@misc{5556, abstract = {MATLAB code and processed datasets available for reproducing the results in: Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast. *equal contributions}, author = {Lukacisin, Martin and Landon, Matthieu and Jajoo, Rishi}, keywords = {transcription, pausing, backtracking, polymerase, RNA, NET-seq, nucleosome, basepairing}, publisher = {Institute of Science and Technology Austria}, title = {{MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'}}, doi = {10.15479/AT:ISTA:45}, year = {2016}, } @misc{5557, abstract = {Small synthetic discrete tomography problems. Sizes are 32x32, 64z64 and 256x256. Projection angles are 2, 4, and 6. Number of labels are 3 and 5.}, author = {Swoboda, Paul}, keywords = {discrete tomography}, publisher = {Institute of Science and Technology Austria}, title = {{Synthetic discrete tomography problems}}, doi = {10.15479/AT:ISTA:46}, year = {2016}, } @misc{5558, abstract = {PhD thesis LaTeX source code}, author = {Bojsen-Hansen, Morten}, publisher = {Institute of Science and Technology Austria}, title = {{Tracking, Correcting and Absorbing Water Surface Waves}}, doi = {10.15479/AT:ISTA:48}, year = {2016}, } @article{5749, abstract = {Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.}, author = {Wielgoss, Sébastien and Bergmiller, Tobias and Bischofberger, Anna M. and Hall, Alex R.}, issn = {1537-1719}, journal = {Molecular Biology and Evolution}, number = {3}, pages = {770--782}, publisher = {Oxford University Press}, title = {{Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria}}, doi = {10.1093/molbev/msv270}, volume = {33}, year = {2016}, } @inbook{5805, abstract = {Discretization of sphere in the integer space follows a particular discretization scheme, which, in principle, conforms to some topological model. This eventually gives rise to interesting topological properties of a discrete spherical surface, which need to be investigated for its analytical characterization. This paper presents some novel results on the local topological properties of the naive model of discrete sphere. They follow from the bijection of each quadraginta octant of naive sphere with its projection map called f -map on the corresponding functional plane and from the characterization of certain jumps in the f-map. As an application, we have shown how these properties can be used in designing an efficient reconstruction algorithm for a naive spherical surface from an input voxel set when it is sparse or noisy.}, author = {Sen, Nabhasmita and Biswas, Ranita and Bhowmick, Partha}, booktitle = {Computational Topology in Image Context}, isbn = {978-3-319-39440-4}, issn = {1611-3349}, location = {Marseille, France}, pages = {253--264}, publisher = {Springer Nature}, title = {{On some local topological properties of naive discrete sphere}}, doi = {10.1007/978-3-319-39441-1_23}, volume = {9667}, year = {2016}, } @inproceedings{5806, abstract = {Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane.}, author = {Biswas, Ranita and Bhowmick, Partha}, booktitle = {Discrete Geometry for Computer Imagery}, isbn = {978-3-319-32359-6}, issn = {0302-9743}, location = {Nantes, France}, pages = {256--267}, publisher = {Springer Nature}, title = {{On functionality of quadraginta octants of naive sphere with application to circle drawing}}, doi = {10.1007/978-3-319-32360-2_20}, volume = {9647}, year = {2016}, } @inbook{5809, abstract = {A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness.}, author = {Biswas, Ranita and Bhowmick, Partha and Brimkov, Valentin E.}, booktitle = {Combinatorial image analysis}, isbn = {978-3-319-26144-7}, issn = {1611-3349}, location = {Kolkata, India}, pages = {86--100}, publisher = {Springer Nature}, title = {{On the connectivity and smoothness of discrete spherical circles}}, doi = {10.1007/978-3-319-26145-4_7}, volume = {9448}, year = {2016}, } @article{1431, abstract = {The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow.}, author = {Tartally, András and Kelager, Andreas and Fürst, Matthias and Nash, David}, journal = {PeerJ}, number = {3}, publisher = {PeerJ}, title = {{Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon}}, doi = {10.7717/peerj.1865}, volume = {2016}, year = {2016}, } @article{1432, abstract = {CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network.}, author = {Mishra, Rajiv Kumar and Kim, Sooyun and Guzmán, José and Jonas, Peter M}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks}}, doi = {10.1038/ncomms11552}, volume = {7}, year = {2016}, } @article{1434, abstract = {We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B on scales down to N−2/3N−2/3.}, author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin}, journal = {Journal of Functional Analysis}, number = {3}, pages = {672 -- 719}, publisher = {Academic Press}, title = {{Local stability of the free additive convolution}}, doi = {10.1016/j.jfa.2016.04.006}, volume = {271}, year = {2016}, } @article{1435, abstract = {ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.}, author = {Guzmán, José and Gerevich, Zoltan}, journal = {Neural Plasticity}, publisher = {Hindawi Publishing Corporation}, title = {{P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction}}, doi = {10.1155/2016/1207393}, volume = {2016}, year = {2016}, } @article{1436, abstract = {We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system.}, author = {Bach, Volker and Breteaux, Sébastien and Petrat, Sören P and Pickl, Peter and Tzaneteas, Tim}, journal = {Journal de Mathématiques Pures et Appliquées}, number = {1}, pages = {1 -- 30}, publisher = {Elsevier}, title = {{Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction}}, doi = {10.1016/j.matpur.2015.09.003}, volume = {105}, year = {2016}, } @inproceedings{1437, abstract = {We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.}, author = {Chatterjee, Krishnendu and Goharshady, Amir and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas}, location = {St. Petersburg, FL, USA}, pages = {733 -- 747}, publisher = {ACM}, title = {{Algorithms for algebraic path properties in concurrent systems of constant treewidth components}}, doi = {10.1145/2837614.2837624}, volume = {20-22}, year = {2016}, } @inproceedings{1438, abstract = {In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.}, author = {Chatterjee, Krishnendu and Fu, Hongfei and Novotny, Petr and Hasheminezhad, Rouzbeh}, location = {St. Petersburg, FL, USA}, pages = {327 -- 342}, publisher = {ACM}, title = {{Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs}}, doi = {10.1145/2837614.2837639}, volume = {20-22}, year = {2016}, } @inproceedings{1439, abstract = {Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification.}, author = {Dragoi, Cezara and Henzinger, Thomas A and Zufferey, Damien}, location = {St. Petersburg, FL, USA}, pages = {400 -- 415}, publisher = {ACM}, title = {{PSYNC: A partially synchronous language for fault-tolerant distributed algorithms}}, doi = {10.1145/2837614.2837650}, volume = {20-22}, year = {2016}, } @article{1440, author = {Janovjak, Harald L}, journal = {Structure}, number = {2}, pages = {213 -- 215}, publisher = {Cell Press}, title = {{Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain}}, doi = {10.1016/j.str.2016.01.002}, volume = {24}, year = {2016}, } @article{1441, abstract = {Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.}, author = {Gschaider-Reichhart, Eva and Inglés Prieto, Álvaro and Tichy, Alexandra-Madelaine and Mckenzie, Catherine and Janovjak, Harald L}, journal = {Angewandte Chemie - International Edition}, number = {21}, pages = {6339 -- 6342}, publisher = {Wiley}, title = {{A phytochrome sensory domain permits receptor activation by red light}}, doi = {10.1002/anie.201601736}, volume = {55}, year = {2016}, } @article{1446, abstract = {The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index.}, author = {Calatrava Moreno, Maria and Auzinger, Thomas and Werthner, Hannes}, journal = {Scientometrics}, number = {1}, pages = {213 -- 232}, publisher = {Springer}, title = {{On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data}}, doi = {10.1007/s11192-016-1842-4}, volume = {107}, year = {2016}, } @article{1448, abstract = {We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.}, author = {Fathi, Max and Maas, Jan}, journal = {The Annals of Applied Probability}, number = {3}, pages = {1774 -- 1806}, publisher = {Institute of Mathematical Statistics}, title = {{Entropic Ricci curvature bounds for discrete interacting systems}}, doi = {10.1214/15-AAP1133}, volume = {26}, year = {2016}, } @article{1475, abstract = {The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.}, author = {Toshima, Junko and Furuya, Eri and Nagano, Makoto and Kanno, Chisa and Sakamoto, Yuta and Ebihara, Masashi and Siekhaus, Daria E and Toshima, Jiro}, journal = {eLife}, number = {February 2016}, publisher = {eLife Sciences Publications}, title = {{Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton}}, doi = {10.7554/eLife.10276}, volume = {5}, year = {2016}, }