@article{443, abstract = {Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited.}, author = {Hardie, Rae and Van Dam, Ellen and Cowley, Mark and Han, Ting and Balaban, Seher and Pajic, Marina and Pinese, Mark and Iconomou, Mary and Shearer, Robert and Mckenna, Jessie and Miller, David and Waddell, Nicola and Pearson, John and Grimmond, Sean and Sazanov, Leonid A and Biankin, Andrew and Villas Boas, Silas and Hoy, Andrew and Turner, Nigel and Saunders, Darren}, journal = {Cancer & Metabolism}, number = {2}, publisher = {BioMed Central}, title = {{Mitochondrial mutations and metabolic adaptation in pancreatic cancer}}, doi = {10.1186/s40170-017-0164-1}, volume = {5}, year = {2017}, } @inbook{444, abstract = {Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations.}, author = {Sazanov, Leonid A}, booktitle = {Mechanisms of primary energy transduction in biology }, editor = {Wikström, Mårten}, isbn = {978-1-78262-865-1}, pages = {25 -- 59}, publisher = {Royal Society of Chemistry}, title = {{Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions}}, doi = {10.1039/9781788010405-00025}, year = {2017}, } @article{445, abstract = {The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase.}, author = {Maksym Serbyn and Abanin, Dimitry A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {1}, publisher = {American Physical Society}, title = {{Loschmidt echo in many body localized phases}}, doi = {10.1103/PhysRevB.96.014202}, volume = {96}, year = {2017}, } @article{447, abstract = {We consider last passage percolation (LPP) models with exponentially distributed random variables, which are linked to the totally asymmetric simple exclusion process (TASEP). The competition interface for LPP was introduced and studied in Ferrari and Pimentel (2005a) for cases where the corresponding exclusion process had a rarefaction fan. Here we consider situations with a shock and determine the law of the fluctuations of the competition interface around its deter- ministic law of large number position. We also study the multipoint distribution of the LPP around the shock, extending our one-point result of Ferrari and Nejjar (2015).}, author = {Ferrari, Patrik and Nejjar, Peter}, journal = {Revista Latino-Americana de Probabilidade e Estatística}, pages = {299 -- 325}, publisher = {Instituto Nacional de Matematica Pura e Aplicada}, title = {{Fluctuations of the competition interface in presence of shocks}}, doi = {10.30757/ALEA.v14-17}, volume = {9}, year = {2017}, } @article{452, abstract = {Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. Yet, due to the exceeding difficulty of creating stably spinning objects of asymmetric shape in a manual trial-and-error process, there has been little departure from rotationally symmetric designs. With modern 3D printing technologies, however, we can manufacture shapes of almost unbounded complexity at the press of a button, shifting this design complexity toward computation. In this article, we describe an algorithm to generate designs for spinning objects by optimizing their mass distribution: as input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the interior mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. To create voids inside the model, we represent its volume with an adaptive multiresolution voxelization and optimize the discrete voxel fill values using a continuous, nonlinear formulation. We further optimize for rotational stability by maximizing the dominant principal moment. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance.}, author = {Bächer, Moritz and Bickel, Bernd and Whiting, Emily and Sorkine Hornung, Olga}, journal = {Communications of the ACM}, number = {8}, pages = {92 -- 99}, publisher = {ACM}, title = {{Spin it: Optimizing moment of inertia for spinnable objects}}, doi = {10.1145/3068766}, volume = {60}, year = {2017}, } @article{453, abstract = {Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.}, author = {Fallesen, Todd and Roostalu, Johanna and Düllberg, Christian F and Pruessner, Gunnar and Surrey, Thomas}, journal = {Biophysical Journal}, number = {9}, pages = {2055 -- 2067}, publisher = {Biophysical Society}, title = {{Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement}}, doi = {10.1016/j.bpj.2017.09.006}, volume = {113}, year = {2017}, } @article{459, abstract = {The social insects bees, wasps, ants, and termites are species-rich, occur in many habitats, and often constitute a large part of the biomass. Many are also invasive, including species of termites, the red imported fire ant, and the Argentine ant. While invasive social insects have been a problem in Southern Europe for some time, Central Europa was free of invasive ant species until recently because most ants are adapted to warmer climates. Only in the 1990s, did Lasius neglectus, a close relative of the common black garden ant, arrive in Germany. First described in 1990 based on individuals collected in Budapest, the species has since been detected for example in France, Germany, Spain, England, and Kyrgyzstan. The species is spread with soil during construction work or plantings, and L. neglectus therefore is often found in parks and botanical gardens. Another invasive ant now spreading in southern Germany is Formica fuscocinerea, which occurs along rivers, including in the sandy floodplains of the river Isar. As is typical of pioneer species, F. fuscocinerea quickly becomes extremely abundant and therefore causes problems for example on playgrounds in Munich. All invasive ant species are characterized by cooperation across nests, leading to strongly interconnected, very large super-colonies. The resulting dominance results in the extinction of native ant species as well as other arthropod species and thus in the reduction of biodiversity.}, author = {Cremer, Sylvia}, issn = {2366-2875}, journal = {Rundgespräche Forum Ökologie}, pages = {105 -- 116}, publisher = {Verlag Dr. Friedrich Pfeil}, title = {{Invasive Ameisen in Europa: Wie sie sich ausbreiten und die heimische Fauna verändern}}, volume = {46}, year = {2017}, } @article{463, abstract = {We investigate transient behaviors induced by magnetic fields on the dynamics of the flow of a ferrofluid in the gap between two concentric, independently rotating cylinders. Without applying any magnetic fields, we uncover emergence of flow states constituted by a combination of a localized spiral state (SPIl) in the top and bottom of the annulus and different multi-cell flow states (SPI2v, SPI3v) with toroidally closed vortices in the interior of the bulk (SPIl+2v = SPIl + SPI2v and SPIl+3v = SPIl + SPI3v). However, when a magnetic field is presented, we observe the transient behaviors between multi-cell states passing through two critical thresholds in a strength of an axial (transverse) magnetic field. Before the first critical threshold of a magnetic field strength, multi-stable states with different number of cells could be observed. After the first critical threshold, we find the transient behavior between the three- and two-cell flow states. For more strength of magnetic field or after the second critical threshold, we discover that multi-cell states are disappeared and a localized spiral state remains to be stimulated. The studied transient behavior could be understood by the investigation of various quantities including a modal kinetic energy, a mode amplitude of the radial velocity, wavenumber, angular momentum, and torque. In addition, the emergence of new flow states and the transient behavior between their states in ferrofluidic flows indicate that richer and potentially controllable dynamics through magnetic fields could be possible in ferrofluic flow.}, author = {Altmeyer, Sebastian and Do, Younghae and Ryu, Soorok}, issn = {10541500}, journal = {Chaos}, number = {11}, publisher = {AIP Publishing}, title = {{Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow}}, doi = {10.1063/1.5002771}, volume = {27}, year = {2017}, } @article{464, abstract = {The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years.}, author = {Chatterjee, Krishnendu and Henzinger, Monika H and Loitzenbauer, Veronika}, issn = {1860-5974}, journal = {Logical Methods in Computer Science}, number = {3}, publisher = {International Federation of Computational Logic}, title = {{Improved algorithms for parity and Streett objectives}}, doi = {10.23638/LMCS-13(3:26)2017}, volume = {13}, year = {2017}, } @article{465, abstract = {The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. }, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Ibsen-Jensen, Rasmus and Otop, Jan}, issn = {18605974}, journal = {Logical Methods in Computer Science}, number = {3}, publisher = {International Federation of Computational Logic}, title = {{Edit distance for pushdown automata}}, doi = {10.23638/LMCS-13(3:23)2017}, volume = {13}, year = {2017}, } @article{466, abstract = {We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. }, author = {Chatterjee, Krishnendu and Křetínská, Zuzana and Kretinsky, Jan}, issn = {18605974}, journal = {Logical Methods in Computer Science}, number = {2}, publisher = {International Federation of Computational Logic}, title = {{Unifying two views on multiple mean-payoff objectives in Markov decision processes}}, doi = {10.23638/LMCS-13(2:15)2017}, volume = {13}, year = {2017}, } @article{467, abstract = {Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan}, issn = {15293785}, journal = {ACM Transactions on Computational Logic (TOCL)}, number = {4}, publisher = {ACM}, title = {{Nested weighted automata}}, doi = {10.1145/3152769}, volume = {18}, year = {2017}, } @article{470, abstract = {This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios.}, author = {Jeschke, Stefan and Wojtan, Christopher J}, issn = {07300301}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Water wave packets}}, doi = {10.1145/3072959.3073678}, volume = {36}, year = {2017}, } @article{471, abstract = {We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. }, author = {Daca, Przemyslaw and Henzinger, Thomas A and Kretinsky, Jan and Petrov, Tatjana}, issn = {15293785}, journal = {ACM Transactions on Computational Logic (TOCL)}, number = {2}, publisher = {ACM}, title = {{Faster statistical model checking for unbounded temporal properties}}, doi = {10.1145/3060139}, volume = {18}, year = {2017}, } @article{472, abstract = {α-Synuclein is a presynaptic protein the function of which has yet to be identified, but its neuronal content increases in patients of synucleinopa-thies including Parkinson’s disease. Chronic overexpression of α-synuclein reportedly expresses various phenotypes of synaptic dysfunction, but the primary target of its toxicity has not been determined. To investigate this, we acutely loaded human recombinant α-synuclein or its pathological mutants in their monomeric forms into the calyces of Held presynaptic terminals in slices from auditorily mature and immature rats of either sex. Membrane capacitance measurements revealed significant and specific inhibitory effects of WT monomeric α-synuclein on vesicle endocytosis throughout development. However, the α-synuclein A53T mutant affected vesicle endocytosis only at immature calyces, where as the A30P mutant had no effect throughout. The endocytic impairment by WTα-synuclein was rescued by intraterminal coloading of the microtubule (MT) polymerization blocker nocodazole. Furthermore, it was reversibly rescued by presynaptically loaded photostatin-1, a pho-toswitcheable inhibitor of MT polymerization, inalight-wavelength-dependent manner. Incontrast, endocyticinhibition by the A53T mutant at immature calyces was not rescued by nocodazole. Functionally, presynaptically loaded WT α-synuclein had no effect on basal synaptic transmission evoked at a low frequency, but significantly attenuated exocytosis and impaired the fidelity of neurotransmission during prolonged high-frequency stimulation. We conclude that monomeric WTα-synuclein primarily inhibits vesicle endocytosis via MT overassembly, thereby impairing high-frequency neurotransmission.}, author = {Eguchi, Kohgaku and Taoufiq, Zachari and Thorn Seshold, Oliver and Trauner, Dirk and Hasegawa, Masato and Takahashi, Tomoyuki}, issn = {02706474}, journal = {European Journal of Neuroscience}, number = {25}, pages = {6043 -- 6052}, publisher = {Wiley-Blackwell}, title = {{Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held}}, doi = {10.1523/JNEUROSCI.0179-17.2017}, volume = {37}, year = {2017}, } @article{481, abstract = {We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.}, author = {Biedl, Therese and Huber, Stefan and Palfrader, Peter}, journal = {International Journal of Computational Geometry and Applications}, number = {3-4}, pages = {211 -- 229}, publisher = {World Scientific Publishing}, title = {{Planar matchings for weighted straight skeletons}}, doi = {10.1142/S0218195916600050}, volume = {26}, year = {2017}, } @article{483, abstract = {We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices.}, author = {Bourgade, Paul and Erdös, László and Yau, Horng and Yin, Jun}, issn = {10950761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {3}, pages = {739 -- 800}, publisher = {International Press}, title = {{Universality for a class of random band matrices}}, doi = {10.4310/ATMP.2017.v21.n3.a5}, volume = {21}, year = {2017}, } @article{484, abstract = {We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory.}, author = {Nam, Phan and Napiórkowski, Marcin M}, issn = {10950761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {3}, pages = {683 -- 738}, publisher = {International Press}, title = {{Bogoliubov correction to the mean-field dynamics of interacting bosons}}, doi = {10.4310/ATMP.2017.v21.n3.a4}, volume = {21}, year = {2017}, } @inproceedings{485, abstract = {We present results on nonlinear electro-optical conversion of microwave radiation into the optical telecommunication band with more than 0.1% photon number conversion efficiency with MHz bandwidth, in a crystalline whispering gallery mode resonator}, author = {Rueda Sanchez, Alfredo R and Sedlmeir, Florian and Collodo, Michele and Vogl, Ulrich and Stiller, Birgit and Schunk, Gerhard and Strekalov, Dmitry and Marquardt, Christoph and Fink, Johannes M and Painter, Oskar and Leuchs, Gerd and Schwefel, Harald}, booktitle = {Optics InfoBase Conference Papers}, isbn = {978-155752820-9}, location = {Waikoloa, HI, United States}, publisher = {Optica Publishing Group}, title = {{Single sideband microwave to optical photon conversion-an-electro-optic-realization}}, doi = {10.1364/NLO.2017.NM3A.1}, volume = {F54}, year = {2017}, } @article{486, abstract = {Color texture reproduction in 3D printing commonly ignores volumetric light transport (cross-talk) between surface points on a 3D print. Such light diffusion leads to significant blur of details and color bleeding, and is particularly severe for highly translucent resin-based print materials. Given their widely varying scattering properties, this cross-talk between surface points strongly depends on the internal structure of the volume surrounding each surface point. Existing scattering-aware methods use simplified models for light diffusion, and often accept the visual blur as an immutable property of the print medium. In contrast, our work counteracts heterogeneous scattering to obtain the impression of a crisp albedo texture on top of the 3D print, by optimizing for a fully volumetric material distribution that preserves the target appearance. Our method employs an efficient numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous scattering, supported by a practical calibration procedure to obtain scattering parameters from a given set of printer materials. Despite the inherent translucency of the medium, we reproduce detailed surface textures on 3D prints. We evaluate our system using a commercial, five-tone 3D print process and compare against the printer’s native color texturing mode, demonstrating that our method preserves high-frequency features well without having to compromise on color gamut.}, author = {Elek, Oskar and Sumin, Denis and Zhang, Ran and Weyrich, Tim and Myszkowski, Karol and Bickel, Bernd and Wilkie, Alexander and Krivanek, Jaroslav}, issn = {07300301}, journal = {ACM Transactions on Graphics}, number = {6}, publisher = {ACM}, title = {{Scattering-aware texture reproduction for 3D printing}}, doi = {10.1145/3130800.3130890}, volume = {36}, year = {2017}, }