@article{481, abstract = {We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.}, author = {Biedl, Therese and Huber, Stefan and Palfrader, Peter}, journal = {International Journal of Computational Geometry and Applications}, number = {3-4}, pages = {211 -- 229}, publisher = {World Scientific Publishing}, title = {{Planar matchings for weighted straight skeletons}}, doi = {10.1142/S0218195916600050}, volume = {26}, year = {2017}, } @article{483, abstract = {We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices.}, author = {Bourgade, Paul and Erdös, László and Yau, Horng and Yin, Jun}, issn = {10950761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {3}, pages = {739 -- 800}, publisher = {International Press}, title = {{Universality for a class of random band matrices}}, doi = {10.4310/ATMP.2017.v21.n3.a5}, volume = {21}, year = {2017}, } @article{484, abstract = {We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory.}, author = {Nam, Phan and Napiórkowski, Marcin M}, issn = {10950761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {3}, pages = {683 -- 738}, publisher = {International Press}, title = {{Bogoliubov correction to the mean-field dynamics of interacting bosons}}, doi = {10.4310/ATMP.2017.v21.n3.a4}, volume = {21}, year = {2017}, } @inproceedings{485, abstract = {We present results on nonlinear electro-optical conversion of microwave radiation into the optical telecommunication band with more than 0.1% photon number conversion efficiency with MHz bandwidth, in a crystalline whispering gallery mode resonator}, author = {Rueda Sanchez, Alfredo R and Sedlmeir, Florian and Collodo, Michele and Vogl, Ulrich and Stiller, Birgit and Schunk, Gerhard and Strekalov, Dmitry and Marquardt, Christoph and Fink, Johannes M and Painter, Oskar and Leuchs, Gerd and Schwefel, Harald}, booktitle = {Optics InfoBase Conference Papers}, isbn = {978-155752820-9}, location = {Waikoloa, HI, United States}, publisher = {Optica Publishing Group}, title = {{Single sideband microwave to optical photon conversion-an-electro-optic-realization}}, doi = {10.1364/NLO.2017.NM3A.1}, volume = {F54}, year = {2017}, } @article{486, abstract = {Color texture reproduction in 3D printing commonly ignores volumetric light transport (cross-talk) between surface points on a 3D print. Such light diffusion leads to significant blur of details and color bleeding, and is particularly severe for highly translucent resin-based print materials. Given their widely varying scattering properties, this cross-talk between surface points strongly depends on the internal structure of the volume surrounding each surface point. Existing scattering-aware methods use simplified models for light diffusion, and often accept the visual blur as an immutable property of the print medium. In contrast, our work counteracts heterogeneous scattering to obtain the impression of a crisp albedo texture on top of the 3D print, by optimizing for a fully volumetric material distribution that preserves the target appearance. Our method employs an efficient numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous scattering, supported by a practical calibration procedure to obtain scattering parameters from a given set of printer materials. Despite the inherent translucency of the medium, we reproduce detailed surface textures on 3D prints. We evaluate our system using a commercial, five-tone 3D print process and compare against the printer’s native color texturing mode, demonstrating that our method preserves high-frequency features well without having to compromise on color gamut.}, author = {Elek, Oskar and Sumin, Denis and Zhang, Ran and Weyrich, Tim and Myszkowski, Karol and Bickel, Bernd and Wilkie, Alexander and Krivanek, Jaroslav}, issn = {07300301}, journal = {ACM Transactions on Graphics}, number = {6}, publisher = {ACM}, title = {{Scattering-aware texture reproduction for 3D printing}}, doi = {10.1145/3130800.3130890}, volume = {36}, year = {2017}, } @inproceedings{487, abstract = {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.}, author = {Baig, Ghufran and Radunovic, Bozidar and Alistarh, Dan-Adrian and Balkwill, Matthew and Karagiannis, Thomas and Qiu, Lili}, booktitle = {Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies}, isbn = {978-145035422-6}, location = {Incheon, South Korea}, pages = {2 -- 14}, publisher = {ACM}, title = {{Towards unlicensed cellular networks in TV white spaces}}, doi = {10.1145/3143361.3143367}, year = {2017}, } @article{512, abstract = {The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and 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. }, author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin}, issn = {20452322}, journal = {Scientific Reports}, number = {1}, publisher = {Nature Publishing Group}, title = {{Amplification on undirected population structures: Comets beat stars}}, doi = {10.1038/s41598-017-00107-w}, volume = {7}, year = {2017}, } @article{513, abstract = {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.}, author = {Klotz, Lukasz and Lemoult, Grégoire M and Frontczak, Idalia and Tuckerman, Laurette and Wesfreid, José}, journal = {Physical Review Fluids}, number = {4}, publisher = {American Physical Society}, title = {{Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence}}, doi = {10.1103/PhysRevFluids.2.043904}, volume = {2}, year = {2017}, } @article{514, abstract = {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.}, author = {Simonnet, Jean and Nassar, Mérie and Stella, Federico and Cohen, Ivan and Mathon, Bertrand and Boccara, Charlotte and Miles, Richard and Fricker, Desdemona}, issn = {20411723}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum}}, doi = {10.1038/ncomms16032}, volume = {8}, year = {2017}, } @article{515, abstract = {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.}, author = {Letts, James A and Sazanov, Leonid A}, issn = {15459993}, journal = {Nature Structural and Molecular Biology}, number = {10}, pages = {800 -- 808}, publisher = {Nature Publishing Group}, title = {{Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain}}, doi = {10.1038/nsmb.3460}, volume = {24}, year = {2017}, } @article{520, abstract = {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.}, author = {Du, Wei and Angermayr, Andreas and Jongbloets, Joeri and Molenaar, Douwe and Bachmann, Herwig and Hellingwerf, Klaas and Branco Dos Santos, Filipe}, issn = {21615063}, journal = {ACS Synthetic Biology}, number = {3}, pages = {395 -- 401}, publisher = {American Chemical Society}, title = {{Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803}}, doi = {10.1021/acssynbio.6b00235}, volume = {6}, year = {2017}, } @article{521, abstract = {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.}, author = {Austin, Kyle and Virk, Ziga}, issn = {01668641}, journal = {Topology and its Applications}, pages = {45 -- 57}, publisher = {Elsevier}, title = {{Higson compactification and dimension raising}}, doi = {10.1016/j.topol.2016.10.005}, volume = {215}, year = {2017}, } @article{525, abstract = {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. }, author = {Daniel von Wangenheim and Goh, Tatsuaki and Dietrich, Daniela and Bennett, Malcolm J}, journal = {Current Biology}, number = {5}, pages = {R172 -- R174}, publisher = {Cell Press}, title = {{Plant biology: Building barriers… in roots}}, doi = {10.1016/j.cub.2017.01.060}, volume = {27}, year = {2017}, } @article{529, abstract = {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.}, author = {Gherghina, Florin L and Tica, Andrei A and Elena Deliu and Abood, Mary E and Brailoiu, G. Christina and Brǎiloiu, Eugen}, journal = {Brain Research}, pages = {297 -- 303}, publisher = {Elsevier}, title = {{Effects of VPAC1 activation in nucleus ambiguus neurons}}, doi = {10.1016/j.brainres.2016.12.026}, volume = {1657}, year = {2017}, } @article{534, abstract = {We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.}, author = {Burton, Benjamin and De Mesmay, Arnaud N and Wagner, Uli}, issn = {01795376}, journal = {Discrete & Computational Geometry}, number = {4}, pages = {871 -- 888}, publisher = {Springer}, title = {{Finding non-orientable surfaces in 3-Manifolds}}, doi = {10.1007/s00454-017-9900-0}, volume = {58}, year = {2017}, } @article{538, abstract = {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. }, author = {Kainrath, Stephanie and Stadler, Manuela and Gschaider-Reichhart, Eva and Distel, Martin and Janovjak, Harald L}, journal = {Angewandte Chemie}, number = {16}, pages = {4679 -- 4682}, publisher = {Wiley}, title = {{Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen}}, doi = {10.1002/ange.201611998}, volume = {129}, year = {2017}, } @article{540, abstract = {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.}, author = {Khamina, Kseniya and Lercher, Alexander and Caldera, Michael and Schliehe, Christopher and Vilagos, Bojan and Sahin, Mehmet and Kosack, Lindsay and Bhattacharya, Anannya and Májek, Peter and Stukalov, Alexey and Sacco, Roberto and James, Leo and Pinschewer, Daniel and Bennett, Keiryn and Menche, Jörg and Bergthaler, Andreas}, issn = {15537366}, journal = {PLoS Pathogens}, number = {12}, publisher = {Public Library of Science}, title = {{Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein}}, doi = {10.1371/journal.ppat.1006758}, volume = {13}, year = {2017}, } @article{541, abstract = {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.}, author = {Nikolic, Nela and Schreiber, Frank and Dal Co, Alma and Kiviet, Daniel and Bergmiller, Tobias and Littmann, Sten and Kuypers, Marcel and Ackermann, Martin}, issn = {15537390}, journal = {PLoS Genetics}, number = {12}, publisher = {Public Library of Science}, title = {{Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations}}, doi = {10.1371/journal.pgen.1007122}, volume = {13}, year = {2017}, } @inbook{545, abstract = {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.}, author = {Mazur, Ewa and Friml, Jirí}, booktitle = {Plant Engineering}, editor = {Jurić, Snježana}, pages = {113 -- 140}, publisher = {InTech}, title = {{Vascular tissue development and regeneration in the model plant arabidopsis}}, doi = {10.5772/intechopen.69712}, year = {2017}, } @techreport{5450, abstract = {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.}, author = {Barbara Petritsch}, publisher = {IST Austria}, title = {{Implementing the institutional data repository IST DataRep}}, year = {2017}, }