Benková, Eva},
journal = {Frontiers in Plant Science},
number = {4},
publisher = {Frontiers Research Foundation},
title = {{Strategies of seedlings to overcome their sessile nature: Auxin in mobility control}},
doi = {10.3389/fpls.2015.00218},
volume = {6},
year = {2015},
}
@inproceedings{1595,
abstract = {A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.},
author = {Fulek, Radoslav and Pelsmajer, Michael and Schaefer, Marcus},
location = {Los Angeles, CA, USA},
pages = {99 -- 110},
publisher = {Springer},
title = {{Hanani-Tutte for radial planarity}},
doi = {10.1007/978-3-319-27261-0_9},
volume = {9411},
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{1598,
abstract = {We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure winning vertices such that the objective can be ensured with probability 1 from these vertices. We study for the first time the average-case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average-case running time is linear (as compared to the worst-case linear number of iterations and quadratic time complexity). Second, for the average-case analysis over all MDPs we show that the expected number of iterations is constant and the average-case running time is linear (again as compared to the worst-case linear number of iterations and quadratic time complexity). Finally we also show that when all MDPs are equally likely, the probability that the classical algorithm requires more than a constant number of iterations is exponentially small.},
author = {Chatterjee, Krishnendu and Joglekar, Manas and Shah, Nisarg},
journal = {Theoretical Computer Science},
number = {3},
pages = {71 -- 89},
publisher = {Elsevier},
title = {{Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives}},
doi = {10.1016/j.tcs.2015.01.050},
volume = {573},
year = {2015},
}
@inproceedings{1601,
abstract = {We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata.},
author = {Babiak, Tomáš and Blahoudek, František and Duret Lutz, Alexandre and Klein, Joachim and Kretinsky, Jan and Mueller, Daniel and Parker, David and Strejček, Jan},
location = {San Francisco, CA, United States},
pages = {479 -- 486},
publisher = {Springer},
title = {{The Hanoi omega-automata format}},
doi = {10.1007/978-3-319-21690-4_31},
volume = {9206},
year = {2015},
}
@article{1602,
abstract = {Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas and Goyal, Prateesh},
journal = {ACM SIGPLAN Notices},
location = {Mumbai, India},
number = {1},
pages = {97 -- 109},
publisher = {ACM},
title = {{Faster algorithms for algebraic path properties in recursive state machines with constant treewidth}},
doi = {10.1145/2676726.2676979},
volume = {50},
year = {2015},
}
@inproceedings{1603,
abstract = {For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation.
The key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.},
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Fellner, Andreas and Kretinsky, Jan},
location = {San Francisco, CA, United States},
pages = {158 -- 177},
publisher = {Springer},
title = {{Counterexample explanation by learning small strategies in Markov decision processes}},
doi = {10.1007/978-3-319-21690-4_10},
volume = {9206},
year = {2015},
}
@inproceedings{1605,
abstract = {Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model.},
author = {Bogomolov, Sergiy and Schilling, Christian and Bartocci, Ezio and Batt, Grégory and Kong, Hui and Grosu, Radu},
location = {Haifa, Israel},
pages = {19 -- 35},
publisher = {Springer},
title = {{Abstraction-based parameter synthesis for multiaffine systems}},
doi = {10.1007/978-3-319-26287-1_2},
volume = {9434},
year = {2015},
}
@inproceedings{1607,
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 multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) 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|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅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},
location = {San Francisco, CA, USA},
pages = {140 -- 157},
publisher = {Springer},
title = {{Faster algorithms for quantitative verification in constant treewidth graphs}},
doi = {10.1007/978-3-319-21690-4_9},
volume = {9206},
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},
}
@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{1614,
abstract = {GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. },
author = {Strüber, Michael and Jonas, Peter M and Bartos, Marlene},
journal = {PNAS},
number = {4},
pages = {1220 -- 1225},
publisher = {National Academy of Sciences},
title = {{Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells}},
doi = {10.1073/pnas.1412996112},
volume = {112},
year = {2015},
}
@article{1615,
abstract = {Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches.},
author = {Hammer, Matthieu and Krueger Burg, Dilja and Tuffy, Liam and Cooper, Benjamin and Taschenberger, Holger and Goswami, Sarit and Ehrenreich, Hannelore and Jonas, Peter M and Varoqueaux, Frederique and Rhee, Jeong and Brose, Nils},
journal = {Cell Reports},
number = {3},
pages = {516 -- 523},
publisher = {Cell Press},
title = {{Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism}},
doi = {10.1016/j.celrep.2015.09.011},
volume = {13},
year = {2015},
}
@article{1618,
abstract = {CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed.},
author = {Veldkamp, Christopher and Kiermaier, Eva and Gabel Eissens, Skylar and Gillitzer, Miranda and Lippner, David and Disilvio, Frank and Mueller, Casey and Wantuch, Paeton and Chaffee, Gary and Famiglietti, Michael and Zgoba, Danielle and Bailey, Asha and Bah, Yaya and Engebretson, Samantha and Graupner, David and Lackner, Emily and Larosa, Vincent and Medeiros, Tysha and Olson, Michael and Phillips, Andrew and Pyles, Harley and Richard, Amanda and Schoeller, Scott and Touzeau, Boris and Williams, Larry and Sixt, Michael K and Peterson, Francis},
journal = {Biochemistry},
number = {27},
pages = {4163 -- 4166},
publisher = {ACS},
title = {{Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites}},
doi = {10.1021/acs.biochem.5b00560},
volume = {54},
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},
}
@article{1624,
abstract = {Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions.},
author = {Pavlogiannis, Andreas and Chatterjee, Krishnendu and Adlam, Ben and Nowak, Martin},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Cellular cooperation with shift updating and repulsion}},
doi = {10.1038/srep17147},
volume = {5},
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},
}
@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},
}
@inproceedings{1632,
abstract = {This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling.
Although our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling.},
author = {Ando, Ryoichi and Thuerey, Nils and Wojtan, Christopher J},
location = {Los Angeles, CA, USA},
number = {4},
publisher = {ACM},
title = {{A stream function solver for liquid simulations}},
doi = {10.1145/2766935},
volume = {34},
year = {2015},
}
@inproceedings{1633,
abstract = {We present a method for simulating brittle fracture under the assumptions of quasi-static linear elastic fracture mechanics (LEFM). Using the boundary element method (BEM) and Lagrangian crack-fronts, we produce highly detailed fracture surfaces. The computational cost of the BEM is alleviated by using a low-resolution mesh and interpolating the resulting stress intensity factors when propagating the high-resolution crack-front.
Our system produces physics-based fracture surfaces with high spatial and temporal resolution, taking spatial variation of material toughness and/or strength into account. It also allows for crack initiation to be handled separately from crack propagation, which is not only more reasonable from a physics perspective, but can also be used to control the simulation.
Separating the resolution of the crack-front from the resolution of the computational mesh increases the efficiency and therefore the amount of visual detail on the resulting fracture surfaces. The BEM also allows us to re-use previously computed blocks of the system matrix.},
author = {Hahn, David and Wojtan, Christopher J},
location = {Los Angeles, CA, United States},
number = {4},
publisher = {ACM},
title = {{High-resolution brittle fracture simulation with boundary elements}},
doi = {10.1145/2766896},
volume = {34},
year = {2015},
}
@inproceedings{1634,
abstract = {Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart.},
author = {Da, Fang and Batty, Christopher and Wojtan, Christopher J and Grinspun, Eitan},
location = {Los Angeles, CA, United States},
number = {4},
publisher = {ACM},
title = {{Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams}},
doi = {10.1145/2767003},
volume = {34},
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},
}
@inproceedings{1636,
abstract = {Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism R→ΓΓ between two relational structures, e.g. between two directed graphs. Analyzing its complexity has been a prominent research direction, especially for the fixed template CSPs where the right side ΓΓ is fixed and the left side R is unconstrained.
Far fewer results are known for the hybrid setting that restricts both sides simultaneously. It assumes that R belongs to a certain class of relational structures (called a structural restriction in this paper). We study which structural restrictions are effective, i.e. there exists a fixed template ΓΓ (from a certain class of languages) for which the problem is tractable when R is restricted, and NP-hard otherwise. We provide a characterization for structural restrictions that are closed under inverse homomorphisms. The criterion is based on the chromatic number of a relational structure defined in this paper; it generalizes the standard chromatic number of a graph.
As our main tool, we use the algebraic machinery developed for fixed template CSPs. To apply it to our case, we introduce a new construction called a “lifted language”. We also give a characterization for structural restrictions corresponding to minor-closed families of graphs, extend results to certain Valued CSPs (namely conservative valued languages), and state implications for (valued) CSPs with ordered variables and for the maximum weight independent set problem on some restricted families of graphs.},
author = {Kolmogorov, Vladimir and Rolinek, Michal and Takhanov, Rustem},
location = {Nagoya, Japan},
pages = {566 -- 577},
publisher = {Springer},
title = {{Effectiveness of structural restrictions for hybrid CSPs}},
doi = {10.1007/978-3-662-48971-0_48},
volume = {9472},
year = {2015},
}
@inproceedings{1637,
abstract = {An instance of the Valued Constraint Satisfaction Problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P ≠ NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one deals only with the feasibility issue and there is no optimization. This case is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which constraint languages CSPs are tractable (i.e. solvable in polynomial time) and for which NP-hard. The case when all allowed functions take only finite values corresponds to finite-valued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Zivny. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e. the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.},
author = {Kolmogorov, Vladimir and Krokhin, Andrei and Rolinek, Michal},
location = {Berkeley, CA, United States},
pages = {1246 -- 1258},
publisher = {IEEE},
title = {{The complexity of general-valued CSPs}},
doi = {10.1109/FOCS.2015.80},
year = {2015},
}
@article{1639,
abstract = {In this paper the optimal transport and the metamorphosis perspectives are combined. For a pair of given input images geodesic paths in the space of images are defined as minimizers of a resulting path energy. To this end, the underlying Riemannian metric measures the rate of transport cost and the rate of viscous dissipation. Furthermore, the model is capable to deal with strongly varying image contrast and explicitly allows for sources and sinks in the transport equations which are incorporated in the metric related to the metamorphosis approach by Trouvé and Younes. In the non-viscous case with source term existence of geodesic paths is proven in the space of measures. The proposed model is explored on the range from merely optimal transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals. These functionals are defined on corresponding pairs of intensity functions and on associated pairwise matching deformations. Existence of time discrete geodesics is demonstrated. Furthermore, a finite element implementation is proposed and applied to instructive test cases and to real images. In the non-viscous case this is compared to the algorithm proposed by Benamou and Brenier including a discretization of the source term. Finally, the model is generalized to define discrete weighted barycentres with applications to textures and objects.},
author = {Maas, Jan and Rumpf, Martin and Schönlieb, Carola and Simon, Stefan},
journal = {ESAIM: Mathematical Modelling and Numerical Analysis},
number = {6},
pages = {1745 -- 1769},
publisher = {EDP Sciences},
title = {{A generalized model for optimal transport of images including dissipation and density modulation}},
doi = {10.1051/m2an/2015043},
volume = {49},
year = {2015},
}
@article{1640,
abstract = {Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.},
author = {Šimášková, Mária and O'Brien, José and Khan-Djamei, Mamoona and Van Noorden, Giel and Ötvös, Krisztina and Vieten, Anne and De Clercq, Inge and Van Haperen, Johanna and Cuesta, Candela and Hoyerová, Klára and Vanneste, Steffen and Marhavy, Peter and Wabnik, Krzysztof T and Van Breusegem, Frank and Nowack, Moritz and Murphy, Angus and Friml, Jiřĺ and Weijers, Dolf and Beeckman, Tom and Benková, Eva},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Cytokinin response factors regulate PIN-FORMED auxin transporters}},
doi = {10.1038/ncomms9717},
volume = {6},
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},
}
@inproceedings{1644,
abstract = {Increasing the computational complexity of evaluating a hash function, both for the honest users as well as for an adversary, is a useful technique employed for example in password-based cryptographic schemes to impede brute-force attacks, and also in so-called proofs of work (used in protocols like Bitcoin) to show that a certain amount of computation was performed by a legitimate user. A natural approach to adjust the complexity of a hash function is to iterate it c times, for some parameter c, in the hope that any query to the scheme requires c evaluations of the underlying hash function. However, results by Dodis et al. (Crypto 2012) imply that plain iteration falls short of achieving this goal, and designing schemes which provably have such a desirable property remained an open problem. This paper formalizes explicitly what it means for a given scheme to amplify the query complexity of a hash function. In the random oracle model, the goal of a secure query-complexity amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability, a random oracle allowing R queries (for the adversary) into one provably allowing only r < R queries. Turned around, this means that making r queries to the scheme requires at least R queries to the actual random oracle. Second, a new scheme, called collision-free iteration, is proposed and proven to achieve c-fold QCA for both the honest parties and the adversary, for any fixed parameter c.},
author = {Demay, Grégory and Gazi, Peter and Maurer, Ueli and Tackmann, Björn},
location = {Lugano, Switzerland},
pages = {159 -- 180},
publisher = {Springer},
title = {{Query-complexity amplification for random oracles}},
doi = {10.1007/978-3-319-17470-9_10},
volume = {9063},
year = {2015},
}
@inproceedings{1646,
abstract = {A pseudorandom function (PRF) is a keyed function F : K × X → Y where, for a random key k ∈ K, the function F(k, ·) is indistinguishable from a uniformly random function, given black-box access. A key-homomorphic PRF has the additional feature that for any keys k, k' and any input x, we have F(k+k', x) = F(k, x)⊕F(k', x) for some group operations +,⊕ on K and Y, respectively. A constrained PRF for a family of setsS ⊆ P(X) has the property that, given any key k and set S ∈ S, one can efficiently compute a “constrained” key kS that enables evaluation of F(k, x) on all inputs x ∈ S, while the values F(k, x) for x /∈ S remain pseudorandom even given kS. In this paper we construct PRFs that are simultaneously constrained and key homomorphic, where the homomorphic property holds even for constrained keys. We first show that the multilinear map-based bit-fixing and circuit-constrained PRFs of Boneh and Waters (Asiacrypt 2013) can be modified to also be keyhomomorphic. We then show that the LWE-based key-homomorphic PRFs of Banerjee and Peikert (Crypto 2014) are essentially already prefix-constrained PRFs, using a (non-obvious) definition of constrained keys and associated group operation. Moreover, the constrained keys themselves are pseudorandom, and the constraining and evaluation functions can all be computed in low depth. As an application of key-homomorphic constrained PRFs,we construct a proxy re-encryption schemewith fine-grained access control. This scheme allows storing encrypted data on an untrusted server, where each file can be encrypted relative to some attributes, so that only parties whose constrained keys match the attributes can decrypt. Moreover, the server can re-key (arbitrary subsets of) the ciphertexts without learning anything about the plaintexts, thus permitting efficient and finegrained revocation.},
author = {Banerjee, Abishek and Fuchsbauer, Georg and Peikert, Chris and Pietrzak, Krzysztof Z and Stevens, Sophie},
location = {Warsaw, Poland},
pages = {31 -- 60},
publisher = {Springer},
title = {{Key-homomorphic constrained pseudorandom functions}},
doi = {10.1007/978-3-662-46497-7_2},
volume = {9015},
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},
}