@article{1476, abstract = {The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis}, author = {Toshima, Junko and Horikomi, Chika and Okada, Asuka and Hatori, Makiko and Nagano, Makoto and Masuda, Atsushi and Yamamoto, Wataru and Siekhaus, Daria E and Toshima, Jiro}, journal = {Journal of Cell Science}, number = {2}, pages = {367 -- 379}, publisher = {Company of Biologists}, title = {{Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis}}, doi = {10.1242/jcs.176651}, volume = {129}, year = {2016}, } @article{1477, abstract = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples.}, author = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu}, journal = {Journal of Computer and System Sciences}, number = {5}, pages = {878 -- 911}, publisher = {Elsevier}, title = {{What is decidable about partially observable Markov decision processes with ω-regular objectives}}, doi = {10.1016/j.jcss.2016.02.009}, volume = {82}, year = {2016}, } @article{1478, abstract = {We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.}, author = {Seiringer, Robert and Warzel, Simone}, journal = {New Journal of Physics}, number = {3}, publisher = {IOP Publishing Ltd.}, title = {{Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas}}, doi = {10.1088/1367-2630/18/3/035002}, volume = {18}, year = {2016}, } @misc{5445, abstract = {We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. }, author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Velner, Yaron}, issn = {2664-1690}, pages = {33}, publisher = {IST Austria}, title = {{Quantitative interprocedural analysis}}, doi = {10.15479/AT:IST-2016-523-v1-1}, year = {2016}, } @misc{5449, abstract = {The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.}, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin}, issn = {2664-1690}, pages = {22}, publisher = {IST Austria}, title = {{Amplification on undirected population structures: Comets beat stars}}, doi = {10.15479/AT:IST-2016-648-v1-1}, year = {2016}, } @misc{5451, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin}, issn = {2664-1690}, pages = {34}, publisher = {IST Austria}, title = {{Strong amplifiers of natural selection}}, doi = {10.15479/AT:IST-2016-728-v1-1}, year = {2016}, } @misc{5452, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin}, issn = {2664-1690}, pages = {32}, publisher = {IST Austria}, title = {{Arbitrarily strong amplifiers of natural selection}}, doi = {10.15479/AT:IST-2017-728-v2-1}, year = {2016}, } @misc{5453, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin}, issn = {2664-1690}, pages = {34}, publisher = {IST Austria}, title = {{Arbitrarily strong amplifiers of natural selection}}, doi = {10.15479/AT:IST-2017-749-v3-1}, year = {2016}, } @misc{5550, abstract = {We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny. For full details of the methods see: Ellis TJ and Field DL "Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)}, author = {Ellis, Thomas and Field, David}, publisher = {Institute of Science and Technology Austria}, title = {{Flower colour data and phylogeny (NEXUS) files}}, doi = {10.15479/AT:ISTA:34}, year = {2016}, } @misc{5551, abstract = {Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016. We placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6. After 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.}, author = {Ellis, Thomas}, publisher = {Institute of Science and Technology Austria}, title = {{Data on pollinator observations and offpsring phenotypes}}, doi = {10.15479/AT:ISTA:35}, year = {2016}, } @misc{5552, abstract = {Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016). Snapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012. Also included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.}, author = {Ellis, Thomas}, publisher = {Institute of Science and Technology Austria}, title = {{Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.}}, doi = {10.15479/AT:ISTA:36}, year = {2016}, } @misc{5553, abstract = {Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016). Tissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset. Other data were retreived from an online database of this population at www.antspec.org.}, author = {Field, David and Ellis, Thomas}, keywords = {paternity assignment, pedigree, matting patterns, assortative mating, Antirrhinum majus, frequency-dependent selection, plant-pollinator interaction}, publisher = {Institute of Science and Technology Austria}, title = {{Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012}}, doi = {10.15479/AT:ISTA:37}, year = {2016}, } @misc{5554, abstract = {The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding. Magdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.}, author = {Tugrul, Murat}, keywords = {RNAP binding, de novo promoter evolution, lac promoter}, publisher = {Institute of Science and Technology Austria}, title = {{Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase}}, doi = {10.15479/AT:ISTA:43}, year = {2016}, } @misc{5555, abstract = {This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.}, author = {Hauschild, Robert}, keywords = {cell migration, wide field microscopy, FIJI}, publisher = {Institute of Science and Technology Austria}, title = {{Fiji script to determine average speed and direction of migration of cells}}, doi = {10.15479/AT:ISTA:44}, year = {2016}, } @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}, }