@article{163, abstract = {For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.}, author = {Reipert, Siegfried and Goldammer, Helmuth and Richardson, Christine and Goldberg, Martin and Hawkins, Timothy and Hollergschwandtner, Elena and Kaufmann, Walter and Antreich, Sebastian and Stierhof, York}, issn = {0022-1554}, journal = {Journal of Histochemistry and Cytochemistry}, number = {12}, pages = {903--921}, publisher = {SAGE Publications}, title = {{Agitation modules: Flexible means to accelerate automated freeze substitution}}, doi = {10.1369/0022155418786698}, volume = {66}, year = {2018}, } @article{17, abstract = {Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow.}, author = {Varshney, Atul and Steinberg, Victor}, journal = {Physical Review Fluids}, number = {10}, publisher = {American Physical Society}, title = {{Drag enhancement and drag reduction in viscoelastic flow}}, doi = {10.1103/PhysRevFluids.3.103302}, volume = {3}, year = {2018}, } @inproceedings{174, abstract = {We survey recent efforts to quantify failures of the Hasse principle in families of rationally connected varieties.}, author = {Browning, Timothy D}, location = {Salt Lake City, Utah, USA}, number = {2}, pages = {89 -- 102}, publisher = {American Mathematical Society}, title = {{How often does the Hasse principle hold?}}, doi = {10.1090/pspum/097.2/01700}, volume = {97}, year = {2018}, } @article{176, abstract = {For a general class of non-negative functions defined on integral ideals of number fields, upper bounds are established for their average over the values of certain principal ideals that are associated to irreducible binary forms with integer coefficients.}, author = {Browning, Timothy D and Sofos, Efthymios}, journal = {International Journal of Nuber Theory}, number = {3}, pages = {547--567}, publisher = {World Scientific Publishing}, title = {{Averages of arithmetic functions over principal ideals}}, doi = {10.1142/S1793042119500283}, volume = {15}, year = {2018}, } @article{178, abstract = {We give an upper bound for the number of rational points of height at most B, lying on a surface defined by a quadratic form Q. The bound shows an explicit dependence on Q. It is optimal with respect to B, and is also optimal for typical forms Q.}, author = {Browning, Timothy D and Heath-Brown, Roger}, issn = {2397-3129}, journal = {Discrete Analysis}, pages = {1 -- 29}, publisher = {Alliance of Diamond Open Access Journals}, title = {{Counting rational points on quadric surfaces}}, doi = {10.19086/da.4375}, volume = {15}, year = {2018}, } @article{18, abstract = {An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17].}, author = {Kolmogorov, Vladimir and Rolinek, Michal}, issn = {0381-7032}, journal = {Ars Combinatoria}, number = {10}, pages = {269 -- 304}, publisher = {Charles Babbage Research Centre}, title = {{Superconcentrators of density 25.3}}, volume = {141}, year = {2018}, } @article{180, abstract = {In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density.}, author = {Lewi, Mathieu and Lieb, Élliott and Seiringer, Robert}, issn = {2270-518X}, journal = {Journal de l'Ecole Polytechnique - Mathematiques}, pages = {79 -- 116}, publisher = {Ecole Polytechnique}, title = {{Statistical mechanics of the uniform electron gas}}, doi = {10.5802/jep.64}, volume = {5}, year = {2018}, } @article{181, abstract = {We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2.}, author = {Erdös, László and Krüger, Torben H and Renfrew, David T}, journal = {SIAM Journal on Mathematical Analysis}, number = {3}, pages = {3271 -- 3290}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Power law decay for systems of randomly coupled differential equations}}, doi = {10.1137/17M1143125}, volume = {50}, year = {2018}, } @inproceedings{182, abstract = {We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice.}, author = {Bakhirkin, Alexey and Ferrere, Thomas and Maler, Oded}, booktitle = {Proceedings of the 21st International Conference on Hybrid Systems}, isbn = {978-1-4503-5642-8 }, location = {Porto, Portugal}, pages = {177 -- 186}, publisher = {ACM}, title = {{Efficient parametric identification for STL}}, doi = {10.1145/3178126.3178132}, year = {2018}, } @inproceedings{183, abstract = {Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.}, author = {Bartocci, Ezio and Ferrere, Thomas and Manjunath, Niveditha and Nickovic, Dejan}, location = {Porto, Portugal}, pages = {197 -- 206}, publisher = {Association for Computing Machinery, Inc}, title = {{Localizing faults in simulink/stateflow models with STL}}, doi = {10.1145/3178126.3178131}, 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{185, abstract = {We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.}, author = {Fulek, Radoslav and Kynčl, Jan}, isbn = {978-3-95977-066-8}, location = {Budapest, Hungary}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Hanani-Tutte for approximating maps of graphs}}, doi = {10.4230/LIPIcs.SoCG.2018.39}, volume = {99}, 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{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}, } @inproceedings{188, abstract = {Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex.}, author = {Edelsbrunner, Herbert and Virk, Ziga and Wagner, Hubert}, location = {Budapest, Hungary}, pages = {35:1 -- 35:13}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Smallest enclosing spheres and Chernoff points in Bregman geometry}}, doi = {10.4230/LIPIcs.SoCG.2018.35}, volume = {99}, year = {2018}, } @article{19, abstract = {Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.}, author = {Palmer, Adam and Chait, Remy P and Kishony, Roy}, issn = {0737-4038}, journal = {Molecular Biology and Evolution}, number = {11}, pages = {2669 -- 2684}, publisher = {Oxford University Press}, title = {{Nonoptimal gene expression creates latent potential for antibiotic resistance}}, doi = {10.1093/molbev/msy163}, volume = {35}, year = {2018}, } @article{190, abstract = {The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control.}, author = {Harrison, Mark and Arning, Nicolas and Kremer, Lucas and Ylla, Guillem and Belles, Xavier and Bornberg Bauer, Erich and Huylmans, Ann K and Jongepier, Evelien and Puilachs, Maria and Richards, Stephen and Schal, Coby}, journal = {Journal of Experimental Zoology Part B: Molecular and Developmental Evolution}, pages = {254--264}, publisher = {Wiley}, title = {{Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest}}, doi = {10.1002/jez.b.22824}, volume = {330}, year = {2018}, } @article{191, abstract = {Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.}, author = {Grones, Peter and Abas, Melinda F and Hajny, Jakub and Jones, Angharad and Waidmann, Sascha and Kleine Vehn, Jürgen and Friml, Jirí}, journal = {Scientific Reports}, number = {1}, publisher = {Springer}, title = {{PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism}}, doi = {10.1038/s41598-018-28188-1}, volume = {8}, year = {2018}, } @article{192, abstract = {The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.}, author = {Fendrych, Matyas and Akhmanova, Maria and Merrin, Jack and Glanc, Matous and Hagihara, Shinya and Takahashi, Koji and Uchida, Naoyuki and Torii, Keiko U and Friml, Jirí}, journal = {Nature Plants}, number = {7}, pages = {453 -- 459}, publisher = {Springer Nature}, title = {{Rapid and reversible root growth inhibition by TIR1 auxin signalling}}, doi = {10.1038/s41477-018-0190-1}, volume = {4}, year = {2018}, } @inproceedings{193, abstract = {We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.}, author = {Alwen, Joel F and Gazi, Peter and Kamath Hosdurg, Chethan and Klein, Karen and Osang, Georg F and Pietrzak, Krzysztof Z and Reyzin, Lenoid and Rolinek, Michal and Rybar, Michal}, booktitle = {Proceedings of the 2018 on Asia Conference on Computer and Communication Security}, location = {Incheon, Republic of Korea}, pages = {51 -- 65}, publisher = {ACM}, title = {{On the memory hardness of data independent password hashing functions}}, doi = {10.1145/3196494.3196534}, year = {2018}, }