@inbook{60, abstract = {Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking.}, author = {Clarke, Edmund and Henzinger, Thomas A and Veith, Helmut}, booktitle = {Handbook of Model Checking}, editor = {Henzinger, Thomas A}, pages = {1 -- 26}, publisher = {Springer}, title = {{Introduction to model checking}}, doi = {10.1007/978-3-319-10575-8_1}, year = {2018}, } @article{6354, abstract = {Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.}, author = {Fan, Shuxia and Lorenz, Michael and Massberg, Steffen and Gärtner, Florian R}, issn = {2331-8325}, journal = {Bio-Protocol}, keywords = {Platelets, Cell migration, Bacteria, Shear flow, Fibrinogen, E. coli}, number = {18}, publisher = {Bio-Protocol}, title = {{Platelet migration and bacterial trapping assay under flow}}, doi = {10.21769/bioprotoc.3018}, volume = {8}, year = {2018}, } @misc{6459, author = {Petritsch, Barbara}, keywords = {Open Access, Publication Analysis}, location = {Graz, Austria}, publisher = {IST Austria}, title = {{Open Access at IST Austria 2009-2017}}, doi = {10.5281/zenodo.1410279}, year = {2018}, } @inbook{6525, abstract = {This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal.}, author = {Hausel, Tamás and Mellit, Anton and Pei, Du}, booktitle = {Geometry and Physics: Volume I}, isbn = {9780198802013}, pages = {189--218}, publisher = {Oxford University Press}, title = {{Mirror symmetry with branes by equivariant verlinde formulas}}, doi = {10.1093/oso/9780198802013.003.0009}, year = {2018}, } @article{690, abstract = {We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1.}, author = {Lee, Jii and Schnelli, Kevin}, journal = {Probability Theory and Related Fields}, number = {1-2}, publisher = {Springer}, title = {{Local law and Tracy–Widom limit for sparse random matrices}}, doi = {10.1007/s00440-017-0787-8}, volume = {171}, year = {2018}, } @article{703, abstract = {We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision.}, author = {Shekhovtsov, Alexander and Swoboda, Paul and Savchynskyy, Bogdan}, issn = {01628828}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {7}, pages = {1668--1682}, publisher = {IEEE}, title = {{Maximum persistency via iterative relaxed inference with graphical models}}, doi = {10.1109/TPAMI.2017.2730884}, volume = {40}, year = {2018}, } @inproceedings{7116, abstract = {Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights.}, author = {Grubic, Demjan and Tam, Leo and Alistarh, Dan-Adrian and Zhang, Ce}, booktitle = {Proceedings of the 21st International Conference on Extending Database Technology}, isbn = {9783893180783}, issn = {2367-2005}, location = {Vienna, Austria}, pages = {145--156}, publisher = {OpenProceedings}, title = {{Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study}}, doi = {10.5441/002/EDBT.2018.14}, year = {2018}, } @inproceedings{7407, abstract = {Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he "wastes" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. }, author = {Pietrzak, Krzysztof Z}, booktitle = {10th Innovations in Theoretical Computer Science Conference (ITCS 2019)}, isbn = {978-3-95977-095-8}, issn = {1868-8969}, location = {San Diego, CA, United States}, pages = {59:1--59:25}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Proofs of catalytic space}}, doi = {10.4230/LIPICS.ITCS.2019.59}, volume = {124}, year = {2018}, } @article{6001, abstract = {The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated. In this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads. Initial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.}, author = {Alistarh, Dan-Adrian and Leiserson, William and Matveev, Alexander and Shavit, Nir}, issn = {2329-4949}, journal = {ACM Transactions on Parallel Computing}, number = {4}, publisher = {Association for Computing Machinery}, title = {{ThreadScan: Automatic and scalable memory reclamation}}, doi = {10.1145/3201897}, volume = {4}, year = {2018}, } @inproceedings{7812, abstract = {Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices.}, author = {Polino, Antonio and Pascanu, Razvan and Alistarh, Dan-Adrian}, booktitle = {6th International Conference on Learning Representations}, location = {Vancouver, Canada}, title = {{Model compression via distillation and quantization}}, year = {2018}, } @unpublished{8547, abstract = {The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.}, author = {Llorca, Alfredo and Ciceri, Gabriele and Beattie, Robert J and Wong, Fong K. and Diana, Giovanni and Serafeimidou, Eleni and Fernández-Otero, Marian and Streicher, Carmen and Arnold, Sebastian J. and Meyer, Martin and Hippenmeyer, Simon and Maravall, Miguel and Marín, Oscar}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture}}, doi = {10.1101/494088}, year = {2018}, } @inbook{86, abstract = {Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, booktitle = {Principles of Modeling}, editor = {Lohstroh, Marten and Derler, Patricia and Sirjani, Marjan}, pages = {143 -- 161}, publisher = {Springer}, title = {{Computing average response time}}, doi = {10.1007/978-3-319-95246-8_9}, volume = {10760}, year = {2018}, } @article{9229, author = {Danzl, Johann G}, issn = {2500-2295}, journal = {Opera Medica et Physiologica}, number = {S1}, pages = {11}, publisher = {Lobachevsky State University of Nizhny Novgorod}, title = {{Diffraction-unlimited optical imaging for synaptic physiology}}, doi = {10.20388/omp2018.00s1.001}, volume = {4}, year = {2018}, } @inproceedings{6005, abstract = {Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting.}, author = {Avni, Guy and Guha, Shibashis and Kupferman, Orna}, issn = {1868-8969}, location = {Liverpool, United Kingdom}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Timed network games with clocks}}, doi = {10.4230/LIPICS.MFCS.2018.23}, volume = {117}, year = {2018}, } @article{315, abstract = {More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.}, author = {Polechova, Jitka}, issn = {15449173}, journal = {PLoS Biology}, number = {6}, publisher = {Public Library of Science}, title = {{Is the sky the limit? On the expansion threshold of a species’ range}}, doi = {10.1371/journal.pbio.2005372}, volume = {16}, year = {2018}, } @inproceedings{186, abstract = {A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.}, author = {Fulek, Radoslav and Kynčl, Jan}, location = {Budapest, Hungary}, pages = {40.1 -- 40.14}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The ℤ2-Genus of Kuratowski minors}}, doi = {10.4230/LIPIcs.SoCG.2018.40}, volume = {99}, year = {2018}, } @inproceedings{433, abstract = {A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n.}, author = {Fulek, Radoslav and Pach, János}, location = {Boston, MA, United States}, pages = {160 -- 166}, publisher = {Springer}, title = {{Thrackles: An improved upper bound}}, doi = {10.1007/978-3-319-73915-1_14}, volume = {10692}, year = {2018}, } @misc{9837, abstract = {Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.}, author = {Faria, Rui and Chaube, Pragya and Morales, Hernán E. and Larsson, Tomas and Lemmon, Alan R. and Lemmon, Emily M. and Rafajlović, Marina and Panova, Marina and Ravinet, Mark and Johannesson, Kerstin and Westram, Anja M and Butlin, Roger K.}, publisher = {Dryad}, title = {{Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes}}, doi = {10.5061/dryad.72cg113}, year = {2018}, } @misc{5457, abstract = {We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well. In this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework. Moreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds.}, author = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3 and Anonymous, 4 and Anonymous, 5 and Anonymous, 6}, issn = {2664-1690}, pages = {27}, publisher = {IST Austria}, title = {{Cost analysis of nondeterministic probabilistic programs}}, year = {2018}, } @inbook{10864, abstract = {We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.}, author = {Kazda, Alexandr and Kozik, Marcin and McKenzie, Ralph and Moore, Matthew}, booktitle = {Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science}, editor = {Czelakowski, J}, isbn = {9783319747712}, issn = {2211-2766}, pages = {203--220}, publisher = {Springer Nature}, title = {{Absorption and directed Jónsson terms}}, doi = {10.1007/978-3-319-74772-9_7}, volume = {16}, year = {2018}, } @inproceedings{184, abstract = {We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes.}, author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, location = {Budapest, Hungary}, pages = {41:1 -- 41:16}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Shellability is NP-complete}}, doi = {10.4230/LIPIcs.SoCG.2018.41}, volume = {99}, year = {2018}, } @inproceedings{285, abstract = {In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).}, author = {Huszár, Kristóf and Spreer, Jonathan and Wagner, Uli}, issn = {18688969}, location = {Budapest, Hungary}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{On the treewidth of triangulated 3-manifolds}}, doi = {10.4230/LIPIcs.SoCG.2018.46}, volume = {99}, year = {2018}, } @misc{13059, abstract = {This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled "Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method". It also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript. The repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`. For details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).}, author = {Garriga, Edgar and di Tommaso, Paolo and Magis, Cedrik and Erb, Ionas and Mansouri, Leila and Baltzis, Athanasios and Laayouni, Hafid and Kondrashov, Fyodor and Floden, Evan and Notredame, Cedric}, publisher = {Zenodo}, title = {{Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method}}, doi = {10.5281/ZENODO.2025846}, year = {2018}, } @phdthesis{49, abstract = {Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits.}, author = {Watzinger, Hannes}, issn = {2663-337X}, pages = {77}, publisher = {Institute of Science and Technology Austria}, title = {{Ge hut wires - from growth to hole spin resonance}}, doi = {10.15479/AT:ISTA:th_1033}, year = {2018}, } @phdthesis{201, abstract = {We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications.}, author = {Iglesias Ham, Mabel}, issn = {2663-337X}, pages = {171}, publisher = {Institute of Science and Technology Austria}, title = {{Multiple covers with balls}}, doi = {10.15479/AT:ISTA:th_1026}, year = {2018}, } @phdthesis{68, abstract = {The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability.}, author = {Zimin, Alexander}, issn = {2663-337X}, pages = {92}, publisher = {Institute of Science and Technology Austria}, title = {{Learning from dependent data}}, doi = {10.15479/AT:ISTA:TH1048}, year = {2018}, } @phdthesis{83, abstract = {A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work. Proofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.}, author = {Abusalah, Hamza M}, issn = {2663-337X}, pages = {59}, publisher = {Institute of Science and Technology Austria}, title = {{Proof systems for sustainable decentralized cryptocurrencies}}, doi = {10.15479/AT:ISTA:TH_1046}, year = {2018}, } @phdthesis{197, abstract = {Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task.}, author = {Kolesnikov, Alexander}, issn = {2663-337X}, pages = {113}, publisher = {Institute of Science and Technology Austria}, title = {{Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images}}, doi = {10.15479/AT:ISTA:th_1021}, year = {2018}, } @article{6774, abstract = {A central problem of algebraic topology is to understand the homotopy groups 𝜋𝑑(𝑋) of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group 𝜋1(𝑋) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with 𝜋1(𝑋) trivial), compute the higher homotopy group 𝜋𝑑(𝑋) for any given 𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of 𝜋𝑑(𝑋) , 𝑑≥2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of 𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere 𝑆𝑑 to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes 𝜋𝑑(𝑋) and represents its elements as simplicial maps from a suitable triangulation of the d-sphere 𝑆𝑑 to X. For fixed d, the algorithm runs in time exponential in size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed 𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of 𝜋𝑑(𝑋) , the size of the triangulation of 𝑆𝑑 on which the map is defined, is exponential in size(𝑋) .}, author = {Filakovský, Marek and Franek, Peter and Wagner, Uli and Zhechev, Stephan Y}, issn = {2367-1734}, journal = {Journal of Applied and Computational Topology}, number = {3-4}, pages = {177--231}, publisher = {Springer}, title = {{Computing simplicial representatives of homotopy group elements}}, doi = {10.1007/s41468-018-0021-5}, volume = {2}, year = {2018}, } @inproceedings{133, abstract = {Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs.}, author = {Kragl, Bernhard and Qadeer, Shaz and Henzinger, Thomas A}, issn = {18688969}, location = {Beijing, China}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Synchronizing the asynchronous}}, doi = {10.4230/LIPIcs.CONCUR.2018.21}, volume = {118}, year = {2018}, } @inproceedings{187, abstract = {Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. }, author = {Edelsbrunner, Herbert and Osang, Georg F}, location = {Budapest, Hungary}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The multi-cover persistence of Euclidean balls}}, doi = {10.4230/LIPIcs.SoCG.2018.34}, volume = {99}, year = {2018}, } @article{692, abstract = {We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them.}, author = {Akopyan, Arseniy}, journal = {Geometriae Dedicata}, number = {1}, pages = {55 -- 64}, publisher = {Springer}, title = {{3-Webs generated by confocal conics and circles}}, doi = {10.1007/s10711-017-0265-6}, volume = {194}, year = {2018}, } @article{77, abstract = {Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.}, author = {Watzinger, Hannes and Kukucka, Josip and Vukusic, Lada and Gao, Fei and Wang, Ting and Schäffler, Friedrich and Zhang, Jian and Katsaros, Georgios}, journal = {Nature Communications}, number = {3902 }, publisher = {Nature Publishing Group}, title = {{A germanium hole spin qubit}}, doi = {10.1038/s41467-018-06418-4}, volume = {9}, year = {2018}, } @article{401, abstract = {The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation.}, author = {Qin, Xiang and Hannezo, Edouard B and Mangeat, Thomas and Liu, Chang and Majumder, Pralay and Liu, Jjiaying and Choesmel Cadamuro, Valerie and Mcdonald, Jocelyn and Liu, Yinyao and Yi, Bin and Wang, Xiaobo}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{A biochemical network controlling basal myosin oscillation}}, doi = {10.1038/s41467-018-03574-5}, volume = {9}, year = {2018}, } @article{318, abstract = {The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.}, author = {Casano, Alessandra M and Sixt, Michael K}, journal = {Developmental Cell}, number = {4}, pages = {405 -- 406}, publisher = {Cell Press}, title = {{A fat lot of good for wound healing}}, doi = {10.1016/j.devcel.2018.02.009}, volume = {44}, year = {2018}, } @article{410, abstract = {Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.}, author = {Masís, Javier and Mankus, David and Wolff, Steffen and Guitchounts, Grigori and Jösch, Maximilian A and Cox, David}, journal = {Scientific Reports}, number = {1}, publisher = {Nature Publishing Group}, title = {{A micro-CT-based method for quantitative brain lesion characterization and electrode localization}}, doi = {10.1038/s41598-018-23247-z}, volume = {8}, year = {2018}, } @article{277, abstract = {Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.}, author = {Dokládal, Ladislav and Benková, Eva and Honys, David and Dupláková, Nikoleta and Lee, Lan and Gelvin, Stanton and Sýkorová, Eva}, journal = {Plant Molecular Biology}, number = {5}, pages = {407 -- 420}, publisher = {Springer}, title = {{An armadillo-domain protein participates in a telomerase interaction network}}, doi = {10.1007/s11103-018-0747-4}, volume = {97}, year = {2018}, } @inproceedings{299, abstract = {We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal.}, author = {Nickovic, Dejan and Lebeltel, Olivier and Maler, Oded and Ferrere, Thomas and Ulus, Dogan}, editor = {Beyer, Dirk and Huisman, Marieke}, location = {Thessaloniki, Greece}, pages = {303 -- 319}, publisher = {Springer}, title = {{AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic}}, doi = {10.1007/978-3-319-89963-3_18}, volume = {10806}, year = {2018}, } @article{413, abstract = {Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk.}, author = {Konrad, Matthias and Pull, Christopher and Metzler, Sina and Seif, Katharina and Naderlinger, Elisabeth and Grasse, Anna V and Cremer, Sylvia}, journal = {PNAS}, number = {11}, pages = {2782 -- 2787}, publisher = {National Academy of Sciences}, title = {{Ants avoid superinfections by performing risk-adjusted sanitary care}}, doi = {10.1073/pnas.1713501115}, volume = {115}, year = {2018}, } @article{195, abstract = {We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.}, author = {Yakaboylu, Enderalp and Lemeshko, Mikhail}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {4}, publisher = {American Physical Society}, title = {{Anyonic statistics of quantum impurities in two dimensions}}, doi = {10.1103/PhysRevB.98.045402}, volume = {98}, year = {2018}, } @inproceedings{144, abstract = {The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines.}, author = {Ferrere, Thomas and Henzinger, Thomas A and Saraç, Ege}, location = {Oxford, UK}, pages = {394 -- 403}, publisher = {IEEE}, title = {{A theory of register monitors}}, doi = {10.1145/3209108.3209194}, volume = {Part F138033}, year = {2018}, } @article{203, abstract = {Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.}, author = {Abbas, Mohamad and Hernández, García J and Pollmann, Stephan and Samodelov, Sophia L and Kolb, Martina and Friml, Jirí and Hammes, Ulrich Z and Zurbriggen, Matias D and Blázquez, Miguel and Alabadí, David}, journal = {PNAS}, number = {26}, pages = {6864--6869}, publisher = {National Academy of Sciences}, title = {{Auxin methylation is required for differential growth in Arabidopsis}}, doi = {10.1073/pnas.1806565115}, volume = {115}, year = {2018}, } @article{399, abstract = {Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.}, author = {Napiórkowski, Marcin M and Reuvers, Robin and Solovej, Jan}, journal = {EPL}, number = {1}, publisher = {IOP Publishing Ltd.}, title = {{Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation}}, doi = {10.1209/0295-5075/121/10007}, volume = {121}, year = {2018}, } @article{5830, abstract = {CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.}, author = {Zhang, Luosha and Shi, Xiong and Zhang, Yutao and Wang, Jiajing and Yang, Jingwei and Ishida, Takashi and Jiang, Wenqian and Han, Xiangyu and Kang, Jingke and Wang, Xuening and Pan, Lixia and Lv, Shuo and Cao, Bing and Zhang, Yonghong and Wu, Jinbin and Han, Huibin and Hu, Zhubing and Cui, Langjun and Sawa, Shinichiro and He, Junmin and Wang, Guodong}, issn = {01407791}, journal = {Plant Cell and Environment}, publisher = {Wiley}, title = {{CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana}}, doi = {10.1111/pce.13475}, year = {2018}, } @article{288, abstract = {Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.}, author = {Lilja, Anna and Rodilla, Veronica and Huyghe, Mathilde and Hannezo, Edouard B and Landragin, Camille and Renaud, Olivier and Leroy, Olivier and Rulands, Steffen and Simons, Benjamin and Fré, Silvia}, journal = {Nature Cell Biology}, number = {6}, pages = {677 -- 687}, publisher = {Nature Publishing Group}, title = {{Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland}}, doi = {10.1038/s41556-018-0108-1}, volume = {20}, year = {2018}, } @article{304, abstract = {Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods. As a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications. In this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process. This requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure. Many of these components should be re-usable for the design of other optical structures at this scale. We show initial results of material samples fabricated based on our designs. While these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.}, author = {Auzinger, Thomas and Heidrich, Wolfgang and Bickel, Bernd}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Computational design of nanostructural color for additive manufacturing}}, doi = {10.1145/3197517.3201376}, volume = {37}, year = {2018}, } @article{12, abstract = {Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.}, author = {Nakashima, Kazutaka and Auzinger, Thomas and Iarussi, Emmanuel and Zhang, Ran and Igarashi, Takeo and Bickel, Bernd}, journal = {ACM Transaction on Graphics}, number = {4}, publisher = {ACM}, title = {{CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds}}, doi = {10.1145/3197517.3201341}, volume = {37}, year = {2018}, } @article{454, abstract = {Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games.}, author = {Reiter, Johannes and Hilbe, Christian and Rand, David and Chatterjee, Krishnendu and Nowak, Martin}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness}}, doi = {10.1038/s41467-017-02721-8}, volume = {9}, year = {2018}, } @article{320, abstract = {Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. }, author = {Hu, Hua and Roth, Fabian and Vandael, David H and Jonas, Peter M}, journal = {Neuron}, number = {1}, pages = {156 -- 165}, publisher = {Elsevier}, title = {{Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons}}, doi = {10.1016/j.neuron.2018.02.024}, volume = {98}, year = {2018}, } @article{423, abstract = {Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.}, author = {Payne, Pavel and Geyrhofer, Lukas and Barton, Nicholas H and Bollback, Jonathan P}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{CRISPR-based herd immunity can limit phage epidemics in bacterial populations}}, doi = {10.7554/eLife.32035}, volume = {7}, year = {2018}, }