TY - JOUR
AB - 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.
AU - Altmeyer, Sebastian
AU - Do, Younghae
AU - Ryu, Soorok
ID - 463
IS - 11
JF - Chaos
SN - 10541500
TI - Transient behavior between multi-cell flow states in ferrofluidic Taylor-Couette flow
VL - 27
ER -
TY - JOUR
AB - 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.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Ibsen-Jensen, Rasmus
AU - Otop, Jan
ID - 465
IS - 3
JF - Logical Methods in Computer Science
SN - 18605974
TI - Edit distance for pushdown automata
VL - 13
ER -
TY - JOUR
AB - 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.
AU - Chatterjee, Krishnendu
AU - Křetínská, Zuzana
AU - Kretinsky, Jan
ID - 466
IS - 2
JF - Logical Methods in Computer Science
SN - 18605974
TI - Unifying two views on multiple mean-payoff objectives in Markov decision processes
VL - 13
ER -
TY - JOUR
AB - 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.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Otop, Jan
ID - 467
IS - 4
JF - ACM Transactions on Computational Logic (TOCL)
SN - 15293785
TI - Nested weighted automata
VL - 18
ER -
TY - JOUR
AB - 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.
AU - Jeschke, Stefan
AU - Wojtan, Christopher J
ID - 470
IS - 4
JF - ACM Transactions on Graphics
SN - 07300301
TI - Water wave packets
VL - 36
ER -
TY - JOUR
AB - 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.
AU - Daca, Przemyslaw
AU - Henzinger, Thomas A
AU - Kretinsky, Jan
AU - Petrov, Tatjana
ID - 471
IS - 2
JF - ACM Transactions on Computational Logic (TOCL)
SN - 15293785
TI - Faster statistical model checking for unbounded temporal properties
VL - 18
ER -
TY - JOUR
AB - 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.
AU - Eguchi, Kohgaku
AU - Taoufiq, Zachari
AU - Thorn Seshold, Oliver
AU - Trauner, Dirk
AU - Hasegawa, Masato
AU - Takahashi, Tomoyuki
ID - 472
IS - 25
JF - European Journal of Neuroscience
SN - 02706474
TI - Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held
VL - 37
ER -
TY - JOUR
AB - 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.
AU - Bourgade, Paul
AU - Erdös, László
AU - Yau, Horng
AU - Yin, Jun
ID - 483
IS - 3
JF - Advances in Theoretical and Mathematical Physics
SN - 10950761
TI - Universality for a class of random band matrices
VL - 21
ER -
TY - JOUR
AB - 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.
AU - Nam, Phan
AU - Napiórkowski, Marcin M
ID - 484
IS - 3
JF - Advances in Theoretical and Mathematical Physics
SN - 10950761
TI - Bogoliubov correction to the mean-field dynamics of interacting bosons
VL - 21
ER -
TY - CONF
AB - 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
AU - Rueda Sanchez, Alfredo R
AU - Sedlmeir, Florian
AU - Collodo, Michele
AU - Vogl, Ulrich
AU - Stiller, Birgit
AU - Schunk, Gerhard
AU - Strekalov, Dmitry
AU - Marquardt, Christoph
AU - Fink, Johannes M
AU - Painter, Oskar
AU - Leuchs, Gerd
AU - Schwefel, Harald
ID - 485
SN - 978-155752820-9
TI - Single sideband microwave to optical photon conversion-an-electro-optic-realization
VL - F54
ER -
TY - JOUR
AB - 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.
AU - Elek, Oskar
AU - Sumin, Denis
AU - Zhang, Ran
AU - Weyrich, Tim
AU - Myszkowski, Karol
AU - Bickel, Bernd
AU - Wilkie, Alexander
AU - Krivanek, Jaroslav
ID - 486
IS - 6
JF - ACM Transactions on Graphics
SN - 07300301
TI - Scattering-aware texture reproduction for 3D printing
VL - 36
ER -
TY - CONF
AB - In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x.
AU - Baig, Ghufran
AU - Radunovic, Bozidar
AU - Alistarh, Dan-Adrian
AU - Balkwill, Matthew
AU - Karagiannis, Thomas
AU - Qiu, Lili
ID - 487
SN - 978-145035422-6
T2 - Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies
TI - Towards unlicensed cellular networks in TV white spaces
ER -
TY - JOUR
AB - The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.
AU - Pavlogiannis, Andreas
AU - Tkadlec, Josef
AU - Chatterjee, Krishnendu
AU - Nowak, Martin
ID - 512
IS - 1
JF - Scientific Reports
SN - 20452322
TI - Amplification on undirected population structures: Comets beat stars
VL - 7
ER -
TY - JOUR
AB - We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction.
AU - Klotz, Lukasz
AU - Lemoult, Grégoire M
AU - Frontczak, Idalia
AU - Tuckerman, Laurette
AU - Wesfreid, José
ID - 513
IS - 4
JF - Physical Review Fluids
TI - Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence
VL - 2
ER -
TY - JOUR
AB - Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.
AU - Simonnet, Jean
AU - Nassar, Mérie
AU - Stella, Federico
AU - Cohen, Ivan
AU - Mathon, Bertrand
AU - Boccara, Charlotte
AU - Miles, Richard
AU - Fricker, Desdemona
ID - 514
JF - Nature Communications
SN - 20411723
TI - Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum
VL - 8
ER -
TY - JOUR
AB - The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.
AU - Letts, James A
AU - Sazanov, Leonid A
ID - 515
IS - 10
JF - Nature Structural and Molecular Biology
SN - 15459993
TI - Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain
VL - 24
ER -
TY - JOUR
AB - Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here.
AU - Du, Wei
AU - Angermayr, Andreas
AU - Jongbloets, Joeri
AU - Molenaar, Douwe
AU - Bachmann, Herwig
AU - Hellingwerf, Klaas
AU - Branco Dos Santos, Filipe
ID - 520
IS - 3
JF - ACS Synthetic Biology
SN - 21615063
TI - Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803
VL - 6
ER -
TY - JOUR
AB - Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension.
AU - Austin, Kyle
AU - Virk, Ziga
ID - 521
JF - Topology and its Applications
SN - 01668641
TI - Higson compactification and dimension raising
VL - 215
ER -
TY - JOUR
AB - The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity.
AU - Daniel von Wangenheim
AU - Goh, Tatsuaki
AU - Dietrich, Daniela
AU - Bennett, Malcolm J
ID - 525
IS - 5
JF - Current Biology
TI - Plant biology: Building barriers… in roots
VL - 27
ER -
TY - JOUR
AB - The pituitary adenylyl cyclase-activating polypeptide (PACAP) and its G protein-coupled receptors, PAC1, VPAC1 and VPAC2 form a system involved in a variety of biological processes. Although some sympathetic stimulatory effects of this system have been reported, its central cardiovascular regulatory properties are poorly characterized. VPAC1 receptors are expressed in the nucleus ambiguus (nAmb), a key center controlling cardiac parasympathetic tone. In this study, we report that selective VPAC1 activation in rhodamine-labeled cardiac vagal preganglionic neurons of the rat nAmb produces inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization, membrane depolarization and activation of P/Q-type Ca2+ channels. In vivo, this pathway converges onto transient reduction in heart rate of conscious rats. Therefore we demonstrate a VPAC1-dependent mechanism in the central parasympathetic regulation of the heart rate, adding to the complexity of PACAP-mediated cardiovascular modulation.
AU - Gherghina, Florin L
AU - Tica, Andrei A
AU - Elena Deliu
AU - Abood, Mary E
AU - Brailoiu, G. Christina
AU - Brǎiloiu, Eugen
ID - 529
JF - Brain Research
TI - Effects of VPAC1 activation in nucleus ambiguus neurons
VL - 1657
ER -
TY - JOUR
AB - We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.
AU - Burton, Benjamin
AU - De Mesmay, Arnaud N
AU - Wagner, Uli
ID - 534
IS - 4
JF - Discrete & Computational Geometry
SN - 01795376
TI - Finding non-orientable surfaces in 3-Manifolds
VL - 58
ER -
TY - JOUR
AB - Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung.
AU - Kainrath, Stephanie
AU - Stadler, Manuela
AU - Gschaider-Reichhart, Eva
AU - Distel, Martin
AU - Janovjak, Harald L
ID - 538
IS - 16
JF - Angewandte Chemie
TI - Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen
VL - 129
ER -
TY - JOUR
AB - RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host.
AU - Khamina, Kseniya
AU - Lercher, Alexander
AU - Caldera, Michael
AU - Schliehe, Christopher
AU - Vilagos, Bojan
AU - Sahin, Mehmet
AU - Kosack, Lindsay
AU - Bhattacharya, Anannya
AU - Májek, Peter
AU - Stukalov, Alexey
AU - Sacco, Roberto
AU - James, Leo
AU - Pinschewer, Daniel
AU - Bennett, Keiryn
AU - Menche, Jörg
AU - Bergthaler, Andreas
ID - 540
IS - 12
JF - PLoS Pathogens
SN - 15537366
TI - Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein
VL - 13
ER -
TY - JOUR
AB - While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed.
AU - Nikolic, Nela
AU - Schreiber, Frank
AU - Dal Co, Alma
AU - Kiviet, Daniel
AU - Bergmiller, Tobias
AU - Littmann, Sten
AU - Kuypers, Marcel
AU - Ackermann, Martin
ID - 541
IS - 12
JF - PLoS Genetics
SN - 15537390
TI - Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations
VL - 13
ER -
TY - CHAP
AB - Development of vascular tissue is a remarkable example of intercellular communication and coordinated development involving hormonal signaling and tissue polarity. Thus far, studies on vascular patterning and regeneration have been conducted mainly in trees—woody plants—with a well-developed layer of vascular cambium and secondary tissues. Trees are difficult to use as genetic models, i.e., due to long generation time, unstable environmental conditions, and lack of available mutants and transgenic lines. Therefore, the use of the main genetic model plant Arabidopsis thaliana (L.) Heynh., with a wealth of available marker and transgenic lines, provides a unique opportunity to address molecular mechanism of vascular tissue formation and regeneration. With specific treatments, the tiny weed Arabidopsis can serve as a model to understand the growth of mighty trees and interconnect a tree physiology with molecular genetics and cell biology of Arabidopsis.
AU - Mazur, Ewa
AU - Friml, Jirí
ED - Jurić, Snježana
ID - 545
T2 - Plant Engineering
TI - Vascular tissue development and regeneration in the model plant arabidopsis
ER -
TY - GEN
AB - In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.
AU - Barbara Petritsch
ID - 5450
TI - Implementing the institutional data repository IST DataRep
ER -
TY - GEN
AB - A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks.
AU - Chatterjee, Krishnendu
AU - Choudhary, Bhavya
AU - Pavlogiannis, Andreas
ID - 5455
SN - 2664-1690
TI - Optimal Dyck reachability for data-dependence and alias analysis
ER -
TY - GEN
AB - We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.
We introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.
1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.
2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence.
Finally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.
AU - Chalupa, Marek
AU - Chatterjee, Krishnendu
AU - Pavlogiannis, Andreas
AU - Sinha, Nishant
AU - Vaidya, Kapil
ID - 5456
SN - 2664-1690
TI - Data-centric dynamic partial order reduction
ER -
TY - JOUR
AB - In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region.
AU - De Martino, Daniele
ID - 548
IS - 6
JF - Physical Review E
SN - 24700045
TI - Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes
VL - 96
ER -
TY - CONF
AB - Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a new class of model checking algorithms that capture the causal relationships in a special data structure called concurrent traces. Concurrent traces identify key events in an execution history and link them through their cause-effect relationships. The model checker builds a tableau of concurrent traces, where the case splits represent different causal explanations of a hypothetical error. Causality-based model checking has been implemented in the ARCTOR tool, and applied to previously intractable multi-threaded benchmarks.
AU - Finkbeiner, Bernd
AU - Kupriyanov, Andrey
ID - 549
SN - 20752180
T2 - Electronic Proceedings in Theoretical Computer Science
TI - Causality-based model checking
VL - 259
ER -
TY - JOUR
AB - For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities.
AU - Alt, Johannes
ID - 550
JF - Electronic Communications in Probability
SN - 1083589X
TI - Singularities of the density of states of random Gram matrices
VL - 22
ER -
TY - CONF
AB - Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs.
AU - Chatterjee, Krishnendu
AU - Ibsen-Jensen, Rasmus
AU - Nowak, Martin
ID - 551
SN - 978-395977046-0
T2 - Leibniz International Proceedings in Informatics
TI - Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs
VL - 83
ER -
TY - CONF
AB - We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary.
AU - Chatterjee, Krishnendu
AU - Hansen, Kristofer
AU - Ibsen-Jensen, Rasmus
ID - 553
SN - 978-395977046-0
T2 - Leibniz International Proceedings in Informatics
TI - Strategy complexity of concurrent safety games
VL - 83
ER -
TY - DATA
AB - Strong amplifiers of natural selection
AU - Pavlogiannis, Andreas
AU - Tkadlec, Josef
AU - Chatterjee, Krishnendu
AU - Nowak , Martin
ID - 5559
KW - natural selection
TI - Strong amplifiers of natural selection
ER -
TY - DATA
AB - This repository contains the data collected for the manuscript "Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity".
The data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.
Data is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic "mother machine" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.
AU - Bergmiller, Tobias
AU - Andersson, Anna M
AU - Tomasek, Kathrin
AU - Balleza, Enrique
AU - Kiviet, Daniel
AU - Hauschild, Robert
AU - Tkacik, Gasper
AU - Guet, Calin C
ID - 5560
KW - single cell microscopy
KW - mother machine microfluidic device
KW - AcrAB-TolC pump
KW - multi-drug efflux
KW - Escherichia coli
TI - Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity
ER -
TY - DATA
AB - Graph matching problems as described in "Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans." by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in "Feature Correspondence via Graph Matching: Models and Global Optimization." by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip.
AU - Kainmueller, Dagmar
AU - Jug, Florian
AU - Rother, Carsten
AU - Meyers, Gene
ID - 5561
KW - graph matching
KW - feature matching
KW - QAP
KW - MAP-inference
TI - Graph matching problems for annotating C. Elegans
ER -
TY - DATA
AB - This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:
[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.
AU - Marre, Olivier
AU - Tkacik, Gasper
AU - Amodei, Dario
AU - Schneidman, Elad
AU - Bialek, William
AU - Berry, Michael
ID - 5562
KW - multi-electrode recording
KW - retinal ganglion cells
TI - Multi-electrode array recording from salamander retinal ganglion cells
ER -
TY - DATA
AB - MATLAB code and processed datasets available for reproducing the results in:
Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.
*equal contributions
AU - Lukacisin, Martin
ID - 5563
TI - MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'
ER -
TY - DATA
AB - Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication.
AU - Steinrück, Magdalena
AU - Guet, Calin C
ID - 5564
TI - Fastq files for "Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection"
ER -
TY - DATA
AB - One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions.
The Video is licensed under a CC BY NC ND license.
AU - Von Wangenheim, Daniel
AU - Hauschild, Robert
AU - Friml, Jirí
ID - 5565
TI - Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel
ER -
TY - DATA
AB - Current minimal version of TipTracker
AU - Hauschild, Robert
ID - 5566
KW - tool
KW - tracking
KW - confocal microscopy
TI - Live tracking of moving samples in confocal microscopy for vertically grown roots
ER -
TY - DATA
AB - Immunological synapse DC-Tcells
AU - Leithner, Alexander F
ID - 5567
KW - Immunological synapse
TI - Immunological synapse DC-Tcells
ER -
TY - DATA
AB - Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)
AU - Hahn, David
ID - 5568
KW - Boundary elements
KW - brittle fracture
KW - computer graphics
KW - fracture simulation
TI - Source codes: Brittle fracture simulation with boundary elements for computer graphics
ER -
TY - JOUR
AB - PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer.
AU - Nickells, Robert
AU - Schmitt, Heather
AU - Maes, Margaret E
AU - Schlamp, Cassandra
ID - 557
IS - 14
JF - Investigative Ophthalmology and Visual Science
SN - 01460404
TI - AAV2 mediated transduction of the mouse retina after optic nerve injury
VL - 58
ER -
TY - DATA
AB - Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files.
AU - Hauschild, Robert
ID - 5570
KW - Cell migration
KW - tracking
KW - forward migration index
KW - FMI
TI - Forward migration indexes
ER -
TY - DATA
AB - This folder contains all the data used in each of the main figures of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures.
AU - Vicoso, Beatriz
ID - 5571
TI - Data for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"
ER -
TY - DATA
AB - Code described in the Supplementary Methods of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.)
AU - Vicoso, Beatriz
ID - 5572
TI - Code for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"
ER -
TY - JOUR
AB - Immune specificity is the degree to which a host’s immune system discriminates among various pathogens or antigenic variants. Vertebrate immune memory is highly specific due to antibody responses. On the other hand, some invertebrates show immune priming, i.e. improved survival after secondary exposure to a previously encountered pathogen. Until now, specificity of priming has only been demonstrated via the septic infection route or when live pathogens were used for priming. Therefore, we tested for specificity in the oral priming route in the red flour beetle, Tribolium castaneum. For priming, we used pathogen-free supernatants derived from three different strains of the entomopathogen, Bacillus thuringiensis, which express different Cry toxin variants known for their toxicity against this beetle. Subsequent exposure to the infective spores showed that oral priming was specific for two naturally occurring strains, while a third engineered strain did not induce any priming effect. Our data demonstrate that oral immune priming with a non-infectious bacterial agent can be specific, but the priming effect is not universal across all bacterial strains.
AU - Futo, Momir
AU - Sell, Marie
AU - Kutzer, Megan
AU - Kurtz, Joachim
ID - 558
IS - 12
JF - Biology Letters
SN - 17449561
TI - Specificity of oral immune priming in the red flour beetle Tribolium castaneum
VL - 13
ER -
TY - CONF
AB - Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).
AU - Abusalah, Hamza M
AU - Alwen, Joel F
AU - Cohen, Bram
AU - Khilko, Danylo
AU - Pietrzak, Krzysztof Z
AU - Reyzin, Leonid
ID - 559
SN - 978-331970696-2
TI - Beyond Hellman’s time-memory trade-offs with applications to proofs of space
VL - 10625
ER -
TY - JOUR
AB - In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.
AU - Gerencser, Mate
AU - Jentzen, Arnulf
AU - Salimova, Diyora
ID - 560
IS - 2207
JF - Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
SN - 13645021
TI - On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions
VL - 473
ER -
TY - JOUR
AB - We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).
AU - Franek, Peter
AU - Krcál, Marek
ID - 568
IS - 2
JF - Homology, Homotopy and Applications
SN - 15320073
TI - Persistence of zero sets
VL - 19
ER -
TY - JOUR
AB - The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.
AU - Spira, Felix
AU - Cuylen Haering, Sara
AU - Mehta, Shalin
AU - Samwer, Matthias
AU - Reversat, Anne
AU - Verma, Amitabh
AU - Oldenbourg, Rudolf
AU - Sixt, Michael K
AU - Gerlich, Daniel
ID - 569
JF - eLife
SN - 2050084X
TI - Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments
VL - 6
ER -
TY - JOUR
AB - Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution.
AU - Lagator, Mato
AU - Sarikas, Srdjan
AU - Acar, Hande
AU - Bollback, Jonathan P
AU - Guet, Calin C
ID - 570
JF - eLife
SN - 2050084X
TI - Regulatory network structure determines patterns of intermolecular epistasis
VL - 6
ER -
TY - JOUR
AB - Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface.
AU - Gärtner, Florian R
AU - Ahmad, Zerkah
AU - Rosenberger, Gerhild
AU - Fan, Shuxia
AU - Nicolai, Leo
AU - Busch, Benjamin
AU - Yavuz, Gökce
AU - Luckner, Manja
AU - Ishikawa Ankerhold, Hellen
AU - Hennel, Roman
AU - Benechet, Alexandre
AU - Lorenz, Michael
AU - Chandraratne, Sue
AU - Schubert, Irene
AU - Helmer, Sebastian
AU - Striednig, Bianca
AU - Stark, Konstantin
AU - Janko, Marek
AU - Böttcher, Ralph
AU - Verschoor, Admar
AU - Leon, Catherine
AU - Gachet, Christian
AU - Gudermann, Thomas
AU - Mederos Y Schnitzler, Michael
AU - Pincus, Zachary
AU - Iannacone, Matteo
AU - Haas, Rainer
AU - Wanner, Gerhard
AU - Lauber, Kirsten
AU - Sixt, Michael K
AU - Massberg, Steffen
ID - 571
IS - 6
JF - Cell Press
SN - 00928674
TI - Migrating platelets are mechano scavengers that collect and bundle bacteria
VL - 171
ER -
TY - JOUR
AB - In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.
AU - Olatunji, Damilola
AU - Geelen, Danny
AU - Verstraeten, Inge
ID - 572
IS - 12
JF - International Journal of Molecular Sciences
TI - Control of endogenous auxin levels in plant root development
VL - 18
ER -
TY - JOUR
AB - We construct a polyhedral surface called a graceful surface, which provides best possible approximation to a given sphere regarding certain criteria. In digital geometry terms, the graceful surface is uniquely characterized by its minimality while guaranteeing the connectivity of certain discrete (polyhedral) curves defined on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva (1999) and shown to be useful for triangular mesh discretization through graceful planes and graceful lines. In this paper we extend the considerations to a nonlinear object such as a sphere. In particular, we investigate the properties of a discrete geodesic path between two voxels and show that discrete 3D circles, circular arcs, and Mobius triangles are all constructible on a graceful sphere, with guaranteed minimum thickness and the desired connectivity in the discrete topological space.
AU - Biswas, Ranita
AU - Bhowmick, Partha
AU - Brimkov, Valentin E.
ID - 5799
JF - Discrete Applied Mathematics
SN - 0166-218X
TI - On the polyhedra of graceful spheres and circular geodesics
VL - 216
ER -
TY - JOUR
AB - This paper presents a novel study on the functional gradation of coordinate planes in connection with the thinnest and tunnel-free (i.e., naive) discretization of sphere in the integer space. For each of the 48-symmetric quadraginta octants of naive sphere with integer radius and integer center, we show that the corresponding voxel set forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as its functional plane. We use this fundamental property to prove several other theoretical results for naive sphere. First, the quadraginta octants form symmetry groups and subgroups with certain equivalent topological properties. Second, a naive sphere is always unique and consists of fewest voxels. Third, it is efficiently constructible from its functional-plane projection. And finally, a special class of 4-symmetric discrete 3D circles can be constructed on a naive sphere based on back projection from the functional plane.
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5800
IS - 1
JF - Journal of Mathematical Imaging and Vision
SN - 09249907
TI - On the functionality and usefulness of Quadraginta octants of naive sphere
VL - 59
ER -
TY - CONF
AB - Space filling circles and spheres have various applications in mathematical imaging and physical modeling. In this paper, we first show how the thinnest (i.e., 2-minimal) model of digital sphere can be augmented to a space filling model by fixing certain “simple voxels” and “filler voxels” associated with it. Based on elementary number-theoretic properties of such voxels, we design an efficient incremental algorithm for generation of these space filling spheres with successively increasing radius. The novelty of the proposed technique is established further through circular space filling on 3D digital plane. As evident from a preliminary set of experimental result, this can particularly be useful for parallel computing of 3D Voronoi diagrams in the digital space.
AU - Dwivedi, Shivam
AU - Gupta, Aniket
AU - Roy, Siddhant
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5801
SN - 0302-9743
T2 - 20th IAPR International Conference
TI - Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space
VL - 10502
ER -
TY - CONF
AB - This papers introduces a definition of digital primitives based on focal points and weighted distances (with positive weights). The proposed definition is applicable to general dimensions and covers in its gamut various regular curves and surfaces like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids, Cartesian k-ovals, etc. Several interesting properties are presented for this class of digital primitives such as space partitioning, topological separation, and connectivity properties. To demonstrate further the potential of this new way of defining digital primitives, we propose, as extension, another class of digital conics defined by focus-directrix combination.
AU - Andres, Eric
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5802
SN - 0302-9743
T2 - 20th IAPR International Conference
TI - Digital primitives defined by weighted focal set
VL - 10502
ER -
TY - CHAP
AB - Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept.
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5803
SN - 0302-9743
T2 - Combinatorial image analysis
TI - Construction of persistent Voronoi diagram on 3D digital plane
VL - 10256
ER -
TY - JOUR
AB - Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements.
AU - Engelsen, Nils
AU - Krishnakumar, Rajiv
AU - Hosten, Onur
AU - Kasevich, Mark
ID - 593
IS - 14
JF - Physical Review Letters
TI - Bell correlations in spin-squeezed states of 500 000 atoms
VL - 118
ER -
TY - JOUR
AB - Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.
AU - Engel, Christoph
AU - Gubbey, Tobias
AU - Neyer, Simon
AU - Sainsbury, Sarah
AU - Oberthuer, Christiane
AU - Baejen, Carlo
AU - Bernecky, Carrie A
AU - Cramer, Patrick
ID - 600
IS - 1
JF - Cell
SN - 00928674
TI - Structural basis of RNA polymerase I transcription initiation
VL - 169
ER -
TY - JOUR
AB - The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin.
AU - Xu, Youwei
AU - Bernecky, Carrie A
AU - Lee, Chung
AU - Maier, Kerstin
AU - Schwalb, Björn
AU - Tegunov, Dimitri
AU - Plitzko, Jürgen
AU - Urlaub, Henning
AU - Cramer, Patrick
ID - 601
JF - Nature Communications
SN - 20411723
TI - Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex
VL - 8
ER -
TY - JOUR
AB - The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”
AU - Camus, Nicolas
AU - Yakaboylu, Enderalp
AU - Fechner, Lutz
AU - Klaiber, Michael
AU - Laux, Martin
AU - Mi, Yonghao
AU - Hatsagortsyan, Karen Z.
AU - Pfeifer, Thomas
AU - Keitel, Christoph H.
AU - Moshammer, Robert
ID - 6013
IS - 2
JF - Physical Review Letters
SN - 0031-9007
TI - Experimental evidence for quantum tunneling time
VL - 119
ER -
TY - JOUR
AB - During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.
AU - Bernecky, Carrie A
AU - Plitzko, Jürgen
AU - Cramer, Patrick
ID - 603
IS - 10
JF - Nature Structural and Molecular Biology
SN - 15459993
TI - Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp
VL - 24
ER -
TY - CHAP
AB - In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.
AU - Lemeshko, Mikhail
AU - Schmidt, Richard
ED - Dulieu, Oliver
ED - Osterwalder, Andreas
ID - 604
SN - 20413181
T2 - Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero
TI - Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets
VL - 11
ER -
TY - CONF
AB - Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.
AU - Brody, Joshua
AU - Dziembowski, Stefan
AU - Faust, Sebastian
AU - Pietrzak, Krzysztof Z
ED - Kalai, Yael
ED - Reyzin, Leonid
ID - 605
SN - 978-331970499-9
TI - Position based cryptography and multiparty communication complexity
VL - 10677
ER -
TY - JOUR
AB - Neutrophils or polymorphonuclear cells (PMN) eliminate bacteria via phagocytosis and/or NETosis. Apartfrom these conventional roles, PMN also have immune-regulatory functions. They can transdifferentiateand upregulate MHCII as well as ligands for costimulatory receptors which enables them to behave asantigen presenting cells (APC). The initial step for activating T-cells is the formation of an immunesynapse between T-cells and antigen-presenting cells. However, the immune synapse that develops atthe PMN/T-cell contact zone is as yet hardly investigated due to the non-availability of methods foranalysis of large number of PMN interactions. In order to overcome these obstacles, we introduce herea workflow to analyse the immune synapse of primary human PMN and T-cells using multispectral imag-ing flow cytometry (InFlow microscopy) and super-resolution microscopy. For that purpose, we used CD3and CD66b as the lineage markers for T-cells and PMN, respectively. Thereafter, we applied and criticallydiscussed various ‘‘masks” for identification of T-cell PMN interactions. Using this approach, we foundthat a small fraction of transdifferentiated PMN (CD66b+CD86high) formed stable PMN/T-cell conjugates.Interestingly, while both CD3 and CD66b accumulation in the immune synapse was dependent on thematuration state of the PMN, only CD3 accumulation was greatly enhanced by the presence of superanti-gen. The actin cytoskeleton was weakly rearranged at the PMN side on the immune synapse upon contactwith a T-cell in the presence of superantigen. A more detailed analysis using super-resolution microscopy(structured-illumination microscopy, SIM) confirmed this finding. Together, we present an InFlow micro-scopy based approach for the large scale analysis of PMN/T-cell interactions and – combined with SIM – apossibility for an in-depth analysis of protein translocation at the site of interactions.
AU - Balta, Emre
AU - Stopp, Julian A
AU - Castelletti, Laura
AU - Kirchgessner, Henning
AU - Samstag, Yvonne
AU - Wabnitz, Guido H.
ID - 6059
IS - 1
JF - Methods
SN - 1046-2023
TI - Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy
VL - 112
ER -
TY - JOUR
AB - It has been known since Stefan Vogel's observations in 1969 that solitary female oil bees collect fatty floral oils from specialized oil-secreting plants with the aid of hairy patches on either their legs or abdomen, a reward used as food for their larvae and/or to line their brood cells. Similar adaptations are also known from male oil bees, although the purpose of their oil-collecting behavior has not yet been clarified. Here, we describe a novel pollination system involving male Paratetrapedia oil bees and the tropical herb Anthurium acutifolium. We present ultrastructural morphological details of bee and plant structures involved in this interaction and the composition of floral scents likely mediating pollinator attraction. Inflorescences of A. acutifolium were visited almost exclusively by male P. chocoensis oil bees. The bees mopped with a hairy patch of their abdominal sterna 3 across the inflorescence surface. During this activity on both staminate and pistillate stage inflorescences, bees’ abdomens and legs became loaded with pollen and contacted receptive stigmas. In contrast to what has been observed in other angiosperms visited for the collection of fatty floral oils, the inflorescences/flowers of A. acutifolium do not have structures specialized in oil secretion, i.e., elaiophores. These inflorescences, nonetheless, were strongly scented during the time interval they were visited by the bees. Gas chromatography/mass spectrometry (GC/MS) analyses of dynamic headspace floral samples revealed that inflorescences of both anthetic phases emitted scent bouquets consisting mainly of aliphatic esters, indole and uncommmon terpenoids (megastigmanes). Interestingly enough, our data suggest that the unusual floral scent of A. acutifolium is a perfume reward collected by male P. chocoensis oil bees. This pollination system thus bears a remarkable resemblence with the interactions between perfume-collecting male euglossine bees and their preferred flowers, discovered by Stefan Vogel half a century ago.
AU - Etl, Florian
AU - Franschitz, Anna
AU - Aguiar, Antonio
AU - Schönenberger, Jürg
AU - Dötterl, Stefan
ID - 695
JF - Flora: Morphology, Distribution, Functional Ecology of Plants
SN - 03672530
TI - A perfume collecting male oil bee? Evidences of a novel pollination system involving Anthurium acutifolium Araceae and Paratetrapedia chocoensis Apidae Tapinotaspidini
VL - 232
ER -
TY - CONF
AB - De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions.
AU - Pietrzak, Krzysztof Z
AU - Skórski, Maciej
ID - 697
SN - 18688969
TI - Non uniform attacks against pseudoentropy
VL - 80
ER -
TY - JOUR
AB - Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases.
AU - Wang, Yejun
AU - Nagarajan, Mallika
AU - Uhler, Caroline
AU - Shivashankar, Gv
ID - 698
IS - 14
JF - Molecular Biology of the Cell
SN - 10591524
TI - Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression
VL - 28
ER -
TY - JOUR
AB - In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts.
AU - Veller, Carl
AU - Hayward, Laura
AU - Nowak, Martin
AU - Hilbe, Christian
ID - 699
IS - 27
JF - PNAS
SN - 00278424
TI - The red queen and king in finite populations
VL - 114
ER -
TY - JOUR
AB - Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.
AU - Barzanjeh, Shabir
AU - Salari, Vahid
AU - Tuszynski, Jack
AU - Cifra, Michal
AU - Simon, Christoph
ID - 700
IS - 1
JF - Physical Review E Statistical Nonlinear and Soft Matter Physics
SN - 24700045
TI - Optomechanical proposal for monitoring microtubule mechanical vibrations
VL - 96
ER -
TY - JOUR
AB - A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2.
AU - Kynčl, Jan
AU - Patakova, Zuzana
ID - 701
IS - 3
JF - The Electronic Journal of Combinatorics
SN - 10778926
TI - On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4
VL - 24
ER -
TY - JOUR
AB - Leading autism-associated mutation in mouse partially mimics human disorder.
AU - Novarino, Gaia
ID - 702
IS - 399
JF - Science Translational Medicine
SN - 19466234
TI - The riddle of CHD8 haploinsufficiency in autism spectrum disorder
VL - 9
ER -
TY - JOUR
AB - A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse.
AU - Geng, Xiaoqi
AU - Maruo, Tomohiko
AU - Mandai, Kenji
AU - Supriyanto, Irwan
AU - Miyata, Muneaki
AU - Sakakibara, Shotaro
AU - Mizoguchi, Akira
AU - Takai, Yoshimi
AU - Mori, Masahiro
ID - 706
IS - 8
JF - Genes to Cells
SN - 13569597
TI - Roles of afadin in functional differentiations of hippocampal mossy fiber synapse
VL - 22
ER -
TY - JOUR
AB - The complex antiferromagnetic orders observed in the honeycomb iridates are a double-edged sword in the search for a quantum spin-liquid: both attesting that the magnetic interactions provide many of the necessary ingredients, while simultaneously impeding access. Focus has naturally been drawn to the unusual magnetic orders that hint at the underlying spin correlations. However, the study of any particular broken symmetry state generally provides little clue about the possibility of other nearby ground states. Here we use magnetic fields approaching 100 Tesla to reveal the extent of the spin correlations in γ-lithium iridate. We find that a small component of field along the magnetic easy-axis melts long-range order, revealing a bistable, strongly correlated spin state. Far from the usual destruction of antiferromagnetism via spin polarization, the high-field state possesses only a small fraction of the total iridium moment, without evidence for long-range order up to the highest attainable magnetic fields.
AU - Modic, Kimberly A
AU - Ramshaw, B. J.
AU - Betts, J. B.
AU - Breznay, Nicholas P.
AU - Analytis, James G.
AU - McDonald, Ross D.
AU - Shekhter, Arkady
ID - 7064
IS - 1
JF - Nature Communications
SN - 2041-1723
TI - Robust spin correlations at high magnetic fields in the harmonic honeycomb iridates
VL - 8
ER -
TY - JOUR
AB - Magneto-quantum oscillation experiments in high-temperature superconductors show a strong thermally induced suppression of the oscillation amplitude approaching the critical dopings [B. J. Ramshaw et al., Science 348, 317 (2014); H. Shishido et al., Phys. Rev. Lett. 104, 057008 (2010); P. Walmsley et al., Phys. Rev. Lett. 110, 257002 (2013)]—in support of a quantum-critical origin of their phase diagrams. We suggest that, in addition to a thermodynamic mass enhancement, these experiments may directly indicate the increasing role of quantum fluctuations that suppress the quantum oscillation amplitude through inelastic scattering. We show that the traditional theoretical approaches beyond Lifshitz-Kosevich to calculate the oscillation amplitude in correlated metals result in a contradiction with the third law of thermodynamics and suggest a way to rectify this problem.
AU - Shekhter, Arkady
AU - Modic, Kimberly A
AU - McDonald, R. D.
AU - Ramshaw, B. J.
ID - 7065
IS - 12
JF - Physical Review B
SN - 2469-9950
TI - Thermodynamic constraints on the amplitude of quantum oscillations
VL - 95
ER -
TY - JOUR
AB - The excitonic insulator phase has long been predicted to form in proximity to a band gap opening in the underlying band structure. The character of the pairing is conjectured to crossover from weak (BCS-like) to strong coupling (BEC-like) as the underlying band structure is tuned from the metallic to the insulating side of the gap opening. Here we report the high-magnetic field phase diagram of graphite to exhibit just such a crossover. By way of comprehensive angle-resolved magnetoresistance measurements, we demonstrate that the underlying band gap opening occurs inside the magnetic field-induced phase, paving the way for a systematic study of the BCS-BEC-like crossover by means of conventional condensed matter probes.
AU - Zhu, Z.
AU - McDonald, R. D.
AU - Shekhter, A.
AU - Ramshaw, B. J.
AU - Modic, Kimberly A
AU - Balakirev, F. F.
AU - Harrison, N.
ID - 7066
JF - Scientific Reports
SN - 2045-2322
TI - Magnetic field tuning of an excitonic insulator between the weak and strong coupling regimes in quantum limit graphite
VL - 7
ER -
TY - JOUR
AB - Broken fourfold rotational (C4) symmetry is observed in the experimental properties of several classes of unconventional superconductors. It has been proposed that this symmetry breaking is important for superconducting pairing in these materials, but in the high-Tc cuprates this broken symmetry has never been observed on the Fermi surface. Here we report a pronounced anisotropy in the angle dependence of the interlayer magnetoresistance of the underdoped high transition temperature (high-Tc) superconductor YBa2Cu3O6.58, directly revealing broken C4 symmetry on the Fermi surface. Moreover, we demonstrate that this Fermi surface has C2 symmetry of the type produced by a uniaxial or anisotropic density-wave phase. This establishes the central role of C4 symmetry breaking in the Fermi surface reconstruction of YBa2Cu3O6+δ , and suggests a striking degree of universality among unconventional superconductors.
AU - Ramshaw, B. J.
AU - Harrison, N.
AU - Sebastian, S. E.
AU - Ghannadzadeh, S.
AU - Modic, Kimberly A
AU - Bonn, D. A.
AU - Hardy, W. N.
AU - Liang, Ruixing
AU - Goddard, P. A.
ID - 7067
IS - 1
JF - npj Quantum Materials
SN - 2397-4648
TI - Broken rotational symmetry on the Fermi surface of a high-Tc superconductor
VL - 2
ER -
TY - JOUR
AB - We answer a question of M. Gromov on the waist of the unit ball.
AU - Akopyan, Arseniy
AU - Karasev, Roman
ID - 707
IS - 4
JF - Bulletin of the London Mathematical Society
SN - 00246093
TI - A tight estimate for the waist of the ball
VL - 49
ER -
TY - JOUR
AB - In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells.
AU - Nagy, Balint
AU - Hovhannisyan, Anahit
AU - Barzan, Ruxandra
AU - Chen, Ting
AU - Kukley, Maria
ID - 708
IS - 8
JF - PLoS Biology
SN - 15449173
TI - Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum
VL - 15
ER -
TY - JOUR
AB - Adipose tissues play key roles in energy homeostasis. Brown adipocytes and beige adipocytes in white adipose tissue (WAT) share the similar characters of thermogenesis, both of them could be potential targets for obesity management. Several thermo-sensitive transient receptor potential channels (thermoTRPs) are shown to be involved in adipocyte biology. However, the expression pattern of thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue (iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed in both iBAT and sWAT, and without significant difference in the mRNA expression level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA expression levels in both iBAT and sWAT were significantly decreased in high fat diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2 mRNA expression level was significantly decreased only in sWAT from HFD-induced obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression levels in iBAT and sWAT were significantly increased in HFD-induced obese mice and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues from HFD-induced obese mice and db/db mice, suggesting a potential involvement in anti-obesity regulations.
AU - Sun, Wuping
AU - Li, Chen
AU - Zhang, Yonghong
AU - Jiang, Changyu
AU - Zhai, Ming-Zhu
AU - Zhou, Qian
AU - Xiao, Lizu
AU - Deng, Qiwen
ID - 709
IS - 8
JF - Cell Biology International
SN - 10656995
TI - Gene expression changes of thermo sensitive transient receptor potential channels in obese mice
VL - 41
ER -
TY - CONF
AB - We revisit the problem of estimating entropy of discrete distributions from independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA 2015), improving their upper and lower bounds on the necessary sample size n. For estimating Renyi entropy of order alpha, up to constant accuracy and error probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha} for integer alpha>1, as the worst case over distributions with Renyi entropy equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha>1, with the constant being an inverse polynomial of the accuracy, as the worst case over all distributions on K elements. Our upper bounds essentially replace the alphabet size by a factor exponential in the entropy, which offers improvements especially in low or medium entropy regimes (interesting for example in anomaly detection). As for the lower bounds, our proof explicitly shows how the complexity depends on both alphabet and accuracy, partially solving the open problem posted in previous works. The argument for upper bounds derives a clean identity for the variance of falling-power sum of a multinomial distribution. Our approach for lower bounds utilizes convex optimization to find a distribution with possibly worse estimation performance, and may be of independent interest as a tool to work with Le Cam’s two point method.
AU - Obremski, Maciej
AU - Skórski, Maciej
ID - 710
SN - 18688969
TI - Renyi entropy estimation revisited
VL - 81
ER -
TY - CONF
AB - Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Otop, Jan
ID - 711
SN - 18688969
TI - Bidirectional nested weighted automata
VL - 85
ER -
TY - JOUR
AB - We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions.
AU - Fischer, Julian L
ID - 712
JF - Nonlinear Analysis: Theory, Methods and Applications
SN - 0362546X
TI - Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations
VL - 159
ER -
TY - JOUR
AB - To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.
AU - Andergassen, Daniel
AU - Dotter, Christoph
AU - Wenzel, Dyniel
AU - Sigl, Verena
AU - Bammer, Philipp
AU - Muckenhuber, Markus
AU - Mayer, Daniela
AU - Kulinski, Tomasz
AU - Theussl, Hans
AU - Penninger, Josef
AU - Bock, Christoph
AU - Barlow, Denise
AU - Pauler, Florian
AU - Hudson, Quanah
ID - 713
JF - eLife
SN - 2050084X
TI - Mapping the mouse Allelome reveals tissue specific regulation of allelic expression
VL - 6
ER -
TY - JOUR
AB - Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients.
AU - Brailoiu, Gabriela
AU - Deliu, Elena
AU - Barr, Jeffrey
AU - Console Bram, Linda
AU - Ciuciu, Alexandra
AU - Abood, Mary
AU - Unterwald, Ellen
AU - Brǎiloiu, Eugen
ID - 714
JF - Drug and Alcohol Dependence
SN - 03768716
TI - HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens
VL - 178
ER -
TY - JOUR
AB - D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome.
AU - Novarino, Gaia
ID - 715
IS - 405
JF - Science Translational Medicine
SN - 19466234
TI - More excitation for Rett syndrome
VL - 9
ER -
TY - JOUR
AB - Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.
AU - Chatterjee, Krishnendu
AU - Velner, Yaron
ID - 716
IS - 5
JF - Journal of the ACM
SN - 00045411
TI - The complexity of mean-payoff pushdown games
VL - 64
ER -
TY - DATA
AB - The de novo genome assemblies generated for this study, and the associated metadata.
AU - Fraisse, Christelle
ID - 7163
TI - Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W"
ER -
TY - JOUR
AB - We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard.
AU - Chatterjee, Krishnendu
AU - Velner, Yaron
ID - 717
JF - Journal of Computer and System Sciences
TI - Hyperplane separation technique for multidimensional mean-payoff games
VL - 88
ER -
TY - JOUR
AB - Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4.
AU - Edelsbrunner, Herbert
AU - Nikitenko, Anton
AU - Reitzner, Matthias
ID - 718
IS - 3
JF - Advances in Applied Probability
SN - 00018678
TI - Expected sizes of poisson Delaunay mosaics and their discrete Morse functions
VL - 49
ER -
TY - JOUR
AB - The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains.
AU - Chatterjee, Krishnendu
AU - Ehlers, Rüdiger
ID - 719
IS - 6
JF - Acta Informatica
SN - 00015903
TI - Special issue: Synthesis and SYNT 2014
VL - 54
ER -
TY - JOUR
AB - Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.
AU - Humplik, Jan
AU - Tkacik, Gasper
ID - 720
IS - 9
JF - PLoS Computational Biology
SN - 1553734X
TI - Probabilistic models for neural populations that naturally capture global coupling and criticality
VL - 13
ER -
TY - JOUR
AB - Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur.
AU - Ajanki, Oskari H
AU - Krüger, Torben H
AU - Erdös, László
ID - 721
IS - 9
JF - Communications on Pure and Applied Mathematics
SN - 00103640
TI - Singularities of solutions to quadratic vector equations on the complex upper half plane
VL - 70
ER -
TY - JOUR
AB - Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises.
AU - Morris, Emily
AU - Griffiths, Marcus
AU - Golebiowska, Agata
AU - Mairhofer, Stefan
AU - Burr Hersey, Jasmine
AU - Goh, Tatsuaki
AU - Von Wangenheim, Daniel
AU - Atkinson, Brian
AU - Sturrock, Craig
AU - Lynch, Jonathan
AU - Vissenberg, Kris
AU - Ritz, Karl
AU - Wells, Darren
AU - Mooney, Sacha
AU - Bennett, Malcolm
ID - 722
IS - 17
JF - Current Biology
SN - 09609822
TI - Shaping 3D root system architecture
VL - 27
ER -
TY - JOUR
AB - We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic.
AU - Hetterich, Daniel
AU - Serbyn, Maksym
AU - Domínguez, Fernando
AU - Pollmann, Frank
AU - Trauzettel, Björn
ID - 724
IS - 10
JF - Physical Review B
SN - 24699950
TI - Noninteracting central site model localization and logarithmic entanglement growth
VL - 96
ER -
TY - JOUR
AB - Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.
AU - Harpaz, Roy
AU - Tkacik, Gasper
AU - Schneidman, Elad
ID - 725
IS - 38
JF - PNAS
SN - 00278424
TI - Discrete modes of social information processing predict individual behavior of fish in a group
VL - 114
ER -
TY - JOUR
AB - The morphogenesis of branched organs remains a subject of abiding interest. Although much is known about the underlying signaling pathways, it remains unclear how macroscopic features of branched organs, including their size, network topology, and spatial patterning, are encoded. Here, we show that, in mouse mammary gland, kidney, and human prostate, these features can be explained quantitatively within a single unifying framework of branching and annihilating random walks. Based on quantitative analyses of large-scale organ reconstructions and proliferation kinetics measurements, we propose that morphogenesis follows from the proliferative activity of equipotent tips that stochastically branch and randomly explore their environment but compete neutrally for space, becoming proliferatively inactive when in proximity with neighboring ducts. These results show that complex branched epithelial structures develop as a self-organized process, reliant upon a strikingly simple but generic rule, without recourse to a rigid and deterministic sequence of genetically programmed events.
AU - Hannezo, Edouard B
AU - Scheele, Colinda
AU - Moad, Mohammad
AU - Drogo, Nicholas
AU - Heer, Rakesh
AU - Sampogna, Rosemary
AU - Van Rheenen, Jacco
AU - Simons, Benjamin
ID - 726
IS - 1
JF - Cell
SN - 00928674
TI - A unifying theory of branching morphogenesis
VL - 171
ER -