@inproceedings{949,
abstract = {The notion of treewidth of graphs has been exploited for faster algorithms for several problems arising in verification and program analysis. Moreover, various notions of balanced tree decompositions have been used for improved algorithms supporting dynamic updates and analysis of concurrent programs. In this work, we present a tool for constructing tree-decompositions of CFGs obtained from Java methods, which is implemented as an extension to the widely used Soot framework. The experimental results show that our implementation on real-world Java benchmarks is very efficient. Our tool also provides the first implementation for balancing tree-decompositions. In summary, we present the first tool support for exploiting treewidth in the static analysis problems on Java programs.},
author = {Chatterjee, Krishnendu and Goharshady, Amir and Pavlogiannis, Andreas},
editor = {D'Souza, Deepak},
issn = {03029743},
location = {Pune, India},
pages = {59 -- 66},
publisher = {Springer},
title = {{JTDec: A tool for tree decompositions in soot}},
doi = {10.1007/978-3-319-68167-2_4},
volume = {10482},
year = {2017},
}
@inproceedings{639,
abstract = {We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.},
author = {Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir},
editor = {Majumdar, Rupak and Kunčak, Viktor},
isbn = {978-331963389-3},
location = {Heidelberg, Germany},
pages = {41 -- 63},
publisher = {Springer},
title = {{Non-polynomial worst case analysis of recursive programs}},
doi = {10.1007/978-3-319-63390-9_3},
volume = {10427},
year = {2017},
}
@inproceedings{8094,
abstract = {With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.},
author = {Martius, Georg S and Hostettler, Rafael and Knoll, Alois and Der, Ralf},
booktitle = {Proceedings of the Artificial Life Conference 2016},
isbn = {9780262339360},
location = {Cancun, Mexico},
pages = {142--143},
publisher = {MIT Press},
title = {{Self-organized control of an tendon driven arm by differential extrinsic plasticity}},
doi = {10.7551/978-0-262-33936-0-ch029},
volume = {28},
year = {2016},
}
@article{1705,
abstract = {Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential.},
author = {Bogomolov, Sergiy and Donzé, Alexandre and Frehse, Goran and Grosu, Radu and Johnson, Taylor and Ladan, Hamed and Podelski, Andreas and Wehrle, Martin},
journal = {International Journal on Software Tools for Technology Transfer},
number = {4},
pages = {449 -- 467},
publisher = {Springer},
title = {{Guided search for hybrid systems based on coarse-grained space abstractions}},
doi = {10.1007/s10009-015-0393-y},
volume = {18},
year = {2016},
}
@article{1794,
abstract = {We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.},
author = {Kolmogorov, Vladimir and Takhanov, Rustem},
journal = {Algorithmica},
number = {1},
pages = {17 -- 46},
publisher = {Springer},
title = {{Inference algorithms for pattern-based CRFs on sequence data}},
doi = {10.1007/s00453-015-0017-7},
volume = {76},
year = {2016},
}
@article{1833,
abstract = {Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. },
author = {Klimova, Anna and Rudas, Tamás},
journal = {Journal of Multivariate Analysis},
pages = {440 -- 452},
publisher = {Elsevier},
title = {{On the closure of relational models}},
doi = {10.1016/j.jmva.2015.10.005},
volume = {143},
year = {2016},
}
@article{1881,
abstract = {We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ>λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ>λ+, while they are completely delocalized for λ<λ+. Similar results hold for the lowest eigenvalues. },
author = {Lee, Jioon and Schnelli, Kevin},
journal = {Probability Theory and Related Fields},
number = {1-2},
pages = {165 -- 241},
publisher = {Springer},
title = {{Extremal eigenvalues and eigenvectors of deformed Wigner matrices}},
doi = {10.1007/s00440-014-0610-8},
volume = {164},
year = {2016},
}
@inproceedings{478,
abstract = {Magic: the Gathering is a game about magical combat for any number of players. Formally it is a zero-sum, imperfect information stochastic game that consists of a potentially unbounded number of steps. We consider the problem of deciding if a move is legal in a given single step of Magic. We show that the problem is (a) coNP-complete in general; and (b) in P if either of two small sets of cards are not used. Our lower bound holds even for single-player Magic games. The significant aspects of our results are as follows: First, in most real-life game problems, the task of deciding whether a given move is legal in a single step is trivial, and the computationally hard task is to find the best sequence of legal moves in the presence of multiple players. In contrast, quite uniquely our hardness result holds for single step and with only one-player. Second, we establish efficient algorithms for important special cases of Magic.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
location = {The Hague, Netherlands},
pages = {1432 -- 1439},
publisher = {IOS Press},
title = {{The complexity of deciding legality of a single step of magic: The gathering}},
doi = {10.3233/978-1-61499-672-9-1432},
volume = {285},
year = {2016},
}
@inproceedings{480,
abstract = {Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph are controlled by two adversarial players, and the other transitions are executed probabilistically. We consider such games where the objective is the conjunction of several quantitative objectives (specified as mean-payoff conditions), which we refer to as generalized mean-payoff objectives. The basic decision problem asks for the existence of a finite-memory strategy for a player that ensures the generalized mean-payoff objective be satisfied with a desired probability against all strategies of the opponent. A special case of the decision problem is the almost-sure problem where the desired probability is 1. Previous results presented a semi-decision procedure for -approximations of the almost-sure problem. In this work, we show that both the almost-sure problem as well as the general basic decision problem are coNP-complete, significantly improving the previous results. Moreover, we show that in the case of 1-player stochastic games, randomized memoryless strategies are sufficient and the problem can be solved in polynomial time. In contrast, in two-player stochastic games, we show that even with randomized strategies exponential memory is required in general, and present a matching exponential upper bound. We also study the basic decision problem with infinite-memory strategies and present computational complexity results for the problem. Our results are relevant in the synthesis of stochastic reactive systems with multiple quantitative requirements.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
location = {New York, NY, USA},
pages = {247 -- 256},
publisher = {IEEE},
title = {{Perfect-information stochastic games with generalized mean-payoff objectives}},
doi = {10.1145/2933575.2934513},
volume = {05-08-July-2016},
year = {2016},
}
@article{510,
abstract = {The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. },
author = {Liu, Zhijun and Yang, Nan and Lv, Yanting and Pan, Lixia and Lv, Shuo and Han, Huibin and Wang, Guodong},
journal = {Plant Signaling & Behavior},
number = {6},
publisher = {Landes Bioscience},
title = {{The CLE gene family in Populus trichocarpa}},
doi = {10.1080/15592324.2016.1191734},
volume = {11},
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{5446,
abstract = {We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-
conquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the
effectiveness of our approach.},
author = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3},
issn = {2664-1690},
pages = {26},
publisher = {IST Austria},
title = {{Termination and worst-case analysis of recursive programs}},
year = {2016},
}
@misc{5447,
abstract = {We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,
linear, or almost-linear (O(log n), O(n), O(n · log n),
respectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase
bounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms.},
author = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3},
issn = {2664-1690},
pages = {20},
publisher = {IST Austria},
title = {{Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds}},
year = {2016},
}
@misc{5448,
abstract = {We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.
We introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.
1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.
2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence.
Finally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.},
author = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3 and Anonymous, 4},
issn = {2664-1690},
pages = {20},
publisher = {IST Austria},
title = {{Data-centric dynamic partial order reduction}},
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 = {IST 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 = {IST 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 = {IST 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 = {IST 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{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 = {IST 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 = {IST 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 = {IST 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 = {IST Austria},
title = {{Tracking, Correcting and Absorbing Water Surface Waves}},
doi = {10.15479/AT:ISTA:48},
year = {2016},
}
@article{1270,
abstract = {A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework.},
author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkacik, Gasper},
journal = {PLoS One},
number = {9},
publisher = {Public Library of Science},
title = {{Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information}},
doi = {10.1371/journal.pone.0163628},
volume = {11},
year = {2016},
}
@article{1271,
abstract = {Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times.},
author = {Diz Muñoz, Alba and Romanczuk, Pawel and Yu, Weimiao and Bergert, Martin and Ivanovitch, Kenzo and Salbreux, Guillame and Heisenberg, Carl-Philipp J and Paluch, Ewa},
journal = {BMC Biology},
number = {1},
publisher = {BioMed Central},
title = {{Steering cell migration by alternating blebs and actin-rich protrusions}},
doi = {10.1186/s12915-016-0294-x},
volume = {14},
year = {2016},
}
@article{1272,
abstract = {We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams.},
author = {Held, Martin and Huber, Stefan and Palfrader, Peter},
journal = {Computer-Aided Design and Applications},
number = {5},
pages = {712 -- 721},
publisher = {Taylor and Francis},
title = {{Generalized offsetting of planar structures using skeletons}},
doi = {10.1080/16864360.2016.1150718},
volume = {13},
year = {2016},
}
@article{1273,
abstract = {Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.},
author = {Porco, Silvana and Larrieu, Antoine and Du, Yujuan and Gaudinier, Allison and Goh, Tatsuaki and Swarup, Kamal and Swarup, Ranjan and Kuempers, Britta and Bishopp, Anthony and Lavenus, Julien and Casimiro, Ilda and Hill, Kristine and Benková, Eva and Fukaki, Hidehiro and Brady, Siobhan and Scheres, Ben and Peéet, Benjamin and Bennett, Malcolm},
journal = {Development},
number = {18},
pages = {3340 -- 3349},
publisher = {Company of Biologists},
title = {{Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3}},
doi = {10.1242/dev.136283},
volume = {143},
year = {2016},
}
@article{1274,
abstract = {Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis.},
author = {Mazur, Ewa and Benková, Eva and Friml, Jirí},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis}},
doi = {10.1038/srep33754},
volume = {6},
year = {2016},
}
@article{1276,
abstract = {The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site.},
author = {Postila, Pekka and Kaszuba, Karol and Kuleta, Patryk and Vattulainen, Ilpo and Sarewicz, Marcin and Osyczka, Artur and Róg, Tomasz},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex}},
doi = {10.1038/srep33607},
volume = {6},
year = {2016},
}
@article{1277,
abstract = {The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.
},
author = {Ortiz Morea, Fausto and Savatin, Daniel and Dejonghe, Wim and Kumar, Rahul and Luo, Yu and Adamowski, Maciek and Van Begin, Jos and Dressano, Keini and De Oliveira, Guilherme and Zhao, Xiuyang and Lu, Qing and Madder, Annemieke and Friml, Jirí and De Moura, Daniel and Russinova, Eugenia},
journal = {PNAS},
number = {39},
pages = {11028 -- 11033},
publisher = {National Academy of Sciences},
title = {{Danger-associated peptide signaling in Arabidopsis requires clathrin}},
doi = {10.1073/pnas.1605588113},
volume = {113},
year = {2016},
}
@article{1278,
abstract = {Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons.},
author = {Matsuno, Hitomi and Kudoh, Moeko and Watakabe, Akiya and Yamamori, Tetsuo and Shigemoto, Ryuichi and Nagao, Soichi},
journal = {PLoS One},
number = {10},
publisher = {Public Library of Science},
title = {{Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies}},
doi = {10.1371/journal.pone.0164037},
volume = {11},
year = {2016},
}
@article{1279,
abstract = {During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles.},
author = {Kovács, Krisztián and O'Neill, Joseph and Schönenberger, Philipp and Penttonen, Markku and Rangel Guerrero, Dámaris K and Csicsvari, Jozsef L},
journal = {PLoS One},
number = {10},
publisher = {Public Library of Science},
title = {{Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus}},
doi = {10.1371/journal.pone.0164675},
volume = {11},
year = {2016},
}
@article{1280,
abstract = {We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics.},
author = {Bourgade, Paul and Erdös, László and Yau, Horngtzer and Yin, Jun},
journal = {Communications on Pure and Applied Mathematics},
number = {10},
pages = {1815 -- 1881},
publisher = {Wiley-Blackwell},
title = {{Fixed energy universality for generalized wigner matrices}},
doi = {10.1002/cpa.21624},
volume = {69},
year = {2016},
}
@article{1281,
abstract = {Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue.},
author = {Bouguyon, Eléonore and Perrine Walker, Francine and Pervent, Marjorie and Rochette, Juliette and Cuesta, Candela and Benková, Eva and Martinière, Alexandre and Bach, Lien and Krouk, Gabriel and Gojon, Alain and Nacry, Philippe},
journal = {Plant Physiology},
number = {2},
pages = {1237 -- 1248},
publisher = {American Society of Plant Biologists},
title = {{Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor}},
doi = {10.1104/pp.16.01047},
volume = {172},
year = {2016},
}
@article{1282,
abstract = {We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k.},
author = {Gundert, Anna and Wagner, Uli},
journal = {Israel Journal of Mathematics},
number = {2},
pages = {545 -- 582},
publisher = {Springer},
title = {{On eigenvalues of random complexes}},
doi = {10.1007/s11856-016-1419-1},
volume = {216},
year = {2016},
}
@article{1286,
abstract = {We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.},
author = {Midya, Bikashkali and Tomza, Michał and Schmidt, Richard and Lemeshko, Mikhail},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {4},
publisher = {American Physical Society},
title = {{Rotation of cold molecular ions inside a Bose-Einstein condensate}},
doi = {10.1103/PhysRevA.94.041601},
volume = {94},
year = {2016},
}
@article{1287,
abstract = {A planar waveguide with an impedance boundary, composed of nonperfect metallic plates, and with passive or active dielectric filling, is considered. We show the possibility of selective mode guiding and amplification when a homogeneous pump is added to the dielectric and analyze differences in TE and TM mode propagation. Such a non-conservative system is also shown to feature exceptional points for specific and experimentally tunable parameters, which are described for a particular case of transparent dielectric.},
author = {Midya, Bikashkali and Konotop, Vladimir},
journal = {Optics Letters},
number = {20},
pages = {4621 -- 4624},
publisher = {OSA},
title = {{Modes and exceptional points in waveguides with impedance boundary conditions}},
doi = {10.1364/OL.41.004621},
volume = {41},
year = {2016},
}
@article{1289,
abstract = {Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI) magnifying endoscopic (ME) images of the stomach, we combine methods from image processing, topology, geometry, and machine learning to classify patterns into three classes: oval, tubular and irregular. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.},
author = {Dunaeva, Olga and Edelsbrunner, Herbert and Lukyanov, Anton and Machin, Michael and Malkova, Daria and Kuvaev, Roman and Kashin, Sergey},
journal = {Pattern Recognition Letters},
number = {1},
pages = {13 -- 22},
publisher = {Elsevier},
title = {{The classification of endoscopy images with persistent homology}},
doi = {10.1016/j.patrec.2015.12.012},
volume = {83},
year = {2016},
}
@article{1290,
abstract = {We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.},
author = {Stone, Laura and Baym, Michael and Lieberman, Tami and Chait, Remy P and Clardy, Jon and Kishony, Roy},
journal = {Nature Chemical Biology},
number = {11},
pages = {902 -- 904},
publisher = {Nature Publishing Group},
title = {{Compounds that select against the tetracycline-resistance efflux pump}},
doi = {10.1038/nchembio.2176},
volume = {12},
year = {2016},
}
@article{1291,
abstract = {We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than dÂ +Â 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for pÂ >Â 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (dÂ =Â 2) or slabs (dÂ =Â 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity.},
author = {Giuliani, Alessandro and Seiringer, Robert},
journal = {Communications in Mathematical Physics},
number = {3},
pages = {983 -- 1007},
publisher = {Springer},
title = {{Periodic striped ground states in Ising models with competing interactions}},
doi = {10.1007/s00220-016-2665-0},
volume = {347},
year = {2016},
}
@article{1292,
abstract = {We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds.},
author = {Durst, Sebastian and Kegel, Marc and Klukas, Mirko D},
journal = {Acta Mathematica Hungarica},
number = {2},
pages = {441 -- 455},
publisher = {Springer},
title = {{Computing the Thurston–Bennequin invariant in open books}},
doi = {10.1007/s10474-016-0648-4},
volume = {150},
year = {2016},
}
@article{1293,
abstract = {For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.},
author = {Solus, Liam T and Uhler, Caroline and Yoshida, Ruriko},
journal = {Linear Algebra and Its Applications},
pages = {247 -- 275},
publisher = {Elsevier},
title = {{Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors}},
doi = {10.1016/j.laa.2016.07.026},
volume = {509},
year = {2016},
}
@article{1322,
abstract = {Direct reciprocity is a major mechanism for the evolution of cooperation. Several classical studies have suggested that humans should quickly learn to adopt reciprocal strategies to establish mutual cooperation in repeated interactions. On the other hand, the recently discovered theory of ZD strategies has found that subjects who use extortionate strategies are able to exploit and subdue cooperators. Although such extortioners have been predicted to succeed in any population of adaptive opponents, theoretical follow-up studies questioned whether extortion can evolve in reality. However, most of these studies presumed that individuals have similar strategic possibilities and comparable outside options, whereas asymmetries are ubiquitous in real world applications. Here we show with a model and an economic experiment that extortionate strategies readily emerge once subjects differ in their strategic power. Our experiment combines a repeated social dilemma with asymmetric partner choice. In our main treatment there is one randomly chosen group member who is unilaterally allowed to exchange one of the other group members after every ten rounds of the social dilemma. We find that this asymmetric replacement opportunity generally promotes cooperation, but often the resulting payoff distribution reflects the underlying power structure. Almost half of the subjects in a better strategic position turn into extortioners, who quickly proceed to exploit their peers. By adapting their cooperation probabilities consistent with ZD theory, extortioners force their co-players to cooperate without being similarly cooperative themselves. Comparison to non-extortionate players under the same conditions indicates a substantial net gain to extortion. Our results thus highlight how power asymmetries can endanger mutually beneficial interactions, and transform them into exploitative relationships. In particular, our results indicate that the extortionate strategies predicted from ZD theory could play a more prominent role in our daily interactions than previously thought.},
author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred},
journal = {PLoS One},
number = {10},
publisher = {Public Library of Science},
title = {{Asymmetric power boosts extortion in an economic experiment}},
doi = {10.1371/journal.pone.0163867},
volume = {11},
year = {2016},
}
@article{1323,
abstract = {Mossy fiber synapses on CA3 pyramidal cells are 'conditional detonators' that reliably discharge postsynaptic targets. The 'conditional' nature implies that burst activity in dentate gyrus granule cells is required for detonation. Whether single unitary excitatory postsynaptic potentials (EPSPs) trigger spikes in CA3 neurons remains unknown. Mossy fiber synapses exhibit both pronounced short-term facilitation and uniquely large post-tetanic potentiation (PTP). We tested whether PTP could convert mossy fiber synapses from subdetonator into detonator mode, using a recently developed method to selectively and noninvasively stimulate individual presynaptic terminals in rat brain slices. Unitary EPSPs failed to initiate a spike in CA3 neurons under control conditions, but reliably discharged them after induction of presynaptic short-term plasticity. Remarkably, PTP switched mossy fiber synapses into full detonators for tens of seconds. Plasticity-dependent detonation may be critical for efficient coding, storage, and recall of information in the granule cell–CA3 cell network.},
author = {Vyleta, Nicholas and Borges Merjane, Carolina and Jonas, Peter M},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses}},
doi = {10.7554/eLife.17977},
volume = {5},
year = {2016},
}
@inproceedings{1325,
abstract = {We study graphs and two-player games in which rewards are assigned to states, and the goal of the players is to satisfy or dissatisfy certain property of the generated outcome, given as a mean payoff property. Since the notion of mean-payoff does not reflect possible fluctuations from the mean-payoff along a run, we propose definitions and algorithms for capturing the stability of the system, and give algorithms for deciding if a given mean payoff and stability objective can be ensured in the system.},
author = {Brázdil, Tomáš and Forejt, Vojtěch and Kučera, Antonín and Novotny, Petr},
location = {Quebec City, Canada},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Stability in graphs and games}},
doi = {10.4230/LIPIcs.CONCUR.2016.10},
volume = {59},
year = {2016},
}
@inproceedings{1326,
abstract = {Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. },
author = {Brázdil, Tomáš and Kučera, Antonín and Novotny, Petr},
location = {Chiba, Japan},
pages = {32 -- 49},
publisher = {Springer},
title = {{Optimizing the expected mean payoff in Energy Markov Decision Processes}},
doi = {10.1007/978-3-319-46520-3_3},
volume = {9938},
year = {2016},
}
@inproceedings{1327,
abstract = {We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. },
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Anchit and Novotny, Petr},
booktitle = {Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems},
location = {Singapore},
pages = {1465 -- 1466},
publisher = {ACM},
title = {{Stochastic shortest path with energy constraints in POMDPs}},
year = {2016},
}
@article{1328,
abstract = {Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples.},
author = {Watzinger, Hannes and Kloeffel, Christoph and Vukusic, Lada and Rossell, Marta and Sessi, Violetta and Kukucka, Josip and Kirchschlager, Raimund and Lausecker, Elisabeth and Truhlar, Alisha and Glaser, Martin and Rastelli, Armando and Fuhrer, Andreas and Loss, Daniel and Katsaros, Georgios},
journal = {Nano Letters},
number = {11},
pages = {6879 -- 6885},
publisher = {American Chemical Society},
title = {{Heavy-hole states in germanium hut wires}},
doi = {10.1021/acs.nanolett.6b02715},
volume = {16},
year = {2016},
}
@article{1329,
abstract = {Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.},
author = {Huylmans, Ann K and López Ezquerra, Alberto and Parsch, John and Cordellier, Mathilde},
journal = {Genome Biology and Evolution},
number = {10},
pages = {3120 -- 3139},
publisher = {Oxford University Press},
title = {{De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata}},
doi = {10.1093/gbe/evw221},
volume = {8},
year = {2016},
}
@article{1330,
abstract = {In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K.},
author = {Akopyan, Arseniy and Balitskiy, Alexey},
journal = {Israel Journal of Mathematics},
number = {2},
pages = {833 -- 845},
publisher = {Springer},
title = {{Billiards in convex bodies with acute angles}},
doi = {10.1007/s11856-016-1429-z},
volume = {216},
year = {2016},
}
@article{1332,
abstract = {Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.},
author = {Chait, Remy P and Palmer, Adam and Yelin, Idan and Kishony, Roy},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments}},
doi = {10.1038/ncomms10333},
volume = {7},
year = {2016},
}
@article{1333,
abstract = {Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most.},
author = {Milinski, Manfred and Hilbe, Christian and Semmann, Dirk and Sommerfeld, Ralf and Marotzke, Jochem},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Humans choose representatives who enforce cooperation in social dilemmas through extortion}},
doi = {10.1038/ncomms10915},
volume = {7},
year = {2016},
}
@article{1334,
abstract = {Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping.},
author = {Schönenberger, Philipp and O'Neill, Joseph and Csicsvari, Jozsef L},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Activity dependent plasticity of hippocampal place maps}},
doi = {10.1038/ncomms11824},
volume = {7},
year = {2016},
}
@inproceedings{1335,
abstract = {In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
location = {Edinburgh, United Kingdom},
pages = {23 -- 38},
publisher = {Springer},
title = {{Quantitative monitor automata}},
doi = {10.1007/978-3-662-53413-7_2},
volume = {9837},
year = {2016},
}
@article{1339,
abstract = {We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive
actuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By
measuring the resonance frequencies of the system, we show that the comb-drive actuator and the
silicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate
(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)
placed close to the silicon beam. In contrast, the effective spring constant of the system is insensitive
to either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator
can be used to switch between different coupling rates with a frequency of at least 10 kHz.
},
author = {Verbiest, Gerard and Xu, Duo and Goldsche, Matthias and Khodkov, Timofiy and Barzanjeh, Shabir and Von Den Driesch, Nils and Buca, Dan and Stampfer, Christoph},
journal = {Applied Physics Letter},
publisher = {American Institute of Physics},
title = {{Tunable mechanical coupling between driven microelectromechanical resonators}},
doi = {10.1063/1.4964122},
volume = {109},
year = {2016},
}
@inproceedings{1340,
abstract = {We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11].},
author = {Hansen, Kristoffer and Ibsen-Jensen, Rasmus and Koucký, Michal},
location = {Liverpool, United Kingdom},
pages = {64 -- 76},
publisher = {Springer},
title = {{The big match in small space}},
doi = {10.1007/978-3-662-53354-3_6},
volume = {9928},
year = {2016},
}
@inproceedings{1341,
abstract = {In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.},
author = {Avni, Guy and Henzinger, Thomas A and Kupferman, Orna},
location = {Liverpool, United Kingdom},
pages = {153 -- 166},
publisher = {Springer},
title = {{Dynamic resource allocation games}},
doi = {10.1007/978-3-662-53354-3_13},
volume = {9928},
year = {2016},
}
@article{1342,
abstract = {A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics.},
author = {Baym, Michael and Lieberman, Tami and Kelsic, Eric and Chait, Remy P and Gross, Rotem and Yelin, Idan and Kishony, Roy},
journal = {Science},
number = {6304},
pages = {1147 -- 1151},
publisher = {American Association for the Advancement of Science},
title = {{Spatiotemporal microbial evolution on antibiotic landscapes}},
doi = {10.1126/science.aag0822},
volume = {353},
year = {2016},
}
@article{1343,
abstract = {The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a
potential for explaining the mystery of high-temperature superconductivity. Recent progress in
ultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using
the tools of quantum simulation, which emerged as a promising alternative to the numerical
calculations plagued by the infamous sign problem. However, the temperatures achieved using
elaborate laser cooling protocols so far have been too high to show the appearance of
antiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate
that using the machinery of dissipative quantum state engineering, one can observe the emergence of
the AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach
is to add incoherent laser scattering in such a way that the AF state emerges as the dark state of
the driven-dissipative dynamics. The proposed controlled dissipation channels described in this work
are straightforward to add to already existing experimental setups.},
author = {Kaczmarczyk, Jan and Weimer, Hendrik and Lemeshko, Mikhail},
journal = {New Journal of Physics},
number = {9},
publisher = {IOP Publishing Ltd.},
title = {{Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model}},
doi = {10.1088/1367-2630/18/9/093042},
volume = {18},
year = {2016},
}
@article{1344,
abstract = {Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.},
author = {Fendrych, Matyas and Leung, Jeffrey and Friml, Jirí},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls}},
doi = {10.7554/eLife.19048},
volume = {5},
year = {2016},
}
@article{1345,
abstract = {The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components.},
author = {Molnar, Gergely and Fendrych, Matyas and Friml, Jirí},
journal = {Nature Plants},
publisher = {Nature Publishing Group},
title = {{Plasma membrane: Negative attraction}},
doi = {10.1038/nplants.2016.102},
volume = {2},
year = {2016},
}
@article{1346,
abstract = {ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.},
author = {Dejonghe, Wim and Kuenen, Sabine and Mylle, Evelien and Vasileva, Mina K and Keech, Olivier and Viotti, Corrado and Swerts, Jef and Fendrych, Matyas and Ortiz Morea, Fausto and Mishev, Kiril and Delang, Simon and Scholl, Stefan and Zarza, Xavier and Heilmann, Mareike and Kourelis, Jiorgos and Kasprowicz, Jaroslaw and Nguyen, Le and Drozdzecki, Andrzej and Van Houtte, Isabelle and Szatmári, Anna and Majda, Mateusz and Baisa, Gary and Bednarek, Sebastian and Robert, Stéphanie and Audenaert, Dominique and Testerink, Christa and Munnik, Teun and Van Damme, Daniël and Heilmann, Ingo and Schumacher, Karin and Winne, Johan and Friml, Jirí and Verstreken, Patrik and Russinova, Eugenia},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification}},
doi = {10.1038/ncomms11710},
volume = {7},
year = {2016},
}
@article{1347,
abstract = {During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem's constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.},
author = {Schmidt, Richard and Lemeshko, Mikhail},
journal = {Physical Review X},
number = {1},
publisher = {American Physical Society},
title = {{Deformation of a quantum many-particle system by a rotating impurity}},
doi = {10.1103/PhysRevX.6.011012},
volume = {6},
year = {2016},
}
@inproceedings{1348,
abstract = {A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest.},
author = {Fulek, Radoslav},
location = {Helsinki, Finland},
pages = {31 -- 42},
publisher = {Springer},
title = {{Bounded embeddings of graphs in the plane}},
doi = {10.1007/978-3-319-44543-4_3},
volume = {9843},
year = {2016},
}
@inproceedings{1349,
abstract = {Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.},
author = {Oliveto, Pietro and Paixao, Tiago and Heredia, Jorge and Sudholt, Dirk and Trubenova, Barbora},
booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference 2016 },
location = {Denver, CO, USA},
pages = {1163 -- 1170},
publisher = {ACM},
title = {{When non-elitism outperforms elitism for crossing fitness valleys}},
doi = {10.1145/2908812.2908909},
year = {2016},
}
@article{1350,
abstract = {The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3
synapses are thought to be the subcellular substrate of pattern completion. However, the
synaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.
Simultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient
memory storage and retrieval in hippocampal networks.},
author = {Guzmán, José and Schlögl, Alois and Frotscher, Michael and Jonas, Peter M},
journal = {Science},
number = {6304},
pages = {1117 -- 1123},
publisher = {American Association for the Advancement of Science},
title = {{Synaptic mechanisms of pattern completion in the hippocampal CA3 network}},
doi = {10.1126/science.aaf1836},
volume = {353},
year = {2016},
}
@article{1352,
abstract = {We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking.},
author = {Kaczmarczyk, Jan and Schickling, Tobias and Bünemann, Jörg},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {8},
publisher = {American Physical Society},
title = {{Coexistence of nematic order and superconductivity in the Hubbard model}},
doi = {10.1103/PhysRevB.94.085152},
volume = {94},
year = {2016},
}
@article{1353,
abstract = {We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations.},
author = {Barto, Libor and Kazda, Alexandr},
journal = {International Journal of Algebra and Computation},
number = {5},
pages = {1033 -- 1060},
publisher = {World Scientific Publishing},
title = {{Deciding absorption}},
doi = {10.1142/S0218196716500430},
volume = {26},
year = {2016},
}
@article{1354,
abstract = {Fabrication processes involving anhydrous hydrofluoric vapor etching are developed to create high-Q aluminum superconducting microwave resonators on free-standing silicon membranes formed from a silicon-on-insulator wafer. Using this fabrication process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave spectroscopy and radiation pressure backaction are used to characterize the coupled system in a dilution refrigerator down to temperatures of Tf=11 mK, yielding a measured electromechanical vacuum coupling rate of g0/2π=24.6 Hz and a mechanical resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being realized at an elevated fridge temperature of Tf=211 mK.},
author = {Dieterle, Paul and Kalaee, Mahmoud and Fink, Johannes M and Painter, Oskar},
journal = {Physical Review Applied},
number = {1},
publisher = {American Physical Society},
title = {{Superconducting cavity electromechanics on a silicon-on-insulator platform}},
doi = {10.1103/PhysRevApplied.6.014013},
volume = {6},
year = {2016},
}
@article{1355,
abstract = {Radiation pressure has recently been used to effectively couple the quantum motion of mechanical elements to the fields of optical or microwave light. Integration of all three degrees of freedom—mechanical, optical and microwave—would enable a quantum interconnect between microwave and optical quantum systems. We present a platform based on silicon nitride nanomembranes for integrating superconducting microwave circuits with planar acoustic and optical devices such as phononic and photonic crystals. Using planar capacitors with vacuum gaps of 60 nm and spiral inductor coils of micron pitch we realize microwave resonant circuits with large electromechanical coupling to planar acoustic structures of nanoscale dimensions and femtoFarad motional capacitance. Using this enhanced coupling, we demonstrate microwave backaction cooling of the 4.48 MHz mechanical resonance of a nanobeam to an occupancy as low as 0.32. These results indicate the viability of silicon nitride nanomembranes as an all-in-one substrate for quantum electro-opto-mechanical experiments.},
author = {Fink, Johannes M and Kalaee, Mahmoud and Pitanti, Alessandro and Norte, Richard and Heinzle, Lukas and Davanço, Marcelo and Srinivasan, Kartik and Painter, Oskar},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Quantum electromechanics on silicon nitride nanomembranes}},
doi = {10.1038/ncomms12396},
volume = {7},
year = {2016},
}
@article{1356,
author = {Barton, Nicholas H},
journal = {Genetics},
number = {1},
pages = {3 -- 4},
publisher = {Genetics Society of America},
title = {{Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”}},
doi = {10.1534/genetics.115.184796},
volume = {202},
year = {2016},
}
@article{1357,
author = {Barton, Nicholas H},
journal = {Genetics},
number = {3},
pages = {865 -- 866},
publisher = {Genetics Society of America},
title = {{Richard Hudson and Norman Kaplan on the coalescent process}},
doi = {10.1534/genetics.116.187542},
volume = {202},
year = {2016},
}
@article{1358,
abstract = {Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.},
author = {Friedlander, Tamar and Prizak, Roshan and Guet, Calin C and Barton, Nicholas H and Tkacik, Gasper},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Intrinsic limits to gene regulation by global crosstalk}},
doi = {10.1038/ncomms12307},
volume = {7},
year = {2016},
}
@article{1359,
abstract = {The role of gene interactions in the evolutionary process has long
been controversial. Although some argue that they are not of
importance, because most variation is additive, others claim that
their effect in the long term can be substantial. Here, we focus on
the long-term effects of genetic interactions under directional
selection assuming no mutation or dominance, and that epistasis is
symmetrical overall. We ask by how much the mean of a complex
trait can be increased by selection and analyze two extreme
regimes, in which either drift or selection dominate the dynamics
of allele frequencies. In both scenarios, epistatic interactions affect
the long-term response to selection by modulating the additive
genetic variance. When drift dominates, we extend Robertson
’
s
[Robertson A (1960)
Proc R Soc Lond B Biol Sci
153(951):234
−
249]
argument to show that, for any form of epistasis, the total response
of a haploid population is proportional to the initial total genotypic
variance. In contrast, the total response of a diploid population is
increased by epistasis, for a given initial genotypic variance. When
selection dominates, we show that the total selection response can
only be increased by epistasis when s
ome initially deleterious alleles
become favored as the genetic background changes. We find a sim-
ple approximation for this effect and show that, in this regime, it is
the structure of the genotype - phenotype map that matters and not
the variance components of the population.},
author = {Paixao, Tiago and Barton, Nicholas H},
journal = {PNAS},
number = {16},
pages = {4422 -- 4427},
publisher = {National Academy of Sciences},
title = {{The effect of gene interactions on the long-term response to selection}},
doi = {10.1073/pnas.1518830113},
volume = {113},
year = {2016},
}
@article{1360,
abstract = {We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. },
author = {Akopyan, Arseniy and Balitskiy, Alexey and Karasev, Roman and Sharipova, Anastasia},
journal = {Proceedings of the American Mathematical Society},
number = {10},
pages = {4501 -- 4513},
publisher = {American Mathematical Society},
title = {{Elementary approach to closed billiard trajectories in asymmetric normed spaces}},
doi = {10.1090/proc/13062},
volume = {144},
year = {2016},
}
@inproceedings{1361,
abstract = {We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes.},
author = {Da, Fang and Hahn, David and Batty, Christopher and Wojtan, Christopher J and Grinspun, Eitan},
location = {Anaheim, CA, USA},
number = {4},
publisher = {ACM},
title = {{Surface only liquids}},
doi = {10.1145/2897824.2925899},
volume = {35},
year = {2016},
}
@inproceedings{1362,
abstract = {We present a boundary element based method for fast simulation of brittle fracture. By introducing simplifying assumptions that allow us to quickly estimate stress intensities and opening displacements during crack propagation, we build a fracture algorithm where the cost of each time step scales linearly with the length of the crackfront. The transition from a full boundary element method to our faster variant is possible at the beginning of any time step. This allows us to build a hybrid method, which uses the expensive but more accurate BEM while the number of degrees of freedom is low, and uses the fast method once that number exceeds a given threshold as the crack geometry becomes more complicated. Furthermore, we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body coupling solves a Neumann boundary value problem by carefully separating translational, rotational and deformational components of the collision forces and then applying a Tikhonov regularizer to the resulting linear system. We show that our method produces physically reasonable results in standard test cases and is capable of dealing with complex scenes faster than previous finite- or boundary element approaches.},
author = {Hahn, David and Wojtan, Christopher J},
location = {Anaheim, CA, USA},
number = {4},
publisher = {ACM},
title = {{Fast approximations for boundary element based brittle fracture simulation}},
doi = {10.1145/2897824.2925902},
volume = {35},
year = {2016},
}
@inproceedings{1363,
abstract = {When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special "non-reflecting" boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation.},
author = {Bojsen-Hansen, Morten and Wojtan, Christopher J},
location = {Anaheim, CA, USA},
number = {4},
publisher = {ACM},
title = {{Generalized non-reflecting boundaries for fluid re-simulation}},
doi = {10.1145/2897824.2925963},
volume = {35},
year = {2016},
}
@inproceedings{1364,
abstract = {We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated.},
author = {Miguel Villalba, Eder and Lepoutre, Mathias and Bickel, Bernd},
location = {Anaheim, CA, USA},
number = {4},
publisher = {ACM},
title = {{Computational design of stable planar-rod structures}},
doi = {10.1145/2897824.2925978},
volume = {35},
year = {2016},
}
@inproceedings{1365,
abstract = {A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest.},
author = {Alwen, Joel F and Blocki, Jeremiah},
location = {Santa Barbara, CA, USA},
pages = {241 -- 271},
publisher = {Springer},
title = {{Efficiently computing data-independent memory-hard functions}},
doi = {10.1007/978-3-662-53008-5_9},
volume = {9815},
year = {2016},
}
@inproceedings{1366,
abstract = {We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions.},
author = {Gazi, Peter and Tessaro, Stefano},
location = {Vienna, Austria},
pages = {87 -- 116},
publisher = {Springer},
title = {{Provably robust sponge-based PRNGs and KDFs}},
doi = {10.1007/978-3-662-49890-3_4},
volume = {9665},
year = {2016},
}
@article{1368,
abstract = {Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.},
author = {Wysokiński, Marcin and Kaczmarczyk, Jan and Spałek, Jozef},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {2},
publisher = {American Physical Society},
title = {{Correlation driven d wave superconductivity in Anderson lattice model: Two gaps}},
doi = {10.1103/PhysRevB.94.024517},
volume = {94},
year = {2016},
}
@inproceedings{1369,
abstract = {We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations.},
author = {Kolesnikov, Alexander and Lampert, Christoph},
location = {Amsterdam, The Netherlands},
pages = {695 -- 711},
publisher = {Springer},
title = {{Seed, expand and constrain: Three principles for weakly-supervised image segmentation}},
doi = {10.1007/978-3-319-46493-0_42},
volume = {9908},
year = {2016},
}
@article{1370,
abstract = {We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction.},
author = {Barzanjeh, Shabir and Vitali, David},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {3},
publisher = {American Physical Society},
title = {{Phonon Josephson junction with nanomechanical resonators}},
doi = {10.1103/PhysRevA.93.033846},
volume = {93},
year = {2016},
}
@article{1372,
abstract = {Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism.},
author = {Pernisová, Markéta and Prat, Tomas and Grones, Peter and Haruštiaková, Danka and Matonohova, Martina and Spíchal, Lukáš and Nodzyński, Tomasz and Friml, Jirí and Hejátko, Jan},
journal = {New Phytologist},
number = {2},
pages = {497 -- 509},
publisher = {Wiley-Blackwell},
title = {{Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis}},
doi = {10.1111/nph.14049},
volume = {212},
year = {2016},
}
@article{1373,
author = {Martin, Olivier and Zagórski, Marcin P},
journal = {Physics of Life Reviews},
pages = {168 -- 171},
publisher = {Elsevier},
title = {{Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"}},
doi = {10.1016/j.plrev.2016.06.006},
volume = {17},
year = {2016},
}
@article{1377,
abstract = {We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.},
author = {Kolmogorov, Vladimir and Pock, Thomas and Rolinek, Michal},
journal = {SIAM Journal on Imaging Sciences},
number = {2},
pages = {605 -- 636},
publisher = {Society for Industrial and Applied Mathematics },
title = {{Total variation on a tree}},
doi = {10.1137/15M1010257},
volume = {9},
year = {2016},
}
@inproceedings{1378,
abstract = {We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M.},
author = {Dotterrer, Dominic and Kaufman, Tali and Wagner, Uli},
location = {Medford, MA, USA},
pages = {35.1 -- 35.10},
publisher = {Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing},
title = {{On expansion and topological overlap}},
doi = {10.4230/LIPIcs.SoCG.2016.35},
volume = {51},
year = {2016},
}
@inproceedings{1379,
abstract = {We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.},
author = {Burton, Benjamin and De Mesmay, Arnaud N and Wagner, Uli},
location = {Medford, MA, USA},
pages = {24.1 -- 24.15},
publisher = {Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing},
title = {{Finding non-orientable surfaces in 3-manifolds}},
doi = {10.4230/LIPIcs.SoCG.2016.24},
volume = {51},
year = {2016},
}
@article{1380,
abstract = {We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP.},
author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James},
journal = {Journal of the ACM},
number = {3},
publisher = {ACM},
title = {{On the complexity of the orbit problem}},
doi = {10.1145/2857050},
volume = {63},
year = {2016},
}
@inproceedings{1381,
abstract = {Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.},
author = {Mabillard, Isaac and Wagner, Uli},
location = {Medford, MA, USA},
pages = {51.1 -- 51.12},
publisher = {Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH},
title = {{Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range}},
doi = {10.4230/LIPIcs.SoCG.2016.51},
volume = {51},
year = {2016},
}
@inproceedings{1389,
abstract = {The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be
described in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can
equivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear
differential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision.},
author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James},
booktitle = {LICS '16},
location = {New York, NY, USA},
pages = {515 -- 524},
publisher = {IEEE},
title = {{On recurrent reachability for continuous linear dynamical systems}},
doi = {10.1145/2933575.2934548},
year = {2016},
}
@inproceedings{1391,
abstract = {We present an extension to the quantifier-free theory of integer arrays which allows us to express counting. The properties expressible in Array Folds Logic (AFL) include statements such as "the first array cell contains the array length," and "the array contains equally many minimal and maximal elements." These properties cannot be expressed in quantified fragments of the theory of arrays, nor in the theory of concatenation. Using reduction to counter machines, we show that the satisfiability problem of AFL is PSPACE-complete, and with a natural restriction the complexity decreases to NP. We also show that adding either universal quantifiers or concatenation leads to undecidability.
AFL contains terms that fold a function over an array. We demonstrate that folding, a well-known concept from functional languages, allows us to concisely summarize loops that count over arrays, which occurs frequently in real-life programs. We provide a tool that can discharge proof obligations in AFL, and we demonstrate on practical examples that our decision procedure can solve a broad range of problems in symbolic testing and program verification.},
author = {Daca, Przemyslaw and Henzinger, Thomas A and Kupriyanov, Andrey},
location = {Toronto, Canada},
pages = {230 -- 248},
publisher = {Springer},
title = {{Array folds logic}},
doi = {10.1007/978-3-319-41540-6_13},
volume = {9780},
year = {2016},
}
@article{1394,
abstract = {The solution space of genome-scale models of cellular metabolism provides a map between physically
viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the
corresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show
that empirical growth rate distributions recently obtained in experiments at single-cell resolution can
be explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the
higher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of
a large bacterial population that captures this trade-off. The scaling relationships observed in
experiments encode, in such frameworks, for the same distance from the maximum achievable growth
rate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being
grounded on genome-scale metabolic network reconstructions, these results allow for multiple
implications and extensions in spite of the underlying conceptual simplicity.},
author = {De Martino, Daniele and Capuani, Fabrizio and De Martino, Andrea},
journal = {Physical Biology},
number = {3},
publisher = {IOP Publishing Ltd.},
title = {{Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli}},
doi = {10.1088/1478-3975/13/3/036005},
volume = {13},
year = {2016},
}
@phdthesis{1398,
abstract = {Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.},
author = {Ellis, Thomas},
pages = {130},
publisher = {IST Austria},
title = {{The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone}},
doi = {10.15479/AT:ISTA:TH_526 },
year = {2016},
}
@article{1408,
abstract = {The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status.},
author = {Franek, Peter and Krcál, Marek},
journal = {Discrete & Computational Geometry},
number = {1},
pages = {126 -- 164},
publisher = {Springer},
title = {{On computability and triviality of well groups}},
doi = {10.1007/s00454-016-9794-2},
volume = {56},
year = {2016},
}
@article{1409,
author = {Abbott, Richard and Barton, Nicholas H and Good, Jeffrey},
journal = {Molecular Ecology},
number = {11},
pages = {2325 -- 2332},
publisher = {Wiley-Blackwell},
title = {{Genomics of hybridization and its evolutionary consequences}},
doi = {10.1111/mec.13685},
volume = {25},
year = {2016},
}