TY - CONF
AB - The analysis of the energy consumption of software is an important goal for quantitative formal methods. Current methods, using weighted transition systems or energy games, model the energy source as an ideal resource whose status is characterized by one number, namely the amount of remaining energy. Real batteries, however, exhibit behaviors that can deviate substantially from an ideal energy resource. Based on a discretization of a standard continuous battery model, we introduce battery transition systems. In this model, a battery is viewed as consisting of two parts-the available-charge tank and the bound-charge tank. Any charge or discharge is applied to the available-charge tank. Over time, the energy from each tank diffuses to the other tank. Battery transition systems are infinite state systems that, being not well-structured, fall into no decidable class that is known to us. Nonetheless, we are able to prove that the !-regular modelchecking problem is decidable for battery transition systems. We also present a case study on the verification of control programs for energy-constrained semi-autonomous robots.
AU - Boker, Udi
AU - Henzinger, Thomas A
AU - Radhakrishna, Arjun
ID - 2239
IS - 1
SN - 978-145032544-8
TI - Battery transition systems
VL - 49
ER -
TY - JOUR
AB - Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.
AU - Gadeyne, Astrid
AU - Sánchez Rodríguez, Clara
AU - Vanneste, Steffen
AU - Di Rubbo, Simone
AU - Zauber, Henrik
AU - Vanneste, Kevin
AU - Van Leene, Jelle
AU - De Winne, Nancy
AU - Eeckhout, Dominique
AU - Persiau, Geert
AU - Van De Slijke, Eveline
AU - Cannoot, Bernard
AU - Vercruysse, Leen
AU - Mayers, Jonathan
AU - Adamowski, Maciek
AU - Kania, Urszula
AU - Ehrlich, Matthias
AU - Schweighofer, Alois
AU - Ketelaar, Tijs
AU - Maere, Steven
AU - Bednarek, Sebastian
AU - Friml, Jirí
AU - Gevaert, Kris
AU - Witters, Erwin
AU - Russinova, Eugenia
AU - Persson, Staffan
AU - De Jaeger, Geert
AU - Van Damme, Daniël
ID - 2240
IS - 4
JF - Cell
SN - 00928674
TI - The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants
VL - 156
ER -
TY - JOUR
AB - The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage.
AU - Beppu, Kaoru
AU - Sasaki, Takuya
AU - Tanaka, Kenji
AU - Yamanaka, Akihiro
AU - Fukazawa, Yugo
AU - Shigemoto, Ryuichi
AU - Matsui, Ko
ID - 2241
IS - 2
JF - Neuron
SN - 08966273
TI - Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage
VL - 81
ER -
TY - JOUR
AB - MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in many cellular pathways. MiRNAs associate with members of the Argonaute protein family and bind to partially complementary sequences on mRNAs and induce translational repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct influence of miR-155 on the expression levels of other miRNAs. For example, miR-455 is negatively regulated in miR-155-deficient cells possibly due to inhibition of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data sets, we propose a model of hierarchical miRNA expression dominated by miR-155 in DCs and macrophages.
AU - Dueck, Anne
AU - Eichner, Alexander
AU - Sixt, Michael K
AU - Meister, Gunter
ID - 2242
IS - 4
JF - FEBS Letters
SN - 00145793
TI - A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage activation
VL - 588
ER -
TY - JOUR
AB - Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain.
AU - Capek, Daniel
AU - Metscher, Brian
AU - Müller, Gerd
ID - 2248
IS - 1
JF - Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
SN - 15525007
TI - Thumbs down: A molecular-morphogenetic approach to avian digit homology
VL - 322
ER -
TY - JOUR
AB - The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.
AU - Chen, Yani
AU - Aung, Kyaw
AU - Rolčík, Jakub
AU - Walicki, Kathryn
AU - Friml, Jirí
AU - Brandizzí, Federica
ID - 2249
IS - 1
JF - Plant Journal
SN - 09607412
TI - Inter-regulation of the unfolded protein response and auxin signaling
VL - 77
ER -
TY - JOUR
AB - The genome sequences of new viruses often contain many "orphan" or "taxon-specific" proteins apparently lacking homologs. However, because viral proteins evolve very fast, commonly used sequence similarity detection methods such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA viruses characterized as "genus specific" by BLAST. More powerful methods developed recently, such as HHblits or HHpred (available through web-based, user-friendly interfaces), could detect distant homologs of a quarter of these proteins, suggesting that these methods should be used to annotate viral genomes. In-depth manual analyses of a subset of the remaining sequences, guided by contextual information such as taxonomy, gene order, or domain cooccurrence, identified distant homologs of another third. Thus, a combination of powerful automated methods and manual analyses can uncover distant homologs of many proteins thought to be orphans. We expect these methodological results to be also applicable to cellular organisms, since they generally evolve much more slowly than RNA viruses. As an application, we reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We could identify homologs of most of its proteins thought to be orphans; in each case, identifying homologs provided functional clues. We discovered that CBPV encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase; a putative membrane protein, SP24, with homologs in unrelated insect viruses and insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses, blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found in negeviruses. SP24 and ORF2 are probably major structural components of the virionsd.
AU - Kuchibhatla, Durga
AU - Sherman, Westley
AU - Chung, Betty
AU - Cook, Shelley
AU - Schneider, Georg
AU - Eisenhaber, Birgit
AU - Karlin, David
ID - 2250
IS - 1
JF - Journal of Virology
SN - 0022538X
TI - Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins
VL - 88
ER -
TY - JOUR
AB - Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps.
AU - Csicsvari, Jozsef L
AU - Dupret, David
ID - 2251
IS - 1635
JF - Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
SN - 09628436
TI - Sharp wave/ripple network oscillations and learning-associated hippocampal maps
VL - 369
ER -
TY - JOUR
AB - The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.
AU - Phadke, Sujal
AU - Paixao, Tiago
AU - Pham, Tuan
AU - Pham, Stephanie
AU - Zufall, Rebecca
ID - 2252
IS - 1
JF - Journal of Heredity
SN - 00221503
TI - Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila
VL - 105
ER -
TY - JOUR
AB - Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.
AU - Bailly, Aurélien
AU - Wang, Bangjun
AU - Zwiewka, Marta
AU - Pollmann, Stephan
AU - Schenck, Daniel
AU - Lüthen, Hartwig
AU - Schulz, Alexander
AU - Friml, Jirí
AU - Geisler, Markus
ID - 2253
IS - 1
JF - Plant Journal
SN - 09607412
TI - Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth
VL - 77
ER -
TY - JOUR
AB - Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus.
AU - Pernia-Andrade, Alejandro
AU - Jonas, Peter M
ID - 2254
IS - 1
JF - Neuron
SN - 08966273
TI - Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations
VL - 81
ER -
TY - CHAP
AB - Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application.
AU - Simon, Sibu
AU - Skůpa, Petr
AU - Dobrev, Petre
AU - Petrášek, Jan
AU - Zažímalová, Eva
AU - Friml, Jirí
ED - Hicks, Glenn
ED - Robert, Stéphanie
ID - 2245
SN - 10643745
T2 - Plant Chemical Genomics
TI - Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters
VL - 1056
ER -
TY - JOUR
AB - Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth.
AU - Grinshpun, Andrey
AU - Phalitnonkiat, Pakawat
AU - Rubin, Sasha
AU - Tarfulea, Andrei
ID - 2246
JF - Theoretical Computer Science
SN - 03043975
TI - Alternating traps in Muller and parity games
VL - 521
ER -
TY - JOUR
AB - To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.
AU - Zhu, Fangfang
AU - Gamboa, Matthew
AU - Farruggio, Alfonso
AU - Hippenmeyer, Simon
AU - Tasic, Bosiljka
AU - Schüle, Birgitt
AU - Chen Tsai, Yanru
AU - Calos, Michele
ID - 2261
IS - 5
JF - Nucleic Acids Research
TI - DICE, an efficient system for iterative genomic editing in human pluripotent stem cells
VL - 42
ER -
TY - CHAP
AB - Coordinated migration of newly-born neurons to their target territories is essential for correct neuronal circuit assembly in the developing brain. Although a cohort of signaling pathways has been implicated in the regulation of cortical projection neuron migration, the precise molecular mechanisms and how a balanced interplay of cell-autonomous and non-autonomous functions of candidate signaling molecules controls the discrete steps in the migration process, are just being revealed. In this chapter, I will focally review recent advances that improved our understanding of the cell-autonomous and possible cell-nonautonomous functions of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential steps of cortical projection neuron migration. I will then elaborate on the emerging concept that the Reelin signaling pathway, acts exactly at precise stages in the course of cortical projection neuron migration. Lastly, I will discuss how finely tuned transcriptional programs and downstream effectors govern particular aspects in driving radial migration at discrete stages and how they regulate the precise positioning of cortical projection neurons in the developing cerebral cortex.
AU - Hippenmeyer, Simon
ED - Nguyen, Laurent
ID - 2265
T2 - Cellular and Molecular Control of Neuronal Migration
TI - Molecular pathways controlling the sequential steps of cortical projection neuron migration
VL - 800
ER -
TY - CONF
AB - Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches.
This partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed.
Our main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach.
AU - Olsson, Carl
AU - Ulen, Johannes
AU - Boykov, Yuri
AU - Kolmogorov, Vladimir
ID - 2275
TI - Partial enumeration and curvature regularization
ER -
TY - JOUR
AB - GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity.
AU - Hosp, Jonas
AU - Strüber, Michael
AU - Yanagawa, Yuchio
AU - Obata, Kunihiko
AU - Vida, Imre
AU - Jonas, Peter M
AU - Bartos, Marlene
ID - 2285
IS - 2
JF - Hippocampus
TI - Morpho-physiological criteria divide dentate gyrus interneurons into classes
VL - 23
ER -
TY - JOUR
AB - We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential.
AU - Guo, Yujin
AU - Seiringer, Robert
ID - 2281
IS - 2
JF - Letters in Mathematical Physics
TI - On the mass concentration for Bose-Einstein condensates with attractive interactions
VL - 104
ER -
TY - JOUR
AB - Two definitions of the effective mass of a particle interacting with a quantum field, such as a polaron, are considered and shown to be equal in models similar to the Fröhlich polaron model. These are: 1. the mass defined by the low momentum energy E(P)≈E(0)+P2/2 M of the translation invariant system constrained to have momentum P and 2. the mass M of a simple particle in an arbitrary slowly varying external potential, V, described by the nonrelativistic Schrödinger equation, whose ground state energy equals that of the combined particle/field system in a bound state in the same V.
AU - Lieb, Élliott
AU - Seiringer, Robert
ID - 2407
IS - 1-2
JF - Journal of Statistical Physics
TI - Equivalence of two definitions of the effective mass of a polaron
VL - 154
ER -
TY - JOUR
AB - For any pencil of conics or higher-dimensional quadrics over ℚ, with all degenerate fibres defined over ℚ, we show that the Brauer–Manin obstruction controls weak approximation. The proof is based on the Hasse principle and weak approximation for some special intersections of quadrics over ℚ, which is a consequence of recent advances in additive combinatorics.
AU - Timothy Browning
AU - Matthiesen, Lilian
AU - Skorobogatov, Alexei N
ID - 248
IS - 1
JF - Annals of Mathematics
TI - Rational points on pencils of conics and quadrics with many degenerate fibres
VL - 180
ER -
TY - JOUR
AB - A version of the Hardy-Littlewood circle method is developed for number fields K/ℚ and is used to show that nonsingular projective cubic hypersurfaces over K always have a K-rational point when they have dimension at least 8.
AU - Timothy Browning
AU - Vishe, Pankaj
ID - 249
IS - 10
JF - Duke Mathematical Journal
TI - Cubic hypersurfaces and a version of the circle method for number fields
VL - 163
ER -
TY - JOUR
AB - For any number field k, upper bounds are established for the number of k-rational points of bounded height on non-singular del Pezzo surfaces defined over k, which are equipped with suitable conic bundle structures over k.
AU - Timothy Browning
AU - Jones, Michael S
ID - 252
IS - 3
JF - Acta Arithmetica
TI - Counting rational points on del Pezzo surfaces with a conic bundle structure
VL - 163
ER -
TY - JOUR
AB - A new "polynomial sieve" is presented and used to show that almost all integers have at most one representation as a sum of two values of a given polynomial of degree at least 3.
AU - Timothy Browning
ID - 254
IS - 7
JF - International Mathematics Research Notices
TI - The polynomial sieve and equal sums of like polynomials
VL - 2015
ER -
TY - JOUR
AB - We investigate the Hasse principle for complete intersections cut out by a quadric hypersurface and a cubic hypersurface defined over the rational numbers.
AU - Timothy Browning
AU - Dietmann, Rainer
AU - Heath-Brown, Roger
ID - 255
IS - 4
JF - Journal of the Institute of Mathematics of Jussieu
TI - Rational points on intersections of cubic and quadric hypersurfaces
VL - 14
ER -
TY - JOUR
AB - Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω ω -regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on vector addition systems with states. Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts.
AU - Chatterjee, Krishnendu
AU - Randour, Mickael
AU - Raskin, Jean
ID - 2716
IS - 3-4
JF - Acta Informatica
TI - Strategy synthesis for multi-dimensional quantitative objectives
VL - 51
ER -
TY - JOUR
AB - We prove the universality of the β-ensembles with convex analytic potentials and for any β >
0, i.e. we show that the spacing distributions of log-gases at any inverse temperature β coincide with those of the Gaussian β-ensembles.
AU - Erdös, László
AU - Bourgade, Paul
AU - Yau, Horng
ID - 2699
IS - 6
JF - Duke Mathematical Journal
TI - Universality of general β-ensembles
VL - 163
ER -
TY - JOUR
AB - Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm.
AU - Edelsbrunner, Herbert
AU - Pausinger, Florian
ID - 2255
IS - 1
JF - Journal of Mathematical Imaging and Vision
SN - 09249907
TI - Stable length estimates of tube-like shapes
VL - 50
ER -
TY - CONF
AB - Persistent homology is a recent grandchild of homology that has found use in
science and engineering as well as in mathematics. This paper surveys the method as well
as the applications, neglecting completeness in favor of highlighting ideas and directions.
AU - Edelsbrunner, Herbert
AU - Morozovy, Dmitriy
ID - 2905
TI - Persistent homology: Theory and practice
ER -
TY - JOUR
AB - The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces, and how to synthesize an interface from incompatible requirements. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies.
AU - Cerny, Pavol
AU - Chmelik, Martin
AU - Henzinger, Thomas A
AU - Radhakrishna, Arjun
ID - 1733
IS - 3
JF - Theoretical Computer Science
TI - Interface simulation distances
VL - 560
ER -
TY - JOUR
AB - The computation of the winning set for Büchi objectives in alternating games on graphs is a central problem in computer-aided verification with a large number of applications. The long-standing best known upper bound for solving the problem is Õ(n ⋅ m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the Õ(n ⋅ m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2)-time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of Õ(n ⋅ m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m>n4/3 an earlier bound of O(m ⋅ √m)). We then show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. Our algorithms are the first dynamic algorithms for this problem. We then consider another core graph theoretic problem in verification of probabilistic systems, namely computing the maximal end-component decomposition of a graph. We present two improved static algorithms for the maximal end-component decomposition problem. Our first algorithm is an O(m ⋅ √m)-time algorithm, and our second algorithm is an O(n2)-time algorithm which is obtained using the same technique as for alternating Büchi games. Thus, we obtain an O(min &lcu;m ⋅ √m,n2})-time algorithm improving the long-standing O(n ⋅ m) time bound. Finally, we show how to maintain the maximal end-component decomposition of a graph under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per edge deletion, and O(m) worst-case time per edge insertion. Again, our algorithms are the first dynamic algorithms for this problem.
AU - Chatterjee, Krishnendu
AU - Henzinger, Monika
ID - 2141
IS - 3
JF - Journal of the ACM
TI - Efficient and dynamic algorithms for alternating Büchi games and maximal end-component decomposition
VL - 61
ER -
TY - JOUR
AB - A robust combiner for hash functions takes two candidate implementations and constructs a hash function which is secure as long as at least one of the candidates is secure. So far, hash function combiners only aim at preserving a single property such as collision-resistance or pseudorandomness. However, when hash functions are used in protocols like TLS they are often required to provide several properties simultaneously. We therefore put forward the notion of robust multi-property combiners and elaborate on different definitions for such combiners. We then propose a combiner that provably preserves (target) collision-resistance, pseudorandomness, and being a secure message authentication code. This combiner satisfies the strongest notion we propose, which requires that the combined function satisfies every security property which is satisfied by at least one of the underlying hash function. If the underlying hash functions have output length n, the combiner has output length 2 n. This basically matches a known lower bound for black-box combiners for collision-resistance only, thus the other properties can be achieved without penalizing the length of the hash values. We then propose a combiner which also preserves the property of being indifferentiable from a random oracle, slightly increasing the output length to 2 n+ω(log n). Moreover, we show how to augment our constructions in order to make them also robust for the one-wayness property, but in this case require an a priory upper bound on the input length.
AU - Fischlin, Marc
AU - Lehmann, Anja
AU - Pietrzak, Krzysztof Z
ID - 2852
IS - 3
JF - Journal of Cryptology
TI - Robust multi-property combiners for hash functions
VL - 27
ER -
TY - JOUR
AB - Adaptation in the retina is thought to optimize the encoding of natural light signals into sequences of spikes sent to the brain. While adaptive changes in retinal processing to the variations of the mean luminance level and second-order stimulus statistics have been documented before, no such measurements have been performed when higher-order moments of the light distribution change. We therefore measured the ganglion cell responses in the tiger salamander retina to controlled changes in the second (contrast), third (skew) and fourth (kurtosis) moments of the light intensity distribution of spatially uniform temporally independent stimuli. The skew and kurtosis of the stimuli were chosen to cover the range observed in natural scenes. We quantified adaptation in ganglion cells by studying linear-nonlinear models that capture well the retinal encoding properties across all stimuli. We found that the encoding properties of retinal ganglion cells change only marginally when higher-order statistics change, compared to the changes observed in response to the variation in contrast. By analyzing optimal coding in LN-type models, we showed that neurons can maintain a high information rate without large dynamic adaptation to changes in skew or kurtosis. This is because, for uncorrelated stimuli, spatio-temporal summation within the receptive field averages away non-gaussian aspects of the light intensity distribution.
AU - Tkacik, Gasper
AU - Ghosh, Anandamohan
AU - Schneidman, Elad
AU - Segev, Ronen
ID - 3263
IS - 1
JF - PLoS One
TI - Adaptation to changes in higher-order stimulus statistics in the salamander retina
VL - 9
ER -
TY - JOUR
AB - Cu2ZnSnS4, based on abundant and environmental friendly elements and with a direct band gap of 1.5 eV, is a main candidate material for solar energy conversion through both photovoltaics and photocatalysis. We detail here the synthesis of quasi-spherical Cu 2ZnSnS4 nanoparticles with unprecedented narrow size distributions. We further detail their use as seeds to produce CZTS-Au and CZTS-Pt heterostructured nanoparticles. Such heterostructured nanoparticles are shown to have excellent photocatalytic properties toward degradation of Rhodamine B and hydrogen generation by water splitting.
AU - Yu, Xuelian
AU - Shavel, Alexey
AU - An, Xiaoqiang
AU - Luo, Zhishan
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 332
IS - 26
JF - Journal of the American Chemical Society
TI - Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation
VL - 136
ER -
TY - CONF
AB - We study two-player concurrent games on finite-state graphs played for an infinite number of rounds, where in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. The objectives are ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). While the qualitative analysis problem for concurrent parity games with infinite-memory, infinite-precision randomized strategies was studied before, we study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies. In terms of precision, strategies can be deterministic, uniform, finite-precision, or infinite-precision; and in terms of memory, strategies can be memoryless, finite-memory, or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies. We show that the winning sets can be computed in (n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. Our symbolic algorithms are based on a characterization of the winning sets as μ-calculus formulas, however, our μ-calculus formulas are crucially different from the ones for concurrent parity games (without bounded rationality); and our memoryless witness strategy constructions are significantly different from the infinite-memory witness strategy constructions for concurrent parity games.
AU - Chatterjee, Krishnendu
ED - Baldan, Paolo
ED - Gorla, Daniele
ID - 2054
T2 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
TI - Qualitative concurrent parity games: Bounded rationality
VL - 8704
ER -
TY - JOUR
AB - We report on the photocatalytic hydrogen evolution under full-arc light irradiation of CuIn1-xGaxS2 wurtzite nanocrystals in the presence of SO3 2- and S2- as sacrificial reagents. We analyzed the hydrogen generation rate as a function of the Ga content and associated it with the energy band positions. For photocatalytic water splitting, the CuInS2 bandgap is slightly too low to efficiently overcome the reaction over-potential. The presence of Ga shifts up the CuInS2 conduction band edge providing a larger driving force for photogenerated carriers to activate the water splitting reduction reaction. The larger the Ga content, the more energetically favorable the electron injection, and thus a more efficient use of the photogenerated carriers is reached. However, the band gap increase associated with the Ga incorporation reduces the concentration of photogenerated carriers available for water splitting, and consequently a lower hydrogen conversion rate is obtained for very high Ga contents. The optimum Ga concentration was experimentally found at CuIn0.3Ga0.7S2.
AU - Yu, Xuelian
AU - An, Xiaoqiang
AU - Shavel, Alexey
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 355
IS - 31
JF - Journal of Materials Chemistry A
TI - The effect of the Ga content on the photocatalytic hydrogen evolution of CuIn1-xGaxS2 nanocrystals
VL - 2
ER -
TY - JOUR
AB - Cu2ZnSnS4, based on abundant and environmental friendly elements and with a direct band gap of 1.5 eV, is a main candidate material for solar energy conversion through both photovoltaics and photocatalysis. We detail here the synthesis of quasi-spherical Cu 2ZnSnS4 nanoparticles with unprecedented narrow size distributions. We further detail their use as seeds to produce CZTS-Au and CZTS-Pt heterostructured nanoparticles. Such heterostructured nanoparticles are shown to have excellent photocatalytic properties toward degradation of Rhodamine B and hydrogen generation by water splitting.
AU - Yu, Xuelian
AU - Shavel, Alexey
AU - An, Xiaoqiang
AU - Luo, Zhishan
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 356
IS - 26
JF - Journal of the American Chemical Society
TI - Cu2ZnSnS4-Pt and Cu2ZnSnS4-Au heterostructured nanoparticles for photocatalytic water splitting and pollutant degradation
VL - 136
ER -
TY - JOUR
AB - Near-resonant Raman scattering measurements of zinc sulfide nanoparticles and thin films have been made and correlated to grain and particle size, respectively, using a 325 nm wavelength excitation source. The area ratios between the first, second, and third order peaks of ZnS identified as the T 2(LO) mode decrease with increasing ZnS grain size. This is an effect attributed to changes in the bandgap energy from quantum confinement due to the varying grain size between the films/particles, as noted by a shift in the room temperature photoluminescence emission corresponding to the free exciton emission energy. While Raman scattering spectroscopy is typically limited to identification of phases and their crystalline properties, it is possible to attain more than such straightforward information by calibrating the spectral features to variations between sets of samples. These results open the possibility of making a quantitative grain size estimation in ZnS thin films and nanostructures, as well as in other material systems where ZnS may be expected as a secondary phase, such as Cu2ZnSnS4. Additionally, more commonly used excitation wavelengths for Raman scattering, such as 514 and 532 nm, are shown to be of limited use in characterizing ZnS thin films due to the extremely low Raman scattering efficiency of ZnS in films with sub-micron thicknesses.
AU - Fairbrother, Andrew
AU - Izquierdo Roca, Victor
AU - Fontané, Xavier
AU - Ibáñez, Maria
AU - Cabot, Andreu
AU - Saucedo, Edgardo
AU - Pérez Rodríguez, Alejandro
ID - 357
IS - 20
JF - CrystEngComm
TI - ZnS grain size effects on near-resonant Raman scattering: Optical non-destructive grain size estimation
VL - 16
ER -
TY - JOUR
AB - Monodispersed Pt3Sn nanoparticles were prepared through a mild thermal synthesis in the presence of surfactants. The performance of Pt3Sn for the electrooxidation of ethanol and adsorbed carbon monoxide (COad) in acid medium was studied by a combination of electrochemical and insitu spectroscopic methods, namely, infrared reflection absorption spectroscopy and differential electrochemical mass spectrometry (DEMS), and the results were compared to those obtained with the use of Pt black. The formation of the Pt3Sn solid solution promoted the oxidation of COad at less-positive potentials than those required for Pt black. Also, the electrooxidation of ethanol, especially at lower potentials, was more favorable with Pt3Sn, as deduced from the higher faradaic currents recorded during the ethanol oxidation reaction (EOR). However, the distribution of products as deduced by DEMS analysis suggested that the formation of C1 products, CO2 inclusive, is less significant on Pt3Sn than on Pt. In fact, the higher faradaic current recorded with the former catalyst can be attributed to the greater amounts of acetaldehyde and acetic acid formed. After the EOR, the surface of both Pt and Pt3Sn remained covered by ethanol adsorbates. Whereas C2 fragments were the main adsorbates at the surface of Pt3Sn after the EOR, both C1 and C2 species remained adsorbed at Pt black.
AU - Herranz, Tirma
AU - Ibáñez, Maria
AU - Gómez De La Fuente, José
AU - Pérez Alonso, Francisco
AU - Peña, Miguel
AU - Cabot, Andreu
AU - Rojas, Sergio
ID - 358
IS - 5
JF - ChemElectroChem
TI - In situ study of ethanol electrooxidation on monodispersed Pt inf 3 inf Sn nanoparticles
VL - 1
ER -
TY - JOUR
AB - An appropriate way of realizing property nanoengineering in complex quaternary chalcogenide nanocrystals is presented for Cu2Cd xSnSey(CCTSe) polypods. The pivotal role of the polarity in determining morphology, growth, and the polytypic branching mechanism is demonstrated. Polarity is considered to be responsible for the formation of an initial seed that takes the form of a tetrahedron with four cation-polar facets. Size and shape confinement of the intermediate pentatetrahedral seed is also attributed to polarity, as their external facets are anion-polar. The final polypod extensions also branch out as a result of a cation-polarity-driven mechanism. Aberration-corrected scanning transmission electron microscopy is used to identify stannite cation ordering, while ab initio studies are used to show the influence of cation ordering/distortion, stoichiometry, and polytypic structural change on the electronic band structure.
AU - Zamani, Reza
AU - Ibáñez, Maria
AU - Luysberg, Martina
AU - García Castelló, Nuria
AU - Houben, Lothar
AU - Prades, Joan
AU - Grillo, Vincenzo
AU - Dunin Borkowski, Rafal
AU - Morante, Joan
AU - Cabot, Andreu
AU - Arbiol, Jordi
ID - 359
IS - 3
JF - ACS Nano
TI - Polarity-driven polytypic branching in Cu-based quaternary chalcogenide nanostructures
VL - 8
ER -
TY - JOUR
AB - Thermoelectricity is a key technology with the potential to improve the efficiency of energy conversion processes, which may strongly benefit from advances in the field of nanotechnology. Nanostructured materials are very appealing for thermoelectric applications, but the full development of their potential requires precise control of their properties at the nanoscale. Bottom-up assembly of nanoparticles provides access to a three-dimensional composition control at the nanoscale not attainable in any other technology. In particular, colloidal nanoheterostructures are especially interesting building blocks for the bottom-up production of functional nanomaterials. In the present work, we use PbTe@PbS core-shell nanoparticles as building blocks for the bottom-up production of PbTe-PbS nanocomposites. We used a ligand exchange strategy and a hot press process to promote the electrical conductivity of the nanocomposite and to increase its density. These two approaches allowed us to improve the performance of bottom-up assembled PbTe-PbS bulk nanostructured materials.
AU - Ortega, Silvia
AU - Ibáñez, Maria
AU - Cadavid, Doris
AU - Cabot, Andreu
ID - 349
IS - 9-11
JF - International Journal of Nanotechnology
TI - Bottom up processing of PbTe PbS thermoelectric nanocomposites
VL - 11
ER -
TY - JOUR
AB - Herein, a colloidal synthetic route to produce highly monodisperse Cu2HgGeSe4 (CHGSe) nanoparticles (NPs) is presented in detail. The high yield of the developed procedure allowed the production of CHGSe NPs at the gram scale. A thorough analysis of their structural and optical properties is shown. CHGSe NPs displayed poly-tetrahedral morphology and narrow size distributions with average size in the range of 10–40 nm and size dispersions below 10 %. A 1.6 eV optical band gap was measured by mean of UV–Vis. By adjusting the cation ratio, an effective control of their electrical conductivity is achieved. The prepared NPs are used as building blocks for the production of CHGSe bulk nanostructured materials. The thermoelectric properties of CHGSe nanomaterials are studied in the temperature range from 300 to 730 K. CHGSe nanomaterials reached electrical conductivities up to 5 × 104 S m−1, Seebeck coefficients above 100 μV K−1, and thermal conductivities below 1.0 W m−1 K−1 which translated into thermoelectric figures of merit up to 0.34 at 730 K.
AU - Li, Wenhua
AU - Ibáñez, Maria
AU - Cadavid, Doris
AU - Zamani, Reza
AU - Rubio Garcia, Javier
AU - Gorsse, Stéphane
AU - Morante, Joan
AU - Arbiol, Jordi
AU - Cabot, Andreu
ID - 350
IS - 3
JF - Journal of Nanoparticle Research
TI - Colloidal synthesis and functional properties of quaternary Cu based semiconductors: Cu2HgGeSe4
VL - 16
ER -
TY - JOUR
AB - Bi2S3-xTex bulk nanocomposites with crystal domain sizes in the range from 50 nm to 100 nm were obtained from the reaction of Bi2S3 nanorods with Te powder. The thermoelectric properties of the obtained nanocomposites were analysed in the temperature range from 0°C to 300°C. We observed how the thermoelectric properties of the material improved with the annealing temperature, being a spark plasma sintering process needed to maintain the material nanostructuration while maximising its electrical properties. Finally thermoelectric dimensionless figures of merit ZT up to 0.42 were obtained before any charge carrier concentration optimisation. Copyright © 2014 Inderscience Enterprises Ltd.
AU - Cadavid, Doris
AU - Ibáñez, Maria
AU - Anselmi Tamburini, Umberto
AU - Durá, Oscar
AU - De La Torre, Marco
AU - Cabot, Andreu
ID - 348
IS - 9-11
JF - International Journal of Nanotechnology
TI - Thermoelectric properties of bottom up assembled Bi2S 3-xTex nanocomposites
VL - 11
ER -
TY - THES
AB - A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis.
AU - Behrndt, Martin
ID - 1403
TI - Forces driving epithelial spreading in zebrafish epiboly
ER -
TY - JOUR
AB - Receptor tyrosine kinases (RTKs) are a large family of cell surface receptors that sense growth factors and hormones and regulate a variety of cell behaviours in health and disease. Contactless activation of RTKs with spatial and temporal precision is currently not feasible. Here, we generated RTKs that are insensitive to endogenous ligands but can be selectively activated by low-intensity blue light. We screened light-oxygen-voltage (LOV)-sensing domains for their ability to activate RTKs by light-activated dimerization. Incorporation of LOV domains found in aureochrome photoreceptors of stramenopiles resulted in robust activation of the fibroblast growth factor receptor 1 (FGFR1), epidermal growth factor receptor (EGFR) and rearranged during transfection (RET). In human cancer and endothelial cells, light induced cellular signalling with spatial and temporal precision. Furthermore, light faithfully mimicked complex mitogenic and morphogenic cell behaviour induced by growth factors. RTKs under optical control (Opto-RTKs) provide a powerful optogenetic approach to actuate cellular signals and manipulate cell behaviour.
AU - Grusch, Michael
AU - Schelch, Karin
AU - Riedler, Robert
AU - Gschaider-Reichhart, Eva
AU - Differ, Christopher
AU - Berger, Walter
AU - Inglés Prieto, Álvaro
AU - Janovjak, Harald L
ID - 2084
IS - 15
JF - EMBO Journal
TI - Spatio-temporally precise activation of engineered receptor tyrosine kinases by light
VL - 33
ER -
TY - CONF
AB - We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in ℝ3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, i.e., an essential curve in the boundary of X bounding a disk in S3 nX with length bounded by a computable function of the number of tetrahedra of X.
AU - Matoušek, Jiří
AU - Sedgwick, Eric
AU - Tancer, Martin
AU - Wagner, Uli
ID - 2157
T2 - Proceedings of the Annual Symposium on Computational Geometry
TI - Embeddability in the 3 sphere is decidable
ER -
TY - JOUR
AB - We introduce algorithms for the computation of homology, cohomology, and related operations on cubical cell complexes, using the technique based on a chain contraction from the original chain complex to a reduced one that represents its homology. This work is based on previous results for simplicial complexes, and uses Serre’s diagonalization for cubical cells. An implementation in C++ of the introduced algorithms is available at http://www.pawelpilarczyk.com/chaincon/ together with some examples. The paper is self-contained as much as possible, and is written at a very elementary level, so that basic knowledge of algebraic topology should be sufficient to follow it.
AU - Pawel Pilarczyk
AU - Real, Pedro
ID - 451
IS - 1
JF - Advances in Computational Mathematics
TI - Computation of cubical homology, cohomology, and (co)homological operations via chain contraction
VL - 41
ER -
TY - CONF
AB - First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard.
AU - Aminof, Benjamin
AU - Rubin, Sasha
ID - 475
T2 - Electronic Proceedings in Theoretical Computer Science, EPTCS
TI - First cycle games
VL - 146
ER -
TY - JOUR
AB - Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance) is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss.
AU - Cimadom, Arno
AU - Ulloa, Angel
AU - Meidl, Patrick
AU - Zöttl, Markus
AU - Zöttl, Elisabet
AU - Fessl, Birgit
AU - Nemeth, Erwin
AU - Dvorak, Michael
AU - Cunninghame, Francesca
AU - Tebbich, Sabine
ID - 468
IS - 9
JF - PLoS One
TI - Invasive parasites habitat change and heavy rainfall reduce breeding success in Darwin's finches
VL - 9
ER -
TY - JOUR
AB - Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.
AU - Chatterjee, Krishnendu
AU - Henzinger, Monika
AU - Krinninger, Sebastian
AU - Nanongkai, Danupon
ID - 535
IS - 3
JF - Algorithmica
TI - Polynomial time algorithms for energy games with special weight structures
VL - 70
ER -
TY - JOUR
AB - Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.
AU - Prizak, Roshan
AU - Ezard, Thomas
AU - Hoyle, Rebecca
ID - 537
IS - 15
JF - Ecology and Evolution
TI - Fitness consequences of maternal and grandmaternal effects
VL - 4
ER -