@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{1581,
  abstract     = {In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation.},
  author       = {Bollenbach, Mark Tobias and Heisenberg, Carl-Philipp J},
  journal      = {Cell},
  number       = {3},
  pages        = {431 -- 432},
  publisher    = {Cell Press},
  title        = {{Gradients are shaping up}},
  doi          = {10.1016/j.cell.2015.04.009},
  volume       = {161},
  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{1585,
  abstract     = {In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004).},
  author       = {Bao, Zhigang and Pan, Guangming and Zhou, Wang},
  journal      = {IEEE Transactions on Information Theory},
  number       = {6},
  pages        = {3413 -- 3426},
  publisher    = {IEEE},
  title        = {{Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices}},
  doi          = {10.1109/TIT.2015.2421894},
  volume       = {61},
  year         = {2015},
}

@article{1586,
  abstract     = {Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass.},
  author       = {Angermayr, Andreas and Gorchs, Aleix and Hellingwerf, Klaas},
  journal      = {Trends in Biotechnology},
  number       = {6},
  pages        = {352 -- 361},
  publisher    = {Elsevier},
  title        = {{Metabolic engineering of cyanobacteria for the synthesis of commodity products}},
  doi          = {10.1016/j.tibtech.2015.03.009},
  volume       = {33},
  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{1588,
  abstract     = {We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids.},
  author       = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying},
  journal      = {Physical Review E},
  number       = {5},
  publisher    = {American Physical Society},
  title        = {{Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows}},
  doi          = {10.1103/PhysRevE.92.053018},
  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},
  isbn         = {978-3-319-27260-3},
  location     = {Los Angeles, CA, United States},
  pages        = {335 -- 347},
  publisher    = {Springer Nature},
  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{1594,
  abstract     = {Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata.},
  author       = {Forejt, Vojtěch and Krčál, Jan and Kretinsky, Jan},
  location     = {Suva, Fiji},
  pages        = {162 -- 177},
  publisher    = {Springer},
  title        = {{Controller synthesis for MDPs and frequency LTL\GU}},
  doi          = {10.1007/978-3-662-48899-7_12},
  volume       = {9450},
  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},
}

@inbook{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},
  booktitle    = {Graph Drawing and Network Visualization},
  isbn         = {978-3-319-27260-3},
  location     = {Los Angeles, CA, United States},
  pages        = {373 -- 379},
  publisher    = {Springer Nature},
  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},
}