TY - JOUR
AU - Kalinin, Nikita
AU - Shkolnikov, Mikhail
ID - 441
IS - 3
JF - European Journal of Mathematics
SN - 2199-675X
TI - Tropical formulae for summation over a part of SL(2,Z)
VL - 5
ER -
TY - JOUR
AB - Cryptographic security is usually defined as a guarantee that holds except when a bad event with negligible probability occurs, and nothing is guaranteed in that bad case. However, in settings where such failure can happen with substantial probability, one needs to provide guarantees even for the bad case. A typical example is where a (possibly weak) password is used instead of a secure cryptographic key to protect a session, the bad event being that the adversary correctly guesses the password. In a situation with multiple such sessions, a per-session guarantee is desired: any session for which the password has not been guessed remains secure, independently of whether other sessions have been compromised. A new formalism for stating such gracefully degrading security guarantees is introduced and applied to analyze the examples of password-based message authentication and password-based encryption. While a natural per-message guarantee is achieved for authentication, the situation of password-based encryption is more delicate: a per-session confidentiality guarantee only holds against attackers for which the distribution of password-guessing effort over the sessions is known in advance. In contrast, for more general attackers without such a restriction, a strong, composable notion of security cannot be achieved.
AU - Demay, Gregory
AU - Gazi, Peter
AU - Maurer, Ueli
AU - Tackmann, Bjorn
ID - 5887
IS - 1
JF - Journal of Computer Security
SN - 0926227X
TI - Per-session security: Password-based cryptography revisited
VL - 27
ER -
TY - JOUR
AB - We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature.
AU - Dyer, Ramsay
AU - Vegter, Gert
AU - Wintraecken, Mathijs
ID - 6515
IS - 1
JF - Journal of Computational Geometry
SN - 1920-180X
TI - Simplices modelled on spaces of constant curvature
VL - 10
ER -
TY - CONF
AB - We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism.
AU - Pietrzak, Krzysztof Z
ID - 6528
SN - 1868-8969
T2 - 10th Innovations in Theoretical Computer Science Conference
TI - Simple verifiable delay functions
VL - 124
ER -
TY - CONF
AB - Knowledge distillation, i.e. one classifier being trained on the outputs of another classifier, is an empirically very successful technique for knowledge transfer between classifiers. It has even been observed that classifiers learn much faster and more reliably if trained with the outputs of another classifier as soft labels, instead of from ground truth data. So far, however, there is no satisfactory theoretical explanation of this phenomenon. In this work, we provide the first insights into the working mechanisms of distillation by studying the special case of linear and deep linear classifiers. Specifically, we prove a generalization bound that establishes fast convergence of the expected risk of a distillation-trained linear classifier. From the bound and its proof we extract three keyfactors that determine the success of distillation: data geometry – geometric properties of the datadistribution, in particular class separation, has an immediate influence on the convergence speed of the risk; optimization bias– gradient descentoptimization finds a very favorable minimum of the distillation objective; and strong monotonicity– the expected risk of the student classifier always decreases when the size of the training set grows.
AU - Bui Thi Mai, Phuong
AU - Lampert, Christoph
ID - 6569
T2 - Proceedings of the 36th International Conference on Machine Learning
TI - Towards understanding knowledge distillation
VL - 97
ER -
TY - CONF
AB - In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example.
AU - Kundu, Atreyee
AU - Garcia Soto, Miriam
AU - Prabhakar, Pavithra
ID - 6565
SN - 978-153866246-5
T2 - 5th Indian Control Conference Proceedings
TI - Formal synthesis of stabilizing controllers for periodically controlled linear switched systems
ER -
TY - CONF
AB - Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space.
AU - Vegter, Gert
AU - Wintraecken, Mathijs
ID - 6628
T2 - The 31st Canadian Conference in Computational Geometry
TI - The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds
ER -
TY - CONF
AB - Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory
needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.
AU - Edelsbrunner, Herbert
AU - Virk, Ziga
AU - Wagner, Hubert
ID - 6648
SN - 9783959771047
T2 - 35th International Symposium on Computational Geometry
TI - Topological data analysis in information space
VL - 129
ER -
TY - JOUR
AB - Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research.
AU - Zenmyo, Naoki
AU - Tokumaru, Hiroki
AU - Uchinomiya, Shohei
AU - Fuchida, Hirokazu
AU - Tabata, Shigekazu
AU - Hamachi, Itaru
AU - Shigemoto, Ryuichi
AU - Ojida, Akio
ID - 6659
IS - 5
JF - Bulletin of the Chemical Society of Japan
SN - 00092673
TI - Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins
VL - 92
ER -
TY - JOUR
AB - In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as "gold" and "green" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.
AU - Danowski, Patrick
ID - 6657
IS - 1
JF - VOEB-Mitteilungen
TI - An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors
VL - 72
ER -
TY - CONF
AB - A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language.
Recent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.
AU - Kolmogorov, Vladimir
ID - 6725
SN - 1868-8969
T2 - 46th International Colloquium on Automata, Languages and Programming
TI - Testing the complexity of a valued CSP language
VL - 132
ER -
TY - CHAP
AB - Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so.
AU - Walter, Michael
ED - Buchmann, J
ED - Nitaj, A
ED - Rachidi, T
ID - 6726
SN - 0302-9743
T2 - Progress in Cryptology – AFRICACRYPT 2019
TI - Sampling the integers with low relative error
VL - 11627
ER -
TY - JOUR
AB - Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported.
AU - Hashemi, Seyyed Ali
AU - Condo, Carlo
AU - Mondelli, Marco
AU - Gross, Warren J
ID - 6750
IS - 22
JF - IEEE Transactions on Signal Processing
SN - 1053587X
TI - Rate-flexible fast polar decoders
VL - 67
ER -
TY - JOUR
AB - We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns.
We also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions.
AU - Jelínek, Vít
AU - Töpfer, Martin
ID - 6759
IS - 3
JF - Electronic Journal of Combinatorics
TI - On grounded L-graphs and their relatives
VL - 26
ER -
TY - CONF
AB - In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the qualitative winner or quantitative payoff of the game. In bidding games, in each turn, we hold an auction between the two players to determine which player moves the token. Bidding games have largely been studied with concrete bidding mechanisms that are variants of a first-price auction: in each turn both players simultaneously submit bids, the higher
bidder moves the token, and pays his bid to the lower bidder in Richman bidding, to the bank in poorman bidding, and in taxman bidding, the bid is split between the other player and the bank according to a predefined constant factor. Bidding games are deterministic games. They have an intriguing connection with a fragment of stochastic games called
randomturn games. We study, for the first time, a combination of bidding games with probabilistic behavior; namely, we study bidding games that are played on Markov decision processes, where the players bid for the right to choose the next action, which determines the probability distribution according to which the next vertex is chosen. We study parity and meanpayoff bidding games on MDPs and extend results from the deterministic bidding setting to the probabilistic one.
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Ibsen-Jensen, Rasmus
AU - Novotny, Petr
ID - 6822
SN - 0302-9743
T2 - Proceedings of the 13th International Conference of Reachability Problems
TI - Bidding games on Markov decision processes
VL - 11674
ER -
TY - JOUR
AB - Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.
AU - Pickup, Melinda
AU - Barton, Nicholas H
AU - Brandvain, Yaniv
AU - Fraisse, Christelle
AU - Yakimowski, Sarah
AU - Dixit, Tanmay
AU - Lexer, Christian
AU - Cereghetti, Eva
AU - Field, David
ID - 6856
IS - 3
JF - New Phytologist
TI - Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow
VL - 224
ER -
TY - CONF
AB - The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors.
AU - Chatterjee, Krishnendu
AU - Dvorák, Wolfgang
AU - Henzinger, Monika H
AU - Svozil, Alexander
ID - 6887
T2 - Leibniz International Proceedings in Informatics
TI - Near-linear time algorithms for Streett objectives in graphs and MDPs
VL - 140
ER -
TY - CONF
AB - In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods.
AU - Lechner, Mathias
AU - Hasani, Ramin
AU - Zimmer, Manuel
AU - Henzinger, Thomas A
AU - Grosu, Radu
ID - 6888
SN - 9781538660270
T2 - Proceedings - IEEE International Conference on Robotics and Automation
TI - Designing worm-inspired neural networks for interpretable robotic control
VL - 2019-May
ER -
TY - CONF
AB - In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets.
AU - Aghajohari, Milad
AU - Avni, Guy
AU - Henzinger, Thomas A
ID - 6886
TI - Determinacy in discrete-bidding infinite-duration games
VL - 140
ER -
TY - CONF
AB - A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Otop, Jan
ID - 6885
TI - Long-run average behavior of vector addition systems with states
VL - 140
ER -
TY - CONF
AB - We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games.
AU - Chatterjee, Krishnendu
AU - Piterman, Nir
ID - 6889
TI - Combinations of Qualitative Winning for Stochastic Parity Games
VL - 140
ER -
TY - CONF
AB - Consider a distributed system with n processors out of which f can be Byzantine faulty. In the
approximate agreement task, each processor i receives an input value xi and has to decide on an
output value yi such that
1. the output values are in the convex hull of the non-faulty processors’ input values,
2. the output values are within distance d of each other.
Classically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.
In this work, we study the task in a discrete setting, where input values with some structure
expressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to
output vertices that are within distance d of each other in G, but still remain in the graph-induced
convex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with
a deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,
we show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,
where ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a
variant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact
variants of these and related tasks over a large class of combinatorial structures.
AU - Nowak, Thomas
AU - Rybicki, Joel
ID - 6931
KW - consensus
KW - approximate agreement
KW - Byzantine faults
KW - chordal graphs
KW - lattice agreement
T2 - 33rd International Symposium on Distributed Computing
TI - Byzantine approximate agreement on graphs
VL - 146
ER -
TY - CONF
AB - In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets.
AU - Hasani, Ramin
AU - Amini, Alexander
AU - Lechner, Mathias
AU - Naser, Felix
AU - Grosu, Radu
AU - Rus, Daniela
ID - 6985
SN - 9781728119854
T2 - Proceedings of the International Joint Conference on Neural Networks
TI - Response characterization for auditing cell dynamics in long short-term memory networks
ER -
TY - JOUR
AB - We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds.
AU - Mondelli, Marco
AU - Hassani, S. Hamed
AU - Urbanke, Rüdiger
ID - 7007
IS - 10
JF - Algorithms
SN - 1999-4893
TI - A new coding paradigm for the primitive relay channel
VL - 12
ER -
TY - CONF
AB - The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.
AU - Geher, Gyorgy Pal
AU - Titkos, Tamas
AU - Virosztek, Daniel
ID - 7035
T2 - Kyoto RIMS Kôkyûroku
TI - Dirac masses and isometric rigidity
VL - 2125
ER -
TY - JOUR
AB - We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas.
AU - Huber, D.
AU - Hammer, H.-W.
AU - Volosniev, Artem
ID - 7190
IS - 3
JF - Physical Review Research
SN - 2643-1564
TI - In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas
VL - 1
ER -
TY - CONF
AB - The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest.
AU - Fulek, Radoslav
AU - Kyncl, Jan
ID - 7401
SN - 1868-8969
T2 - 35th International Symposium on Computational Geometry (SoCG 2019)
TI - Z_2-Genus of graphs and minimum rank of partial symmetric matrices
VL - 129
ER -
TY - CHAP
AB - We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement.
AU - Alur, Rajeev
AU - Giacobbe, Mirco
AU - Henzinger, Thomas A
AU - Larsen, Kim G.
AU - Mikučionis, Marius
ED - Steffen, Bernhard
ED - Woeginger, Gerhard
ID - 7453
SN - 1611-3349
T2 - Computing and Software Science
TI - Continuous-time models for system design and analysis
VL - 10000
ER -
TY - JOUR
AB - We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems.
AU - Portinale, Lorenzo
AU - Stefanelli, Ulisse
ID - 7550
IS - 2
JF - Advances in Mathematical Sciences and Applications
SN - 1343-4373
TI - Penalization via global functionals of optimal-control problems for dissipative evolution
VL - 28
ER -
TY - GEN
AB - There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests.
AU - Bialek, William
AU - Gregor, Thomas
AU - Tkačik, Gašper
ID - 7552
T2 - arXiv:1912.08579
TI - Action at a distance in transcriptional regulation
ER -
TY - CONF
AB - We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.
AU - Immler, Fabian
AU - Althoff, Matthias
AU - Benet, Luis
AU - Chapoutot, Alexandre
AU - Chen, Xin
AU - Forets, Marcelo
AU - Geretti, Luca
AU - Kochdumper, Niklas
AU - Sanders, David P.
AU - Schilling, Christian
ID - 7576
T2 - EPiC Series in Computing
TI - ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics
VL - 61
ER -
TY - CONF
AB - We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices.
AU - Betea, Dan
AU - Bouttier, Jérémie
AU - Nejjar, Peter
AU - Vuletíc, Mirjana
ID - 8175
T2 - Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics
TI - New edge asymptotics of skew Young diagrams via free boundaries
ER -
TY - CONF
AB - This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.
AU - Althoff, Matthias
AU - Bak, Stanley
AU - Forets, Marcelo
AU - Frehse, Goran
AU - Kochdumper, Niklas
AU - Ray, Rajarshi
AU - Schilling, Christian
AU - Schupp, Stefan
ID - 8570
T2 - EPiC Series in Computing
TI - ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics
VL - 61
ER -
TY - JOUR
AB - Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome.
AU - Antoniou, Michael N.
AU - Nicolas, Armel
AU - Mesnage, Robin
AU - Biserni, Martina
AU - Rao, Francesco V.
AU - Martin, Cristina Vazquez
ID - 6819
JF - BMC Research Notes
TI - Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells
VL - 12
ER -
TY - GEN
AB - Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.
AU - Antoniou, Michael N.
AU - Nicolas, Armel
AU - Mesnage, Robin
AU - Biserni, Martina
AU - Rao, Francesco V.
AU - Martin, Cristina Vazquez
ID - 9784
TI - MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells
ER -
TY - GEN
AB - More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.
AU - Polechova, Jitka
ID - 9839
TI - Data from: Is the sky the limit? On the expansion threshold of a species' range
ER -
TY - GEN
AB - In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1=2.
AU - Fulek, Radoslav
AU - Gärtner, Bernd
AU - Kupavskii, Andrey
AU - Valtr, Pavel
AU - Wagner, Uli
ID - 6647
SN - 1868-8969
T2 - 35th International Symposium on Computational Geometry
TI - The crossing Tverberg theorem
VL - 129
ER -
TY - CONF
AB - In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the "bank" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding.
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Zikelic, Dorde
ID - 6884
TI - Bidding mechanisms in graph games
VL - 138
ER -
TY - DATA
AU - Guseinov, Ruslan
ID - 7154
TI - Supplementary data for "Programming temporal morphing of self-actuated shells"
ER -
TY - DATA
AB - Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.
AU - Tomanek, Isabella
ID - 7016
KW - Escherichia coli
KW - gene amplification
KW - galactose
KW - DOG
KW - experimental evolution
KW - Illumina sequence data
KW - FACS data
KW - microfluidics data
TI - Data for the paper "Gene amplification as a form of population-level gene expression regulation"
ER -
TY - JOUR
AB - In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.
AU - Boissonnat, Jean-Daniel
AU - Lieutier, André
AU - Wintraecken, Mathijs
ID - 6671
IS - 1-2
JF - Journal of Applied and Computational Topology
SN - 2367-1726
TI - The reach, metric distortion, geodesic convexity and the variation of tangent spaces
VL - 3
ER -
TY - JOUR
AB - A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.
AU - Gerencser, Mate
AU - Gyöngy, István
ID - 301
IS - 3
JF - Stochastic Processes and their Applications
TI - A Feynman–Kac formula for stochastic Dirichlet problems
VL - 129
ER -
TY - JOUR
AB - We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.
AU - Deuchert, Andreas
AU - Seiringer, Robert
AU - Yngvason, Jakob
ID - 80
IS - 2
JF - Communications in Mathematical Physics
TI - Bose–Einstein condensation in a dilute, trapped gas at positive temperature
VL - 368
ER -
TY - JOUR
AB - Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.
AU - Faria, Rui
AU - Johannesson, Kerstin
AU - Butlin, Roger K.
AU - Westram, Anja M
ID - 5911
IS - 3
JF - Trends in Ecology and Evolution
SN - 01695347
TI - Evolving inversions
VL - 34
ER -
TY - JOUR
AB - We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the
possibility of a P = W conjecture for a suitable wild Hitchin system.
AU - Hausel, Tamas
AU - Mereb, Martin
AU - Wong, Michael
ID - 439
IS - 10
JF - Journal of the European Mathematical Society
TI - Arithmetic and representation theory of wild character varieties
VL - 21
ER -
TY - JOUR
AB - Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.
AU - Marsh, Ashley
AU - Novarino, Gaia
AU - Lockhart, Paul
AU - Leventer, Richard
ID - 105
JF - European Journal of Human Genetics
TI - CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63
VL - 27
ER -
TY - JOUR
AB - We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2.
AU - Dareiotis, Konstantinos
AU - Gerencser, Mate
AU - Gess, Benjamin
ID - 65
IS - 6
JF - Journal of Differential Equations
TI - Entropy solutions for stochastic porous media equations
VL - 266
ER -
TY - JOUR
AB - Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.
AU - Mócsai, Réka
AU - Figl, Rudolf
AU - Troschl, Clemens
AU - Strasser, Richard
AU - Svehla, Elisabeth
AU - Windwarder, Markus
AU - Thader, Andreas
AU - Altmann, Friedrich
ID - 5907
IS - 1
JF - Scientific Reports
TI - N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated
VL - 9
ER -
TY - JOUR
AB - The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants.
AU - Lee, Eunkyoung
AU - Vanneste, Steffen
AU - Pérez-Sancho, Jessica
AU - Benitez-Fuente, Francisco
AU - Strelau, Matthew
AU - Macho, Alberto P.
AU - Botella, Miguel A.
AU - Friml, Jiří
AU - Rosado, Abel
ID - 5908
IS - 4
JF - Proceedings of the National Academy of Sciences of the United States of America
TI - Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis
VL - 116
ER -
TY - JOUR
AB - We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.
AU - Ferrari, Patrick
AU - Ghosal, Promit
AU - Nejjar, Peter
ID - 72
IS - 3
JF - Annales de l'institut Henri Poincare (B) Probability and Statistics
SN - 02460203
TI - Limit law of a second class particle in TASEP with non-random initial condition
VL - 55
ER -
TY - JOUR
AB - The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest.
AU - Chaplick, Steven
AU - Fulek, Radoslav
AU - Klavík, Pavel
ID - 5790
IS - 4
JF - Journal of Graph Theory
SN - 03649024
TI - Extending partial representations of circle graphs
VL - 91
ER -
TY - JOUR
AB - We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently.
AU - Virosztek, Daniel
ID - 405
JF - Linear Algebra and Its Applications
TI - Jointly convex quantum Jensen divergences
VL - 576
ER -
TY - JOUR
AB - An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.
AU - Browning, Timothy D
AU - Loughran, Daniel
ID - 175
IS - 8
JF - Transactions of the American Mathematical Society
SN - 00029947
TI - Sieving rational points on varieties
VL - 371
ER -
TY - JOUR
AB - We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition.
AU - Gerencser, Mate
AU - Hairer, Martin
ID - 319
IS - 3-4
JF - Probability Theory and Related Fields
SN - 01788051
TI - Singular SPDEs in domains with boundaries
VL - 173
ER -
TY - JOUR
AB - We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent.
AU - Ajanki, Oskari H
AU - Erdös, László
AU - Krüger, Torben H
ID - 429
IS - 1-2
JF - Probability Theory and Related Fields
SN - 01788051
TI - Stability of the matrix Dyson equation and random matrices with correlations
VL - 173
ER -
TY - CONF
AB - Graph algorithms applied in many applications, including social networks, communication networks, VLSI design, graphics, and several others, require dynamic modifications - addition and removal of vertices and/or edges - in the graph. This paper presents a novel concurrent non-blocking algorithm to implement a dynamic unbounded directed graph in a shared-memory machine. The addition and removal operations of vertices and edges are lock-free. For a finite sized graph, the lookup operations are wait-free. Most significant component of the presented algorithm is the reachability query in a concurrent graph. The reachability queries in our algorithm are obstruction-free and thus impose minimal additional synchronization cost over other operations. We prove that each of the data structure operations are linearizable. We extensively evaluate a sample C/C++ implementation of the algorithm through a number of micro-benchmarks. The experimental results show that the proposed algorithm scales well with the number of threads and on an average provides 5 to 7x performance improvement over a concurrent graph implementation using coarse-grained locking.
AU - Chatterjee, Bapi
AU - Peri, Sathya
AU - Sa, Muktikanta
AU - Singhal, Nandini
ID - 5947
SN - 978-1-4503-6094-4
T2 - ACM International Conference Proceeding Series
TI - A simple and practical concurrent non-blocking unbounded graph with linearizable reachability queries
ER -
TY - JOUR
AB - A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is [Formula presented](n−1), and that this bound is best possible for infinitely many values of n.
AU - Fulek, Radoslav
AU - Pach, János
ID - 5857
IS - 4
JF - Discrete Applied Mathematics
SN - 0166218X
TI - Thrackles: An improved upper bound
VL - 259
ER -
TY - JOUR
AB - Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.
AU - Corominas-Murtra, Bernat
ID - 5944
IS - 1
JF - Life
TI - Thermodynamics of duplication thresholds in synthetic protocell systems
VL - 9
ER -
TY - JOUR
AB - Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy.
AU - Lindner, Marco
AU - Tresztenyak, Aliz
AU - Fülöp, Gergö
AU - Jahr, Wiebke
AU - Prinz, Adrian
AU - Prinz, Iris
AU - Danzl, Johann G
AU - Schütz, Gerhard J.
AU - Sevcsik, Eva
ID - 6029
JF - Frontiers in Chemistry
TI - A fast and simple contact printing approach to generate 2D protein nanopatterns
VL - 6
ER -
TY - JOUR
AB - We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small.
AU - Gerencser, Mate
AU - Hairer, Martin
ID - 6028
IS - 9
JF - Communications on Pure and Applied Mathematics
TI - A solution theory for quasilinear singular SPDEs
VL - 72
ER -
TY - JOUR
AB - In developing organisms, spatially prescribed cell identities are thought to be determined by the expression levels of multiple genes. Quantitative tests of this idea, however, require a theoretical framework capable of exposing the rules and precision of cell specification over developmental time. We use the gap gene network in the early fly embryo as an example to show how expression levels of the four gap genes can be jointly decoded into an optimal specification of position with 1% accuracy. The decoder correctly predicts, with no free parameters, the dynamics of pair-rule expression patterns at different developmental time points and in various mutant backgrounds. Precise cellular identities are thus available at the earliest stages of development, contrasting the prevailing view of positional information being slowly refined across successive layers of the patterning network. Our results suggest that developmental enhancers closely approximate a mathematically optimal decoding strategy.
AU - Petkova, Mariela D.
AU - Tkacik, Gasper
AU - Bialek, William
AU - Wieschaus, Eric F.
AU - Gregor, Thomas
ID - 5945
IS - 4
JF - Cell
TI - Optimal decoding of cellular identities in a genetic network
VL - 176
ER -
TY - JOUR
AB - The hairpin instability of a jet in a crossflow (JICF) for a low jet-to-crossflow velocity ratio is investigated experimentally for a velocity ratio range of R ∈ (0.14, 0.75) and crossflow Reynolds numbers ReD ∈ (260, 640). From spectral analysis we characterize the Strouhal number and amplitude of the hairpin instability as a function of R and ReD. We demonstrate that the dynamics of the hairpins is well described by the Landau model, and, hence, that the instability occurs through Hopf bifurcation, similarly to other hydrodynamical oscillators such as wake behind different bluff bodies. Using the Landau model, we determine the precise threshold values of hairpin shedding. We also study the spatial dependence of this hydrodynamical instability, which shows a global behaviour.
AU - Klotz, Lukasz
AU - Gumowski, Konrad
AU - Wesfreid, José Eduardo
ID - 5943
JF - Journal of Fluid Mechanics
TI - Experiments on a jet in a crossflow in the low-velocity-ratio regime
VL - 863
ER -
TY - CONF
AB - Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques.
AU - Christakis, Maria
AU - Heizmann, Matthias
AU - Mansur, Muhammad Numair
AU - Schilling, Christian
AU - Wüstholz, Valentin
ID - 6042
T2 - 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems
TI - Semantic fault localization and suspiciousness ranking
VL - 11427
ER -
TY - CONF
AB - We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.
AU - Bogomolov, Sergiy
AU - Forets, Marcelo
AU - Frehse, Goran
AU - Potomkin, Kostiantyn
AU - Schilling, Christian
ID - 6035
KW - reachability analysis
KW - hybrid systems
KW - lazy computation
SN - 9781450362825
T2 - Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control
TI - JuliaReach: A toolbox for set-based reachability
VL - 22
ER -
TY - JOUR
AB - Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis.
AU - Truckenbrodt, Sven M
AU - Sommer, Christoph M
AU - Rizzoli, Silvio O
AU - Danzl, Johann G
ID - 6052
IS - 3
JF - Nature Protocols
TI - A practical guide to optimization in X10 expansion microscopy
VL - 14
ER -
TY - JOUR
AB - Non-canonical Wnt signaling plays a central role for coordinated cell polarization and directed migration in metazoan development. While spatiotemporally restricted activation of non-canonical Wnt-signaling drives cell polarization in epithelial tissues, it remains unclear whether such instructive activity is also critical for directed mesenchymal cell migration. Here, we developed a light-activated version of the non-canonical Wnt receptor Frizzled 7 (Fz7) to analyze how restricted activation of non-canonical Wnt signaling affects directed anterior axial mesendoderm (prechordal plate, ppl) cell migration within the zebrafish gastrula. We found that Fz7 signaling is required for ppl cell protrusion formation and migration and that spatiotemporally restricted ectopic activation is capable of redirecting their migration. Finally, we show that uniform activation of Fz7 signaling in ppl cells fully rescues defective directed cell migration in fz7 mutant embryos. Together, our findings reveal that in contrast to the situation in epithelial cells, non-canonical Wnt signaling functions permissively rather than instructively in directed mesenchymal cell migration during gastrulation.
AU - Capek, Daniel
AU - Smutny, Michael
AU - Tichy, Alexandra Madelaine
AU - Morri, Maurizio
AU - Janovjak, Harald L
AU - Heisenberg, Carl-Philipp J
ID - 6025
JF - eLife
TI - Light-activated Frizzled7 reveals a permissive role of non-canonical wnt signaling in mesendoderm cell migration
VL - 8
ER -
TY - JOUR
AB - The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation.
AU - Merrill, Richard M.
AU - Rastas, Pasi
AU - Martin, Simon H.
AU - Melo Hurtado, Maria C
AU - Barker, Sarah
AU - Davey, John
AU - Mcmillan, W. Owen
AU - Jiggins, Chris D.
ID - 6022
IS - 2
JF - PLoS Biology
TI - Genetic dissection of assortative mating behavior
VL - 17
ER -
TY - JOUR
AB - Multicellular development requires coordinated cell polarization relative to body axes, and translation to oriented cell division 1–3 . In plants, it is unknown how cell polarities are connected to organismal axes and translated to division. Here, we identify Arabidopsis SOSEKI proteins that integrate apical–basal and radial organismal axes to localize to polar cell edges. Localization does not depend on tissue context, requires cell wall integrity and is defined by a transferrable, protein-specific motif. A Domain of Unknown Function in SOSEKI proteins resembles the DIX oligomerization domain in the animal Dishevelled polarity regulator. The DIX-like domain self-interacts and is required for edge localization and for influencing division orientation, together with a second domain that defines the polar membrane domain. Our work shows that SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation. Furthermore, this work reveals that, despite fundamental differences, cell polarity mechanisms in plants and animals converge on a similar protein domain.
AU - Yoshida, Saiko
AU - Van Der Schuren, Alja
AU - Van Dop, Maritza
AU - Van Galen, Luc
AU - Saiga, Shunsuke
AU - Adibi, Milad
AU - Möller, Barbara
AU - Ten Hove, Colette A.
AU - Marhavy, Peter
AU - Smith, Richard
AU - Friml, Jiří
AU - Weijers, Dolf
ID - 6023
IS - 2
JF - Nature Plants
TI - A SOSEKI-based coordinate system interprets global polarity cues in arabidopsis
VL - 5
ER -
TY - JOUR
AB - Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information.
AU - Kalaee, Mahmoud
AU - Mirhosseini, Mohammad
AU - Dieterle, Paul B.
AU - Peruzzo, Matilda
AU - Fink, Johannes M
AU - Painter, Oskar
ID - 6053
IS - 4
JF - Nature Nanotechnology
SN - 1748-3387
TI - Quantum electromechanics of a hypersonic crystal
VL - 14
ER -
TY - JOUR
AB - We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible.
AU - Akopyan, Arseniy
AU - Fedorov, Roman
ID - 6050
JF - Proceedings of the American Mathematical Society
TI - Two circles and only a straightedge
VL - 147
ER -
TY - JOUR
AB - Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.
AU - Faria, Rui
AU - Chaube, Pragya
AU - Morales, Hernán E.
AU - Larsson, Tomas
AU - Lemmon, Alan R.
AU - Lemmon, Emily M.
AU - Rafajlović, Marina
AU - Panova, Marina
AU - Ravinet, Mark
AU - Johannesson, Kerstin
AU - Westram, Anja M
AU - Butlin, Roger K.
ID - 6095
IS - 6
JF - Molecular Ecology
SN - 0962-1083
TI - Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes
VL - 28
ER -
TY - JOUR
AB - In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape.
AU - De Martino, Daniele
ID - 6049
IS - 4
JF - Journal of Physics A: Mathematical and Theoretical
TI - Feedback-induced self-oscillations in large interacting systems subjected to phase transitions
VL - 52
ER -
TY - JOUR
AB - Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.
AU - Fraisse, Christelle
AU - Puixeu Sala, Gemma
AU - Vicoso, Beatriz
ID - 6089
IS - 3
JF - Molecular biology and evolution
SN - 0737-4038
TI - Pleiotropy modulates the efficacy of selection in drosophila melanogaster
VL - 36
ER -
TY - JOUR
AB - Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons.
AU - Henderson, Nathan T.
AU - Le Marchand, Sylvain J.
AU - Hruska, Martin
AU - Hippenmeyer, Simon
AU - Luo, Liqun
AU - Dalva, Matthew B.
ID - 6091
JF - eLife
TI - Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs
VL - 8
ER -
TY - JOUR
AB - Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.
AU - Mitosch, Karin
AU - Rieckh, Georg
AU - Bollenbach, Mark Tobias
ID - 6046
IS - 2
JF - Molecular systems biology
TI - Temporal order and precision of complex stress responses in individual bacteria
VL - 15
ER -
TY - JOUR
AB - In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales.
AU - Mentink, Johann H
AU - Katsnelson, Mikhail
AU - Lemeshko, Mikhail
ID - 6092
IS - 6
JF - Physical Review B
TI - Quantum many-body dynamics of the Einstein-de Haas effect
VL - 99
ER -
TY - JOUR
AB - Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.
AU - Carballo-Pacheco, Martín
AU - Desponds, Jonathan
AU - Gavrilchenko, Tatyana
AU - Mayer, Andreas
AU - Prizak, Roshan
AU - Reddy, Gautam
AU - Nemenman, Ilya
AU - Mora, Thierry
ID - 6090
IS - 2
JF - Physical Review E
TI - Receptor crosstalk improves concentration sensing of multiple ligands
VL - 99
ER -
TY - JOUR
AB - Hosts can alter their strategy towards pathogens during their lifetime; that is, they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e., resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fecundity consequences that result from a high pathogen burden. Finally, previous exposure may also lead to life‐history adjustments, such as terminal investment into reproduction.
Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested whether previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute‐phase infection (one day post‐challenge). We then asked whether previous pathogen exposure affects chronic‐phase pathogen persistence and longer‐term survival (28 days post‐challenge).
We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long‐term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses.
We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection.
To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi‐faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host–pathogen system and that infection persistence may be bacterium‐specific.
AU - Kutzer, Megan
AU - Kurtz, Joachim
AU - Armitage, Sophie A.O.
ID - 6105
IS - 4
JF - Journal of Animal Ecology
SN - 00218790
TI - A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance
VL - 88
ER -
TY - JOUR
AB - Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity.
AU - Xia, Peng
AU - Gütl, Daniel J
AU - Zheden, Vanessa
AU - Heisenberg, Carl-Philipp J
ID - 6087
IS - 6
JF - Cell
TI - Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity
VL - 176
ER -
TY - GEN
AB - 1. Hosts can alter their strategy towards pathogens during their lifetime, i.e., they can show phenotypic plasticity in immunity or life history. Immune priming is one such example, where a previous encounter with a pathogen confers enhanced protection upon secondary challenge, resulting in reduced pathogen load (i.e. resistance) and improved host survival. However, an initial encounter might also enhance tolerance, particularly to less virulent opportunistic pathogens that establish persistent infections. In this scenario, individuals are better able to reduce the negative fitness consequences that result from a high pathogen load. Finally, previous exposure may also lead to life history adjustments, such as terminal investment into reproduction. 2. Using different Drosophila melanogaster host genotypes and two bacterial pathogens, Lactococcus lactis and Pseudomonas entomophila, we tested if previous exposure results in resistance or tolerance and whether it modifies immune gene expression during an acute-phase infection (one day post-challenge). We then asked if previous pathogen exposure affects chronic-phase pathogen persistence and longer-term survival (28 days post-challenge). 3. We predicted that previous exposure would increase host resistance to an early stage bacterial infection while it might come at a cost to host fecundity tolerance. We reasoned that resistance would be due in part to stronger immune gene expression after challenge. We expected that previous exposure would improve long-term survival, that it would reduce infection persistence, and we expected to find genetic variation in these responses. 4. We found that previous exposure to P. entomophila weakened host resistance to a second infection independent of genotype and had no effect on immune gene expression. Fecundity tolerance showed genotypic variation but was not influenced by previous exposure. However, L. lactis persisted as a chronic infection, whereas survivors cleared the more pathogenic P. entomophila infection. 5. To our knowledge, this is the first study that addresses host tolerance to bacteria in relation to previous exposure, taking a multi-faceted approach to address the topic. Our results suggest that previous exposure comes with transient costs to resistance during the early stage of infection in this host-pathogen system and that infection persistence may be bacterium-specific.
AU - Kutzer, Megan
AU - Kurtz, Joachim
AU - Armitage, Sophie A.O.
ID - 9806
TI - Data from: A multi-faceted approach testing the effects of previous bacterial exposure on resistance and tolerance
ER -
TY - JOUR
AB - We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part.
AU - Sadel, Christian
AU - Xu, Disheng
ID - 6086
IS - 4
JF - Ergodic Theory and Dynamical Systems
TI - Singular analytic linear cocycles with negative infinite Lyapunov exponents
VL - 39
ER -
TY - JOUR
AB - Light is a union of electric and magnetic fields, and nowhere is the complex relationship between these fields more evident than in the near fields of nanophotonic structures. There, complicated electric and magnetic fields varying over subwavelength scales are generally present, which results in photonic phenomena such as extraordinary optical momentum, superchiral fields, and a complex spatial evolution of optical singularities. An understanding of such phenomena requires nanoscale measurements of the complete optical field vector. Although the sensitivity of near- field scanning optical microscopy to the complete electromagnetic field was recently demonstrated, a separation of different components required a priori knowledge of the sample. Here, we introduce a robust algorithm that can disentangle all six electric and magnetic field components from a single near-field measurement without any numerical modeling of the structure. As examples, we unravel the fields of two prototypical nanophotonic structures: a photonic crystal waveguide and a plasmonic nanowire. These results pave the way for new studies of complex photonic phenomena at the nanoscale and for the design of structures that optimize their optical behavior.
AU - Le Feber, B.
AU - Sipe, J. E.
AU - Wulf, Matthias
AU - Kuipers, L.
AU - Rotenberg, N.
ID - 6102
IS - 1
JF - Light: Science and Applications
SN - 20955545
TI - A full vectorial mapping of nanophotonic light fields
VL - 8
ER -
TY - JOUR
AB - The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a minimal model combining tissue mechanics with morphogen turnover and transport to explore routes to patterning. Our active description couples morphogen reaction and diffusion, which impact cell differentiation and tissue mechanics, to a two-phase poroelastic rheology, where one tissue phase consists of a poroelastic cell network and the other one of a permeating extracellular fluid, which provides a feedback by actively transporting morphogens. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction–diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics due to mechanically induced cross-diffusion flows. Moreover, we describe a qualitatively different advection-driven Keller–Segel instability which allows for the formation of patterns with a single morphogen and whose fundamental mode pattern robustly scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis.
AU - Recho, Pierre
AU - Hallou, Adrien
AU - Hannezo, Edouard B
ID - 6191
IS - 12
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 00278424
TI - Theory of mechanochemical patterning in biphasic biological tissues
VL - 116
ER -
TY - JOUR
AB - Increased levels of the chemokine CCL2 in cancer patients are associated with poor prognosis. Experimental evidence suggests that CCL2 correlates with inflammatory monocyte recruitment and induction of vascular activation, but the functionality remains open. Here, we show that endothelial Ccr2 facilitates pulmonary metastasis using an endothelial-specific Ccr2-deficient mouse model (Ccr2ecKO). Similar levels of circulating monocytes and equal leukocyte recruitment to metastatic lesions of Ccr2ecKO and Ccr2fl/fl littermates were observed. The absence of endothelial Ccr2 strongly reduced pulmonary metastasis, while the primary tumor growth was unaffected. Despite a comparable cytokine milieu in Ccr2ecKO and Ccr2fl/fl littermates the absence of vascular permeability induction was observed only in Ccr2ecKO mice. CCL2 stimulation of pulmonary endothelial cells resulted in increased phosphorylation of MLC2, endothelial cell retraction, and vascular leakiness that was blocked by an addition of a CCR2 inhibitor. These data demonstrate that endothelial CCR2 expression is required for tumor cell extravasation and pulmonary metastasis.
Implications: The findings provide mechanistic insight into how CCL2–CCR2 signaling in endothelial cells promotes their activation through myosin light chain phosphorylation, resulting in endothelial retraction and enhanced tumor cell migration and metastasis.
AU - Roblek, Marko
AU - Protsyuk, Darya
AU - Becker, Paul F.
AU - Stefanescu, Cristina
AU - Gorzelanny, Christian
AU - Glaus Garzon, Jesus F.
AU - Knopfova, Lucia
AU - Heikenwalder, Mathias
AU - Luckow, Bruno
AU - Schneider, Stefan W.
AU - Borsig, Lubor
ID - 6190
IS - 3
JF - Molecular Cancer Research
SN - 15417786
TI - CCL2 is a vascular permeability factor inducing CCR2-dependent endothelial retraction during lung metastasis
VL - 17
ER -
TY - JOUR
AB - Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.
AU - Barton, Nicholas H
AU - Hermisson, Joachim
AU - Nordborg, Magnus
ID - 6230
JF - eLife
TI - Why structure matters
VL - 8
ER -
TY - JOUR
AB - The boundary behaviour of solutions of stochastic PDEs with Dirichlet boundary conditions can be surprisingly—and in a sense, arbitrarily—bad: as shown by Krylov[ SIAM J. Math. Anal.34(2003) 1167–1182], for any α>0 one can find a simple 1-dimensional constant coefficient linear equation whose solution at the boundary is not α-Hölder continuous.We obtain a positive counterpart of this: under some mild regularity assumptions on the coefficients, solutions of semilinear SPDEs on C1 domains are proved to be α-Hölder continuous up to the boundary with some α>0.
AU - Gerencser, Mate
ID - 6232
IS - 2
JF - Annals of Probability
SN - 00911798
TI - Boundary regularity of stochastic PDEs
VL - 47
ER -
TY - JOUR
AB - Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric
distribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and
shoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing
cells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-
branes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin
feedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-
formed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic
response. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological
outputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of
hypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-
lated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed
defects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-
ping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis
specification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.
The hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell
polarity and plant adaptive development.
AU - Rakusová, Hana
AU - Han, Huibin
AU - Valošek, Petr
AU - Friml, Jiří
ID - 6262
IS - 6
JF - The Plant Journal
SN - 0960-7412
TI - Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls
VL - 98
ER -
TY - JOUR
AB - Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow.
AU - Davies, Heather S.
AU - Baranova, Natalia S.
AU - El Amri, Nouha
AU - Coche-Guérente, Liliane
AU - Verdier, Claude
AU - Bureau, Lionel
AU - Richter, Ralf P.
AU - Débarre, Delphine
ID - 6297
JF - Matrix Biology
SN - 0945-053X
TI - An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments
VL - 78-79
ER -
TY - JOUR
AB - An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariskiopen subset of an arbitrary smooth biquadratic hypersurface in sufficiently many variables. The proof uses the Hardy–Littlewood circle method.
AU - Browning, Timothy D
AU - Hu, L.Q.
ID - 6310
JF - Advances in Mathematics
SN - 00018708
TI - Counting rational points on biquadratic hypersurfaces
VL - 349
ER -
TY - JOUR
AB - Nitrate regulation of root stem cell activity is auxin-dependent.
AU - Wang, Y
AU - Gong, Z
AU - Friml, Jiří
AU - Zhang, J
ID - 6261
IS - 1
JF - Plant Physiology
SN - 0032-0889
TI - Nitrate modulates the differentiation of root distal stem cells
VL - 180
ER -
TY - JOUR
AB - Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure.
AU - Temnov, Andrey Alexandrovich
AU - Rogov, Konstantin Arkadevich
AU - Sklifas, Alla Nikolaevna
AU - Klychnikova, Elena Valerievna
AU - Hartl, Markus
AU - Djinovic-Carugo, Kristina
AU - Charnagalov, Alexej
ID - 6352
JF - Molecular Biology Reports
SN - 03014851
TI - Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure
ER -
TY - JOUR
AB - High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.
AU - Rueda Sanchez, Alfredo R
AU - Sedlmeir, Florian
AU - Kumari, Madhuri
AU - Leuchs, Gerd
AU - Schwefel, Harald G.L.
ID - 6348
IS - 7752
JF - Nature
SN - 00280836
TI - Resonant electro-optic frequency comb
VL - 568
ER -
TY - JOUR
AB - Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning.
AU - Stella, Federico
AU - Baracskay, Peter
AU - O'Neill, Joseph
AU - Csicsvari, Jozsef L
ID - 6338
JF - Neuron
TI - Hippocampal reactivation of random trajectories resembling Brownian diffusion
VL - 102
ER -
TY - JOUR
AB - We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al.
AU - Budanur, Nazmi B
AU - Fleury, Marc
ID - 5878
IS - 1
JF - Chaos: An Interdisciplinary Journal of Nonlinear Science
SN - 1054-1500
TI - State space geometry of the chaotic pilot-wave hydrodynamics
VL - 29
ER -
TY - CONF
AB - Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.
AU - Ferrere, Thomas
AU - Nickovic, Dejan
AU - Donzé, Alexandre
AU - Ito, Hisahiro
AU - Kapinski, James
ID - 6428
SN - 9781450362825
T2 - Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control
TI - Interface-aware signal temporal logic
ER -
TY - JOUR
AB - This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples.
AU - Schreck, Camille
AU - Hafner, Christian
AU - Wojtan, Christopher J
ID - 6442
IS - 4
JF - ACM Transactions on Graphics
TI - Fundamental solutions for water wave animation
VL - 38
ER -
TY - JOUR
AB - Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase.
AU - Song, Baofang
AU - Plana, Carlos
AU - Lopez Alonso, Jose M
AU - Avila, Marc
ID - 6413
JF - International Journal of Multiphase Flow
SN - 03019322
TI - Phase-field simulation of core-annular pipe flow
VL - 117
ER -