TY - JOUR
AB - Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd
AU - Schilling, Christian
AU - Bogomolov, Sergiy
AU - Henzinger, Thomas A
AU - Podelski, Andreas
AU - Ruess, Jakob
ID - 1148
JF - Biosystems
TI - Adaptive moment closure for parameter inference of biochemical reaction networks
VL - 149
ER -
TY - JOUR
AB - We study the usefulness of two most prominent publicly available rigorous ODE integrators: one provided by the CAPD group (capd.ii.uj.edu.pl), the other based on the COSY Infinity project (cosyinfinity.org). Both integrators are capable of handling entire sets of initial conditions and provide tight rigorous outer enclosures of the images under a time-T map. We conduct extensive benchmark computations using the well-known Lorenz system, and compare the computation time against the final accuracy achieved. We also discuss the effect of a few technical parameters, such as the order of the numerical integration method, the value of T, and the phase space resolution. We conclude that COSY may provide more precise results due to its ability of avoiding the variable dependency problem. However, the overall cost of computations conducted using CAPD is typically lower, especially when intervals of parameters are involved. Moreover, access to COSY is limited (registration required) and the rigorous ODE integrators are not publicly available, while CAPD is an open source free software project. Therefore, we recommend the latter integrator for this kind of computations. Nevertheless, proper choice of the various integration parameters turns out to be of even greater importance than the choice of the integrator itself. © 2016 IMACS. Published by Elsevier B.V. All rights reserved.
AU - Miyaji, Tomoyuki
AU - Pilarczyk, Pawel
AU - Gameiro, Marcio
AU - Kokubu, Hiroshi
AU - Mischaikow, Konstantin
ID - 1149
JF - Applied Numerical Mathematics
TI - A study of rigorous ODE integrators for multi scale set oriented computations
VL - 107
ER -
TY - JOUR
AB - When neutrophils infiltrate a site of inflammation, they have to stop at the right place to exert their effector function. In this issue of Developmental Cell, Wang et al. (2016) show that neutrophils sense reactive oxygen species via the TRPM2 channel to arrest migration at their target site. © 2016 Elsevier Inc.
AU - Renkawitz, Jörg
AU - Sixt, Michael K
ID - 1150
IS - 5
JF - Developmental Cell
TI - A Radical Break Restraining Neutrophil Migration
VL - 38
ER -
TY - JOUR
AB - Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al.
AU - Simonini, Sara
AU - Deb, Joyita
AU - Moubayidin, Laila
AU - Stephenson, Pauline
AU - Valluru, Manoj
AU - Freire Rios, Alejandra
AU - Sorefan, Karim
AU - Weijers, Dolf
AU - Friml, Jirí
AU - Östergaard, Lars
ID - 1151
IS - 20
JF - Genes and Development
TI - A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis
VL - 30
ER -
TY - JOUR
AB - Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. © 2016 American Society of Plant Biologists. All rights reserved.
AU - Žádníková, Petra
AU - Wabnik, Krzysztof T
AU - Abuzeineh, Anas
AU - Gallemí, Marçal
AU - Van Der Straeten, Dominique
AU - Smith, Richard
AU - Inze, Dirk
AU - Friml, Jirí
AU - Prusinkiewicz, Przemysław
AU - Benková, Eva
ID - 1153
IS - 10
JF - Plant Cell
TI - A model of differential growth guided apical hook formation in plants
VL - 28
ER -
TY - JOUR
AB - Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluidic chamber that allows measurement of cell migration in combined response to surface immobilized and soluble molecular gradients. As a proof of principle we study the response of dendritic cells to their major guidance cues, chemokines. The majority of data on chemokine gradient sensing is based on in vitro studies employing soluble gradients. Despite evidence suggesting that in vivo chemokines are often immobilized to sugar residues, limited information is available how cells respond to immobilized chemokines. We tracked migration of dendritic cells towards immobilized gradients of the chemokine CCL21 and varying superimposed soluble gradients of CCL19. Differential migratory patterns illustrate the potential of our setup to quantitatively study the competitive response to both types of gradients. Beyond chemokines our approach is broadly applicable to alternative systems of chemo- and haptotaxis such as cells migrating along gradients of adhesion receptor ligands vs. any soluble cue.
AU - Schwarz, Jan
AU - Bierbaum, Veronika
AU - Merrin, Jack
AU - Frank, Tino
AU - Hauschild, Robert
AU - Bollenbach, Mark Tobias
AU - Tay, Savaş
AU - Sixt, Michael K
AU - Mehling, Matthias
ID - 1154
JF - Scientific Reports
TI - A microfluidic device for measuring cell migration towards substrate bound and soluble chemokine gradients
VL - 6
ER -
TY - JOUR
AB - Let k, n, and r be positive integers with k < n and r≤⌊nk⌋. We determine the facets of the r-stable n, k-hypersimplex. As a result, it turns out that the r-stable n, k-hypersimplex has exactly 2n facets for every r<⌊nk⌋. We then utilize the equations of the facets to study when the r-stable hypersimplex is Gorenstein. For every k > 0 we identify an infinite collection of Gorenstein r-stable hypersimplices, consequently expanding the collection of r-stable hypersimplices known to have unimodal Ehrhart δ-vectors.
AU - Hibi, Takayugi
AU - Liam Solus
ID - 1156
IS - 4
JF - Annals of Combinatorics
TI - Facets of the r-stable (n, k)-hypersimplex
VL - 20
ER -
TY - JOUR
AB - We consider sample covariance matrices of the form Q = ( σ1/2X)(σ1/2X)∗, where the sample X is an M ×N random matrix whose entries are real independent random variables with variance 1/N and whereσ is an M × M positive-definite deterministic matrix. We analyze the asymptotic fluctuations of the largest rescaled eigenvalue of Q when both M and N tend to infinity with N/M →d ϵ (0,∞). For a large class of populations σ in the sub-critical regime, we show that the distribution of the largest rescaled eigenvalue of Q is given by the type-1 Tracy-Widom distribution under the additional assumptions that (1) either the entries of X are i.i.d. Gaussians or (2) that σ is diagonal and that the entries of X have a sub-exponential decay.
AU - Lee, Ji
AU - Schnelli, Kevin
ID - 1157
IS - 6
JF - Annals of Applied Probability
TI - Tracy-widom distribution for the largest eigenvalue of real sample covariance matrices with general population
VL - 26
ER -
TY - JOUR
AB - Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.
AU - Roux, Camille
AU - Fraisse, Christelle
AU - Romiguier, Jonathan
AU - Anciaux, Youann
AU - Galtier, Nicolas
AU - Bierne, Nicolas
ID - 1158
IS - 12
JF - PLoS Biology
TI - Shedding light on the grey zone of speciation along a continuum of genomic divergence
VL - 14
ER -
TY - CONF
AB - A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, … , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. A pair of edges e and f in a graph is independent if e and f do not share a vertex. We show that a graph G is radial planar if G has a radial drawing in which every two independent edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the strong Hanani-Tutte theorem for radial planarity. This characterization yields a very simple algorithm for radial planarity testing.
AU - Fulek, Radoslav
AU - Pelsmajer, Michael
AU - Schaefer, Marcus
ID - 1164
TI - Hanani-Tutte for radial planarity II
VL - 9801
ER -
TY - CONF
AB - We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.
AU - Fulek, Radoslav
ID - 1165
TI - C-planarity of embedded cyclic c-graphs
VL - 9801
ER -
TY - CONF
AB - POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIMEcomplete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. © 2016, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.
AU - Chatterjee, Krishnendu
AU - Chmelik, Martin
AU - Davies, Jessica
ID - 1166
T2 - Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence
TI - A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps
VL - 2016
ER -
TY - JOUR
AB - Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K > 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task.
AU - Zagórski, Marcin P
AU - Burda, Zdzisław
AU - Wacław, Bartłomiej
ID - 1167
IS - 12
JF - PLoS Computational Biology
TI - Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks
VL - 12
ER -
TY - JOUR
AB - The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.
AU - Lang, Moritz
AU - Stelling, Jörg
ID - 1170
IS - 6
JF - SIAM Journal on Scientific Computing
TI - Modular parameter identification of biomolecular networks
VL - 38
ER -
TY - JOUR
AU - Tkacik, Gasper
ID - 1171
JF - Physics of Life Reviews
TI - Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" by O. C. Martin et al.
VL - 17
ER -
TY - JOUR
AB - A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.
AU - Sachdeva, Himani
AU - Barma, Mustansir
AU - Rao, Madan
ID - 1172
JF - Scientific Reports
TI - Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae
VL - 6
ER -
TY - JOUR
AB - Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent.
AU - Kamath Hosdurg, Chethan
AU - Chatterjee, Sanjit
ID - 1177
IS - 4
JF - Algorithmica
TI - A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound
VL - 74
ER -
TY - CONF
AB - Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.
Such chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)
A variable X has k bits of HILL entropy of quality (ϵ,s)
if there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ
by distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.
We first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)
, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)
in circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).
The chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)
, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound.
AU - Pietrzak, Krzysztof Z
AU - Maciej, Skorski
ID - 1179
TI - Pseudoentropy: Lower-bounds for chain rules and transformations
VL - 9985
ER -
TY - JOUR
AB - This review accompanies a 2016 SFN mini-symposium presenting examples of current studies that address a central question: How do neural stem cells (NSCs) divide in different ways to produce heterogeneous daughter types at the right time and in proper numbers to build a cerebral cortex with the appropriate size and structure? We will focus on four aspects of corticogenesis: cytokinesis events that follow apical mitoses of NSCs; coordinating abscission with delamination from the apical membrane; timing of neurogenesis and its indirect regulation through emergence of intermediate progenitors; and capacity of single NSCs to generate the correct number and laminar fate of cortical neurons. Defects in these mechanisms can cause microcephaly and other brain malformations, and understanding them is critical to designing diagnostic tools and preventive and corrective therapies.
AU - Dwyer, Noelle
AU - Chen, Bin
AU - Chou, Shen
AU - Hippenmeyer, Simon
AU - Nguyen, Laurent
AU - Ghashghaei, Troy
ID - 1181
IS - 45
JF - Journal of Neuroscience
TI - Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and productivity
VL - 36
ER -
TY - CONF
AB - Balanced knockout tournaments are ubiquitous in sports competitions and are also used in decisionmaking and elections. The traditional computational question, that asks to compute a draw (optimal draw) that maximizes the winning probability for a distinguished player, has received a lot of attention. Previous works consider the problem where the pairwise winning probabilities are known precisely, while we study how robust is the winning probability with respect to small errors in the pairwise winning probabilities. First, we present several illuminating examples to establish: (a) there exist deterministic tournaments (where the pairwise winning probabilities are 0 or 1) where one optimal draw is much more robust than the other; and (b) in general, there exist tournaments with slightly suboptimal draws that are more robust than all the optimal draws. The above examples motivate the study of the computational problem of robust draws that guarantee a specified winning probability. Second, we present a polynomial-time algorithm for approximating the robustness of a draw for sufficiently small errors in pairwise winning probabilities, and obtain that the stated computational problem is NP-complete. We also show that two natural cases of deterministic tournaments where the optimal draw could be computed in polynomial time also admit polynomial-time algorithms to compute robust optimal draws.
AU - Chatterjee, Krishnendu
AU - Ibsen-Jensen, Rasmus
AU - Tkadlec, Josef
ID - 1182
TI - Robust draws in balanced knockout tournaments
VL - 2016-January
ER -
TY - JOUR
AB - Across multicellular organisms, the costs of reproduction and self-maintenance result in a life history trade-off between fecundity and longevity. Queens of perennial social Hymenoptera are both highly fertile and long-lived, and thus, this fundamental trade-off is lacking. Whether social insect males similarly evade the fecundity/longevity trade-off remains largely unstudied. Wingless males of the ant genus Cardiocondyla stay in their natal colonies throughout their relatively long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla obscurior males that were allowed to mate with large numbers of female sexuals had a shortened life span compared to males that mated at a low frequency or virgin males. Although frequent mating negatively affects longevity, males clearly benefit from a “live fast, die young strategy” by inseminating as many female sexuals as possible at a cost to their own survival.
AU - Metzler, Sina
AU - Heinze, Jürgen
AU - Schrempf, Alexandra
ID - 1184
IS - 24
JF - Ecology and Evolution
TI - Mating and longevity in ant males
VL - 6
ER -
TY - JOUR
AB - The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk.
AU - Cucinotta, Mara
AU - Manrique, Silvia
AU - Guazzotti, Andrea
AU - Quadrelli, Nadia
AU - Mendes, Marta
AU - Benková, Eva
AU - Colombo, Lucia
ID - 1185
IS - 23
JF - Development
TI - Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development
VL - 143
ER -
TY - JOUR
AB - The human pathogen Streptococcus pneumoniae is decorated with a special class of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine (PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography, NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies, we provide structural information of choline-binding protein L (CbpL) and demonstrate its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported in this work for the very first time-, (ii) an unprecedented anchorage module showing alternate disposition of canonical and non-canonical choline-binding sites that allows vine-like binding of fully-PCho-substituted teichoic acids (with two choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural and infection assays indicate an important role of the whole multimodular protein allowing both to locate CbpL at specific places on the cell wall and to interact with host components in order to facilitate pneumococcal lung infection and transmigration from nasopharynx to the lungs and blood. CbpL implication in both resistance against killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein as relevant among the pathogenic arsenal of the pneumococcus.
AU - Gutierrez-Fernandez, Javier
AU - Saleh, Malek
AU - Alcorlo, Martín
AU - Gómez Mejóa, Alejandro
AU - Pantoja Uceda, David
AU - Treviño, Miguel
AU - Vob, Franziska
AU - Abdullah, Mohammed
AU - Galán Bartual, Sergio
AU - Seinen, Jolien
AU - Sánchez Murcia, Pedro
AU - Gago, Federico
AU - Bruix, Marta
AU - Hammerschmidt, Sven
AU - Hermoso, Juan
ID - 1186
JF - Scientific Reports
TI - Modular architecture and unique teichoic acid recognition features of choline-binding protein L CbpL contributing to pneumococcal pathogenesis
VL - 6
ER -
TY - JOUR
AB - We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling.
In the asymptotic regime of slow
diffusion, that coincides with the relevant experimental range, the resulting
non-linear Fokker–Planck equation is solved for the steady state in the WKB
approximation that maps it into the ground state of a quantum particle in an
Airy potential plus a centrifugal term. We retrieve scaling laws for growth rate
fluctuations and time response with respect to the distance from the maximum
growth rate suggesting that suboptimal populations can have a faster response
to perturbations.
AU - De Martino, Daniele
AU - Masoero, Davide
ID - 1188
IS - 12
JF - Journal of Statistical Mechanics: Theory and Experiment
TI - Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth
VL - 2016
ER -
TY - THES
AB - Within the scope of this thesis, we show that a driven-dissipative system with
few ultracold atoms can exhibit dissipatively bound states, even if the atom-atom
interaction is purely repulsive. This bond arises due to the dipole-dipole inter-
action, which is restricted to one of the lower electronic energy states, resulting
in the distance-dependent coherent population trapping. The quality of this al-
ready established method of dissipative binding is improved and the application
is extended to higher dimensions and a larger number of atoms. Here, we simu-
late two- and three-atom systems using an adapted approach to the Monte Carlo
wave-function method and analyse the results. Finally, we examine the possi-
bility of finding a setting allowing trimer states but prohibiting dimer states.
In the context of open quantum systems, such a three-body bound states corre-
sponds to the driven-dissipative analogue of a Borromean state. These states can
be detected in modern experiments with dipolar and Rydberg-dressed ultracold
atomic gases.
AU - Jochum, Clemens
ID - 1189
TI - Dissipative Few-Body Quantum Systems
ER -
TY - CONF
AB - We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid "bad features", or "flaws". It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and "resamples" it using a "resampling oracle" provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new "commutativity" condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately.
AU - Kolmogorov, Vladimir
ID - 1193
T2 - Proceedings - Annual IEEE Symposium on Foundations of Computer Science
TI - Commutativity in the algorithmic Lovasz local lemma
VL - 2016-December
ER -
TY - JOUR
AB - The genetic analysis of experimentally evolving populations typically relies on short reads from pooled individuals (Pool-Seq). While this method provides reliable allele frequency estimates, the underlying haplotype structure remains poorly characterized. With small population sizes and adaptive variants that start from low frequencies, the interpretation of selection signatures in most Evolve and Resequencing studies remains challenging. To facilitate the characterization of selection targets, we propose a new approach that reconstructs selected haplotypes from replicated time series, using Pool-Seq data. We identify selected haplotypes through the correlated frequencies of alleles carried by them. Computer simulations indicate that selected haplotype-blocks of several Mb can be reconstructed with high confidence and low error rates, even when allele frequencies change only by 20% across three replicates. Applying this method to real data from D. melanogaster populations adapting to a hot environment, we identify a selected haplotype-block of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations by experimental haplotyping, demonstrating the power and accuracy of our haplotype reconstruction from Pool-Seq data. We propose that the combination of allele frequency estimates with haplotype information will provide the key to understanding the dynamics of adaptive alleles.
AU - Franssen, Susan
AU - Barton, Nicholas H
AU - Schlötterer, Christian
ID - 1195
IS - 1
JF - Molecular Biology and Evolution
TI - Reconstruction of haplotype-blocks selected during experimental evolution.
VL - 34
ER -
TY - JOUR
AB - Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.
AU - Prentice, Jason
AU - Marre, Olivier
AU - Ioffe, Mark
AU - Loback, Adrianna
AU - Tkacik, Gasper
AU - Berry, Michael
ID - 1197
IS - 11
JF - PLoS Computational Biology
TI - Error-robust modes of the retinal population code
VL - 12
ER -
TY - JOUR
AU - Hilbe, Christian
AU - Traulsen, Arne
ID - 1200
JF - Physics of Life Reviews
TI - Only the combination of mathematics and agent based simulations can leverage the full potential of evolutionary modeling: Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze
VL - 19
ER -
TY - JOUR
AB - In this issue of Cell, Skau et al. show that the formin FMN2 organizes a perinuclear actin cytoskeleton that protects the nucleus and its genomic content of migrating cells squeezing through small spaces.
AU - Renkawitz, Jörg
AU - Sixt, Michael K
ID - 1201
IS - 6
JF - Cell
TI - Formin’ a nuclear protection
VL - 167
ER -
TY - JOUR
AU - Milutinovic, Barbara
AU - Peuß, Robert
AU - Ferro, Kevin
AU - Kurtz, Joachim
ID - 1202
IS - 4
JF - Zoology
TI - Immune priming in arthropods: an update focusing on the red flour beetle
VL - 119
ER -
TY - JOUR
AB - Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae.
AU - Hu, Fang
AU - Rishishwar, Lavanya
AU - Sivadas, Ambily
AU - Mitchell, Gabriel
AU - King, Jordan
AU - Murphy, Timothy
AU - Gilsdorf, Janet
AU - Mayer, Leonard
AU - Wang, Xin
ID - 1203
IS - 12
JF - Journal of Clinical Microbiology
TI - Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination
VL - 54
ER -
TY - JOUR
AB - In science, as in life, "surprises" can be adequately appreciated only in the presence of a null model, what we expect a priori. In physics, theories sometimes express the values of dimensionless physical constants as combinations of mathematical constants like π or e. The inverse problem also arises, whereby the measured value of a physical constant admits a "surprisingly" simple approximation in terms of well-known mathematical constants. Can we estimate the probability for this to be a mere coincidence, rather than an inkling of some theory? We answer the question in the most naive form.
AU - Amir, Ariel
AU - Lemeshko, Mikhail
AU - Tokieda, Tadashi
ID - 1204
IS - 6
JF - American Mathematical Monthly
TI - Surprises in numerical expressions of physical constants
VL - 123
ER -
TY - CONF
AB - In this paper, we present a formal model-driven engineering approach to establishing a safety-assured implementation of Multifunction vehicle bus controller (MVBC) based on the generic reference models and requirements described in the International Electrotechnical Commission (IEC) standard IEC-61375. First, the generic models described in IEC-61375 are translated into a network of timed automata, and some safety requirements tested in IEC-61375 are formalized as timed computation tree logic (TCTL) formulas. With the help of Uppaal, we check and debug whether the timed automata satisfy the formulas or not. Within this step, several logic inconsistencies in the original standard are detected and corrected. Then, we apply the tool Times to generate C code from the verified model, which was later synthesized into a real MVBC chip. Finally, the runtime verification tool RMOR is applied to verify some safety requirements at the implementation level. We set up a real platform with worldwide mostly used MVBC D113, and verify the correctness and the scalability of the synthesized MVBC chip more comprehensively. The errors in the standard has been confirmed and the resulted MVBC has been deployed in real train communication network.
AU - Jiang, Yu
AU - Liu, Han
AU - Song, Houbing
AU - Kong, Hui
AU - Gu, Ming
AU - Sun, Jiaguang
AU - Sha, Lui
ID - 1205
TI - Safety assured formal model driven design of the multifunction vehicle bus controller
VL - 9995
ER -
TY - JOUR
AB - We study a polar molecule immersed in a superfluid environment, such as a helium nanodroplet or a Bose–Einstein condensate, in the presence of a strong electrostatic field. We show that coupling of the molecular pendular motion, induced by the field, to the fluctuating bath leads to formation of pendulons—spherical harmonic librators dressed by a field of many-particle excitations. We study the behavior of the pendulon in a broad range of molecule–bath and molecule–field interaction strengths, and reveal that its spectrum features a series of instabilities which are absent in the field-free case of the angulon quasiparticle. Furthermore, we show that an external field allows to fine-tune the positions of these instabilities in the molecular rotational spectrum. This opens the door to detailed experimental studies of redistribution of orbital angular momentum in many-particle systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
AU - Redchenko, Elena
AU - Lemeshko, Mikhail
ID - 1206
IS - 22
JF - ChemPhysChem
TI - Libration of strongly oriented polar molecules inside a superfluid
VL - 17
ER -
TY - JOUR
AB - NADH-ubiquinone oxidoreductase (complex I) is the largest (∼1 MDa) and the least characterized complex of the mitochondrial electron transport chain. Because of the ease of sample availability, previous work has focused almost exclusively on bovine complex I. However, only medium resolution structural analyses of this complex have been reported. Working with other mammalian complex I homologues is a potential approach for overcoming these limitations. Due to the inherent difficulty of expressing large membrane protein complexes, screening of complex I homologues is limited to large mammals reared for human consumption. The high sequence identity among these available sources may preclude the benefits of screening. Here, we report the characterization of complex I purified from Ovis aries (ovine) heart mitochondria. All 44 unique subunits of the intact complex were identified by mass spectrometry. We identified differences in the subunit composition of subcomplexes of ovine complex I as compared with bovine, suggesting differential stability of inter-subunit interactions within the complex. Furthermore, the 42-kDa subunit, which is easily lost from the bovine enzyme, remains tightly bound to ovine complex I. Additionally, we developed a novel purification protocol for highly active and stable mitochondrial complex I using the branched-chain detergent lauryl maltose neopentyl glycol. Our data demonstrate that, although closely related, significant differences exist between the biochemical properties of complex I prepared from ovine and bovine mitochondria and that ovine complex I represents a suitable alternative target for further structural studies.
AU - Letts, James A
AU - Degliesposti, Gianluca
AU - Fiedorczuk, Karol
AU - Skehel, Mark
AU - Sazanov, Leonid A
ID - 1209
IS - 47
JF - Journal of Biological Chemistry
TI - Purification of ovine respiratory complex i results in a highly active and stable preparation
VL - 291
ER -
TY - CHAP
AB - Mechanisms for cell protection are essential for survival of multicellular organisms. In plants, the apical hook, which is transiently formed in darkness when the germinating seedling penetrates towards the soil surface, plays such protective role and shields the vitally important shoot apical meristem and cotyledons from damage. The apical hook is formed by bending of the upper hypocotyl soon after germination, and it is maintained in a closed stage while the hypocotyl continues to penetrate through the soil and rapidly opens when exposed to light in proximity of the soil surface. To uncover the complex molecular network orchestrating this spatiotemporally tightly coordinated process, monitoring of the apical hook development in real time is indispensable. Here we describe an imaging platform that enables high-resolution kinetic analysis of this dynamic developmental process. © Springer Science+Business Media New York 2017.
AU - Zhu, Qiang
AU - Žádníková, Petra
AU - Smet, Dajo
AU - Van Der Straeten, Dominique
AU - Benková, Eva
ID - 1210
T2 - Plant Hormones
TI - Real time analysis of the apical hook development
VL - 1497
ER -
TY - JOUR
AB - Plants adjust their growth according to gravity. Gravitropism involves gravity perception, signal transduction, and asymmetric growth response, with organ bending as a consequence [1]. Asymmetric growth results from the asymmetric distribution of the plant-specific signaling molecule auxin [2] that is generated by lateral transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3 (PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal cells, correlating with increased auxin accumulation in adjacent tissues at the lower side of the stimulated organ, where auxin induces cell elongation and, hence, organ bending. A curvature response allows the hypocotyl to resume straight growth at a defined angle [6], implying that at some point auxin symmetry is restored to prevent overbending. Here, we present initial insights into cellular and molecular mechanisms that lead to the termination of the tropic response. We identified an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization events redirect auxin fluxes at different time points of the gravity response: first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower hypocotyl side, where auxin gradually accumulates and promotes growth, and later PIN3 polarization to the opposite cell side, depleting this auxin maximum to end the bending. Accordingly, genetic or pharmacological interference with the late PIN3 polarization prevents termination of the response and leads to hypocotyl overbending. This observation reveals a role of auxin feedback on PIN polarity in the termination of the tropic response. © 2016 Elsevier Ltd
AU - Rakusová, Hana
AU - Abbas, Mohamad
AU - Han, Huibin
AU - Song, Siyuan
AU - Robert, Hélène
AU - Friml, Jirí
ID - 1212
IS - 22
JF - Current Biology
TI - Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity
VL - 26
ER -
TY - CONF
AB - With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.
AU - Martius, Georg S
AU - Hostettler, Raphael
AU - Knoll, Alois
AU - Der, Ralf
ID - 1214
TI - Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm
VL - 2016-November
ER -
TY - JOUR
AB - A framework fo r extracting features in 2D transient flows, based on the acceleration field to ensure Galilean invariance is proposed in this paper. The minima of the acceleration magnitude (a superset of acceleration zeros) are extracted and discriminated into vortices and saddle points, based on the spectral properties of the velocity Jacobian. The extraction of topological features is performed with purely combinatorial algorithms from discrete computational topology. The feature points are prioritized with persistence, as a physically meaningful importance measure. These feature points are tracked in time with a robust algorithm for tracking features. Thus, a space-time hierarchy of the minima is built and vortex merging events are detected. We apply the acceleration feature extraction strategy to three two-dimensional shear flows: (1) an incompressible periodic cylinder wake, (2) an incompressible planar mixing layer and (3) a weakly compressible planar jet. The vortex-like acceleration feature points are shown to be well aligned with acceleration zeros, maxima of the vorticity magnitude, minima of the pressure field and minima of λ2.
AU - Kasten, Jens
AU - Reininghaus, Jan
AU - Hotz, Ingrid
AU - Hege, Hans
AU - Noack, Bernd
AU - Daviller, Guillaume
AU - Morzyński, Marek
ID - 1216
IS - 1
JF - Archives of Mechanics
TI - Acceleration feature points of unsteady shear flows
VL - 68
ER -
TY - JOUR
AB - Understanding the regulation of T-cell responses during inflammation and auto-immunity is fundamental for designing efficient therapeutic strategies against immune diseases. In this regard, prostaglandin E 2 (PGE 2) is mostly considered a myeloid-derived immunosuppressive molecule. We describe for the first time that T cells secrete PGE 2 during T-cell receptor stimulation. In addition, we show that autocrine PGE 2 signaling through EP receptors is essential for optimal CD4 + T-cell activation in vitro and in vivo, and for T helper 1 (Th1) and regulatory T cell differentiation. PGE 2 was found to provide additive co-stimulatory signaling through AKT activation. Intravital multiphoton microscopy showed that triggering EP receptors in T cells is also essential for the stability of T cell-dendritic cell (DC) interactions and Th-cell accumulation in draining lymph nodes (LNs) during inflammation. We further demonstrated that blocking EP receptors in T cells during the initial phase of collagen-induced arthritis in mice resulted in a reduction of clinical arthritis. This could be attributable to defective T-cell activation, accompanied by a decline in activated and interferon-γ-producing CD4 + Th1 cells in draining LNs. In conclusion, we prove that T lymphocytes secret picomolar concentrations of PGE 2, which in turn provide additive co-stimulatory signaling, enabling T cells to attain a favorable activation threshold. PGE 2 signaling in T cells is also required for maintaining long and stable interactions with DCs within LNs. Blockade of EP receptors in vivo impairs T-cell activation and development of T cell-mediated inflammatory responses. This may have implications in various pathophysiological settings.
AU - Sreeramkumar, Vinatha
AU - Hons, Miroslav
AU - Punzón, Carmen
AU - Stein, Jens
AU - Sancho, David
AU - Fresno Forcelledo, Manuel
AU - Cuesta, Natalia
ID - 1217
IS - 1
JF - Immunology and Cell Biology
TI - Efficient T-cell priming and activation requires signaling through prostaglandin E2 (EP) receptors
VL - 94
ER -
TY - JOUR
AB - Investigating the physiology of cyanobacteria cultured under a diel light regime is relevant for a better understanding of the resulting growth characteristics and for specific biotechnological applications that are foreseen for these photosynthetic organisms. Here, we present the results of a multiomics study of the model cyanobacterium Synechocystis sp. strain PCC 6803, cultured in a lab-scale photobioreactor in physiological conditions relevant for large-scale culturing. The culture was sparged withN2 andCO2, leading to an anoxic environment during the dark period. Growth followed the availability of light. Metabolite analysis performed with 1Hnuclear magnetic resonance analysis showed that amino acids involved in nitrogen and sulfur assimilation showed elevated levels in the light. Most protein levels, analyzed through mass spectrometry, remained rather stable. However, several high-light-response proteins and stress-response proteins showed distinct changes at the onset of the light period. Microarray-based transcript analysis found common patterns of~56% of the transcriptome following the diel regime. These oscillating transcripts could be grouped coarsely into genes that were upregulated and downregulated in the dark period. The accumulated glycogen was degraded in the anaerobic environment in the dark. A small part was degraded gradually, reflecting basic maintenance requirements of the cells in darkness. Surprisingly, the largest part was degraded rapidly in a short time span at the end of the dark period. This degradation could allow rapid formation of metabolic intermediates at the end of the dark period, preparing the cells for the resumption of growth at the start of the light period.
AU - Angermayr, Andreas
AU - Van Alphen, Pascal
AU - Hasdemir, Dicle
AU - Kramer, Gertjan
AU - Iqbal, Muzamal
AU - Van Grondelle, Wilmar
AU - Hoefsloot, Huub
AU - Choi, Younghae
AU - Hellingwerf, Klaas
ID - 1218
IS - 14
JF - Applied and Environmental Microbiology
TI - Culturing synechocystis sp. Strain pcc 6803 with N2 and CO2 in a diel regime reveals multiphase glycogen dynamics with low maintenance costs
VL - 82
ER -
TY - JOUR
AB - We consider N×N random matrices of the form H = W + V where W is a real symmetric or complex Hermitian Wigner matrix and V is a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W, and we choose V so that the eigenvalues ofW and V are typically of the same order. For a large class of diagonal matrices V , we show that the local statistics in the bulk of the spectrum are universal in the limit of large N.
AU - Lee, Jioon
AU - Schnelli, Kevin
AU - Stetler, Ben
AU - Yau, Horngtzer
ID - 1219
IS - 3
JF - Annals of Probability
TI - Bulk universality for deformed wigner matrices
VL - 44
ER -
TY - JOUR
AB - Four rigid panels connected by hinges that meet at a point form a four-vertex, the fundamental building block of origami metamaterials. Most materials designed so far are based on the same four-vertex geometry, and little is known regarding how different geometries affect folding behavior. Here we systematically categorize and analyze the geometries and resulting folding motions of Euclidean four-vertices. Comparing the relative sizes of sector angles, we identify three types of generic vertices and two accompanying subtypes. We determine which folds can fully close and the possible mountain-valley assignments. Next, we consider what occurs when sector angles or sums thereof are set equal, which results in 16 special vertex types. One of these, flat-foldable vertices, has been studied extensively, but we show that a wide variety of qualitatively different folding motions exist for the other 15 special and 3 generic types. Our work establishes a straightforward set of rules for understanding the folding motion of both generic and special four-vertices and serves as a roadmap for designing origami metamaterials.
AU - Waitukaitis, Scott R
AU - Van Hecke, Martin
ID - 122
IS - 2
JF - Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
TI - Origami building blocks: Generic and special four-vertices
VL - 93
ER -
TY - CONF
AB - Theoretical and numerical aspects of aerodynamic efficiency of propulsion systems coupled to the boundary layer of a fuselage are studied. We discuss the effects of local flow fields, which are affected both by conservative flow acceleration as well as total pressure losses, on the efficiency of boundary layer immersed propulsion devices. We introduce the concept of a boundary layer retardation turbine that helps reduce skin friction over the fuselage. We numerically investigate efficiency gains offered by boundary layer and wake interacting devices. We discuss the results in terms of a total energy consumption framework and show that efficiency gains of any device depend on all the other elements of the propulsion system.
AU - Mikić, Gregor
AU - Stoll, Alex
AU - Bevirt, Joe
AU - Grah, Rok
AU - Moore, Mark
ID - 1220
TI - Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency
ER -
TY - JOUR
AB - The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles.
AU - Michalko, Jaroslav
AU - Glanc, Matous
AU - Perrot Rechenmann, Catherine
AU - Friml, Jirí
ID - 1221
JF - F1000 Research
TI - Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein
VL - 5
ER -
TY - JOUR
AB - We consider packings of congruent circles on a square flat torus, i.e., periodic (w.r.t. a square lattice) planar circle packings, with the maximal circle radius. This problem is interesting due to a practical reason—the problem of “super resolution of images.” We have found optimal arrangements for N=6, 7 and 8 circles. Surprisingly, for the case N=7 there are three different optimal arrangements. Our proof is based on a computer enumeration of toroidal irreducible contact graphs.
AU - Musin, Oleg
AU - Nikitenko, Anton
ID - 1222
IS - 1
JF - Discrete & Computational Geometry
TI - Optimal packings of congruent circles on a square flat torus
VL - 55
ER -
TY - JOUR
AB - We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder.
AU - Froese, Richard
AU - Lee, Darrick
AU - Sadel, Christian
AU - Spitzer, Wolfgang
AU - Stolz, Günter
ID - 1223
IS - 3
JF - Journal of Spectral Theory
TI - Localization for transversally periodic random potentials on binary trees
VL - 6
ER -
TY - JOUR
AB - Sexual dimorphism in resource allocation is expected to change during the life cycle of dioecious plants because of temporal differences between the sexes in reproductive investment. Given the potential for sex-specific differences in reproductive costs, resource availability may contribute to variation in reproductive allocation in females and males. Here, we used Rumex hastatulus, a dioecious, wind-pollinated annual plant, to investigate whether sexual dimorphism varies with life-history stage and nutrient availability, and determine whether allocation patterns differ depending on reproductive commitment. To examine if the costs of reproduction varied between the sexes, reproduction was either allowed or prevented through bud removal, and biomass allocation was measured at maturity. In a second experiment to assess variation in sexual dimorphism across the life cycle, and whether this varied with resource availability, plants were grown in high and low nutrients and allocation to roots, aboveground vegetative growth and reproduction were measured at three developmental stages. Males prevented from reproducing compensated with increased above- and belowground allocation to a much larger degree than females, suggesting that male reproductive costs reduce vegetative growth. The proportional allocation to roots, reproductive structures and aboveground vegetative growth varied between the sexes and among life-cycle stages, but not with nutrient treatment. Females allocated proportionally more resources to roots than males at peak flowering, but this pattern was reversed at reproductive maturity under low-nutrient conditions. Our study illustrates the importance of temporal dynamics in sex-specific resource allocation and provides support for high male reproductive costs in wind-pollinated plants.
AU - Teitel, Zachary
AU - Pickup, Melinda
AU - Field, David
AU - Barrett, Spencer
ID - 1224
IS - 1
JF - Plant Biology
TI - The dynamics of resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant
VL - 18
ER -
TY - CONF
AB - At Crypto 2015 Fuchsbauer, Hanser and Slamanig (FHS) presented the first standard-model construction of efficient roundoptimal blind signatures that does not require complexity leveraging. It is conceptually simple and builds on the primitive of structure-preserving signatures on equivalence classes (SPS-EQ). FHS prove the unforgeability of their scheme assuming EUF-CMA security of the SPS-EQ scheme and hardness of a version of the DH inversion problem. Blindness under adversarially chosen keys is proven under an interactive variant of the DDH assumption. We propose a variant of their scheme whose blindness can be proven under a non-interactive assumption, namely a variant of the bilinear DDH assumption. We moreover prove its unforgeability assuming only unforgeability of the underlying SPS-EQ but no additional assumptions as needed for the FHS scheme.
AU - Fuchsbauer, Georg
AU - Hanser, Christian
AU - Kamath Hosdurg, Chethan
AU - Slamanig, Daniel
ID - 1225
TI - Practical round-optimal blind signatures in the standard model from weaker assumptions
VL - 9841
ER -