@phdthesis{838,
abstract = {In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. },
author = {Rybar, Michal},
pages = {86},
publisher = {IST Austria},
title = {{(The exact security of) Message authentication codes}},
doi = {10.15479/AT:ISTA:th_828},
year = {2017},
}
@phdthesis{837,
abstract = {The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. },
author = {Xu, Haibing},
pages = {93},
publisher = {IST Austria},
title = {{Reactivation of the hippocampal cognitive map in goal-directed spatial tasks}},
doi = {10.15479/AT:ISTA:th_858},
year = {2017},
}
@inproceedings{1001,
abstract = {We present a computational approach for designing CurveUps, curvy shells that form from an initially flat state. They consist of small rigid tiles that are tightly held together by two pre-stretched elastic sheets attached to them. Our method allows the realization of smooth, doubly curved surfaces that can be fabricated as a flat piece. Once released, the restoring forces of the pre-stretched sheets support the object to take shape in 3D. CurveUps are structurally stable in their target configuration. The design process starts with a target surface. Our method generates a tile layout in 2D and optimizes the distribution, shape, and attachment areas of the tiles to obtain a configuration that is fabricable and in which the curved up state closely matches the target. Our approach is based on an efficient approximate model and a local optimization strategy for an otherwise intractable nonlinear optimization problem. We demonstrate the effectiveness of our approach for a wide range of shapes, all realized as physical prototypes.},
author = {Guseinov, Ruslan and Miguel, Eder and Bickel, Bernd},
location = {Los Angeles, CA, United States},
number = {4},
publisher = {ACM},
title = {{CurveUps: Shaping objects from flat plates with tension-actuated curvature}},
doi = {10.1145/3072959.3073709},
volume = {36},
year = {2017},
}
@article{6196,
abstract = {PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem.},
author = {Gazi, Peter and Pietrzak, Krzysztof Z and Rybar, Michal},
issn = {2519-173X},
journal = {IACR Transactions on Symmetric Cryptology},
number = {2},
pages = {145--161},
publisher = {Ruhr University Bochum},
title = {{The exact security of PMAC}},
doi = {10.13154/TOSC.V2016.I2.145-161},
volume = {2016},
year = {2017},
}
@article{1120,
abstract = {The existence of a self-localization transition in the polaron problem has been under an active debate ever since Landau suggested it 83 years ago. Here we reveal the self-localization transition for the rotational analogue of the polaron -- the angulon quasiparticle. We show that, unlike for the polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of the symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. The predicted effects can potentially be addressed in experiments on cold molecules trapped in superfluid helium droplets and ultracold quantum gases, as well as on electronic excitations in solids and Bose-Einstein condensates. },
author = {Li, Xiang and Seiringer, Robert and Lemeshko, Mikhail},
issn = {24699926},
journal = {Physical Review A},
number = {3},
publisher = {American Physical Society},
title = {{Angular self-localization of impurities rotating in a bosonic bath}},
doi = {10.1103/PhysRevA.95.033608},
volume = {95},
year = {2017},
}
@article{955,
abstract = {Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.},
author = {Friedlander, Tamar and Prizak, Roshan and Barton, Nicholas H and Tkacik, Gasper},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Evolution of new regulatory functions on biophysically realistic fitness landscapes}},
doi = {10.1038/s41467-017-00238-8},
volume = {8},
year = {2017},
}
@article{956,
abstract = {We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance.},
author = {Carlen, Eric and Maas, Jan},
issn = {00221236},
journal = {Journal of Functional Analysis},
number = {5},
pages = {1810 -- 1869},
publisher = {Academic Press},
title = {{Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance}},
doi = {10.1016/j.jfa.2017.05.003},
volume = {273},
year = {2017},
}
@article{959,
abstract = {In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.},
author = {De Martino, Daniele},
issn = {24700045},
journal = { Physical Review E Statistical Nonlinear and Soft Matter Physics },
number = {6},
pages = {062419},
publisher = {American Institute of Physics},
title = {{Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics}},
doi = {10.1103/PhysRevE.95.062419},
volume = {95},
year = {2017},
}
@article{960,
abstract = {The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context.},
author = {Hansen, Andi H and Düllberg, Christian F and Mieck, Christine and Loose, Martin and Hippenmeyer, Simon},
issn = {16625102},
journal = {Frontiers in Cellular Neuroscience},
publisher = {Frontiers Research Foundation},
title = {{Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks}},
doi = {10.3389/fncel.2017.00176},
volume = {11},
year = {2017},
}
@article{676,
abstract = {The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.},
author = {Krens, Gabriel and Veldhuis, Jim and Barone, Vanessa and Capek, Daniel and Maître, Jean-Léon and Brodland, Wayne and Heisenberg, Carl-Philipp J},
issn = {09501991},
journal = {Development},
number = {10},
pages = {1798 -- 1806},
publisher = {Company of Biologists},
title = {{Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation}},
doi = {10.1242/dev.144964},
volume = {144},
year = {2017},
}
@inproceedings{963,
abstract = {Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. },
author = {Avni, Guy and Guha, Shibashis and Kupferman, Orna},
issn = {18688969},
location = {Aalborg, Denmark},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Timed network games with clocks}},
doi = {10.4230/LIPIcs.MFCS.2017.37},
volume = {83},
year = {2017},
}
@article{988,
abstract = {The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement.},
author = {Nanda, Gaurav and Aguilera Servin, Juan L and Rakyta, Péter and Kormányos, Andor and Kleiner, Reinhold and Koelle, Dieter and Watanabe, Kazuo and Taniguchi, Takashi and Vandersypen, Lieven and Goswami, Srijit},
issn = {15306984},
journal = {Nano Letters},
number = {6},
pages = {3396 -- 3401},
publisher = {American Chemical Society},
title = {{Current-phase relation of ballistic graphene Josephson junctions}},
doi = {10.1021/acs.nanolett.7b00097},
volume = {17},
year = {2017},
}
@article{990,
abstract = {Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.},
author = {Sachdeva, Himani and Barton, Nicholas H},
issn = {00143820},
journal = {Evolution; International Journal of Organic Evolution},
number = {6},
pages = {1478 -- 1493 },
publisher = {Wiley-Blackwell},
title = {{Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow}},
doi = {10.1111/evo.13252},
volume = {71},
year = {2017},
}
@phdthesis{992,
abstract = {An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of
variables, a finite domain of labels, and a set of constraints, each constraint acting on
a subset of the variables. The goal is to find an assignment of labels to its variables
that satisfies all constraints (or decide whether one exists). If we allow more general
“soft” constraints, which come with (possibly infinite) costs of particular assignments,
we obtain instances from a richer class called Valued Constraint Satisfaction Problem
(VCSP). There the goal is to find an assignment with minimum total cost.
In this thesis, we focus (assuming that P
6
=
NP) on classifying computational com-
plexity of CSPs and VCSPs under certain restricting conditions. Two results are the core
content of the work. In one of them, we consider VCSPs parametrized by a constraint
language, that is the set of “soft” constraints allowed to form the instances, and finish
the complexity classification modulo (missing pieces of) complexity classification for
analogously parametrized CSP. The other result is a generalization of Edmonds’ perfect
matching algorithm. This generalization contributes to complexity classfications in two
ways. First, it gives a new (largest known) polynomial-time solvable class of Boolean
CSPs in which every variable may appear in at most two constraints and second, it
settles full classification of Boolean CSPs with planar drawing (again parametrized by a
constraint language).},
author = {Rolinek, Michal},
pages = {97},
publisher = {IST Austria},
title = {{Complexity of constraint satisfaction}},
doi = {10.15479/AT:ISTA:th_815},
year = {2017},
}
@article{993,
abstract = {In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development.},
author = {Levina (Martius), Anna and Priesemann, Viola},
issn = {20411723},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Subsampling scaling}},
doi = {10.1038/ncomms15140},
volume = {8},
year = {2017},
}
@article{994,
abstract = {The formation of vortices is usually considered to be the main mechanism of angular momentum disposal in superfluids. Recently, it was predicted that a superfluid can acquire angular momentum via an alternative, microscopic route -- namely, through interaction with rotating impurities, forming so-called `angulon quasiparticles' [Phys. Rev. Lett. 114, 203001 (2015)]. The angulon instabilities correspond to transfer of a small number of angular momentum quanta from the impurity to the superfluid, as opposed to vortex instabilities, where angular momentum is quantized in units of ℏ per atom. Furthermore, since conventional impurities (such as molecules) represent three-dimensional (3D) rotors, the angular momentum transferred is intrinsically 3D as well, as opposed to a merely planar rotation which is inherent to vortices. Herein we show that the angulon theory can explain the anomalous broadening of the spectroscopic lines observed for CH 3 and NH 3 molecules in superfluid helium nanodroplets, thereby providing a fingerprint of the emerging angulon instabilities in experiment.},
author = {Cherepanov, Igor and Lemeshko, Mikhail},
journal = {Physical Review Materials},
number = {3},
publisher = {American Physical Society},
title = {{Fingerprints of angulon instabilities in the spectra of matrix-isolated molecules}},
doi = {10.1103/PhysRevMaterials.1.035602},
volume = {1},
year = {2017},
}
@article{995,
abstract = {Recently it was shown that an impurity exchanging orbital angular momentum with a surrounding bath can be described in terms of the angulon quasiparticle [Phys. Rev. Lett. 118, 095301 (2017)]. The angulon consists of a quantum rotor dressed by a many-particle field of boson excitations, and can be formed out of, for example, a molecule or a nonspherical atom in superfluid helium, or out of an electron coupled to lattice phonons or a Bose condensate. Here we develop an approach to the angulon based on the path-integral formalism, which sets the ground for a systematic, perturbative treatment of the angulon problem. The resulting perturbation series can be interpreted in terms of Feynman diagrams, from which, in turn, one can derive a set of diagrammatic rules. These rules extend the machinery of the graphical theory of angular momentum - well known from theoretical atomic spectroscopy - to the case where an environment with an infinite number of degrees of freedom is present. In particular, we show that each diagram can be interpreted as a 'skeleton', which enforces angular momentum conservation, dressed by an additional many-body contribution. This connection between the angulon theory and the graphical theory of angular momentum is particularly important as it allows to systematically and substantially simplify the analytical representation of each diagram. In order to exemplify the technique, we calculate the 1- and 2-loop contributions to the angulon self-energy, the spectral function, and the quasiparticle weight. The diagrammatic theory we develop paves the way to investigate next-to-leading order quantities in a more compact way compared to the variational approaches.},
author = {Bighin, Giacomo and Lemeshko, Mikhail},
issn = {24699950},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {8},
publisher = {American Physical Society},
title = {{Diagrammatic approach to orbital quantum impurities interacting with a many-particle environment}},
doi = {10.1103/PhysRevB.96.085410},
volume = {96},
year = {2017},
}
@article{996,
abstract = {Iodine (I 2 ) molecules embedded in He nanodroplets are aligned by a 160 ps long laser pulse. The highest degree of alignment, occurring at the peak of the pulse and quantified by ⟨cos 2 θ 2D ⟩ , is measured as a function of the laser intensity. The results are well described by ⟨cos 2 θ 2D ⟩ calculated for a gas of isolated molecules each with an effective rotational constant of 0.6 times the gas-phase value, and at a temperature of 0.4 K. Theoretical analysis using the angulon quasiparticle to describe rotating molecules in superfluid helium rationalizes why the alignment mechanism is similar to that of isolated molecules with an effective rotational constant. A major advantage of molecules in He droplets is that their 0.4 K temperature leads to stronger alignment than what can generally be achieved for gas phase molecules -- here demonstrated by a direct comparison of the droplet results to measurements on a ∼ 1 K supersonic beam of isolated molecules. This point is further illustrated for more complex system by measurements on 1,4-diiodobenzene and 1,4-dibromobenzene. For all three molecular species studied the highest values of ⟨cos 2 θ 2D ⟩ achieved in He droplets exceed 0.96. },
author = {Shepperson, Benjamin and Chatterley, Adam and Søndergaard, Anders and Christiansen, Lars and Lemeshko, Mikhail and Stapelfeldt, Henrik},
issn = {00219606},
journal = {The Journal of Chemical Physics},
number = {1},
publisher = {AIP},
title = {{Strongly aligned molecules inside helium droplets in the near-adiabatic regime}},
doi = {10.1063/1.4983703},
volume = {147},
year = {2017},
}
@article{997,
abstract = {Recently it was shown that molecules rotating in superfluid helium can be described in terms of the angulon quasiparticles (Phys. Rev. Lett. 118, 095301 (2017)). Here we demonstrate that in the experimentally realized regime the angulon can be seen as a point charge on a 2-sphere interacting with a gauge field of a non-abelian magnetic monopole. Unlike in several other settings, the gauge fields of the angulon problem emerge in the real coordinate space, as opposed to the momentum space or some effective parameter space. Furthermore, we find a topological transition associated with making the monopole abelian, which takes place in the vicinity of the previously reported angulon instabilities. These results pave the way for studying topological phenomena in experiments on molecules trapped in superfluid helium nanodroplets, as well as on other realizations of orbital impurity problems.},
author = {Yakaboylu, Enderalp and Deuchert, Andreas and Lemeshko, Mikhail},
issn = {00319007},
journal = {APS Physics, Physical Review Letters},
number = {23},
publisher = {American Physiological Society},
title = {{Emergence of non-abelian magnetic monopoles in a quantum impurity problem}},
doi = {10.1103/PhysRevLett.119.235301},
volume = {119},
year = {2017},
}
@inproceedings{998,
abstract = {A major open problem on the road to artificial intelligence is the development of incrementally learning systems that learn about more and more concepts over time from a stream of data. In this work, we introduce a new training strategy, iCaRL, that allows learning in such a class-incremental way: only the training data for a small number of classes has to be present at the same time and new classes can be added progressively. iCaRL learns strong classifiers and a data representation simultaneously. This distinguishes it from earlier works that were fundamentally limited to fixed data representations and therefore incompatible with deep learning architectures. We show by experiments on CIFAR-100 and ImageNet ILSVRC 2012 data that iCaRL can learn many classes incrementally over a long period of time where other strategies quickly fail. },
author = {Rebuffi, Sylvestre Alvise and Kolesnikov, Alexander and Sperl, Georg and Lampert, Christoph},
isbn = {978-153860457-1},
location = {Honolulu, HA, United States},
pages = {5533 -- 5542},
publisher = {IEEE},
title = {{iCaRL: Incremental classifier and representation learning}},
doi = {10.1109/CVPR.2017.587},
volume = {2017},
year = {2017},
}
@inproceedings{999,
abstract = {In multi-task learning, a learner is given a collection of prediction tasks and needs to solve all of them. In contrast to previous work, which required that annotated training data must be available for all tasks, we consider a new setting, in which for some tasks, potentially most of them, only unlabeled training data is provided. Consequently, to solve all tasks, information must be transferred between tasks with labels and tasks without labels. Focusing on an instance-based transfer method we analyze two variants of this setting: when the set of labeled tasks is fixed, and when it can be actively selected by the learner. We state and prove a generalization bound that covers both scenarios and derive from it an algorithm for making the choice of labeled tasks (in the active case) and for transferring information between the tasks in a principled way. We also illustrate the effectiveness of the algorithm on synthetic and real data. },
author = {Pentina, Anastasia and Lampert, Christoph},
issn = {978-151085514-4},
location = {Sydney, Australia},
pages = {2807 -- 2816},
publisher = {Omnipress},
title = {{Multi-task learning with labeled and unlabeled tasks}},
volume = {70},
year = {2017},
}
@phdthesis{961,
abstract = {Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation.},
author = {Barone, Vanessa},
pages = {109},
publisher = {IST Austria},
title = {{Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation}},
doi = {10.15479/AT:ISTA:th_825},
year = {2017},
}
@article{739,
abstract = {We study the norm approximation to the Schrödinger dynamics of N bosons in with an interaction potential of the form . Assuming that in the initial state the particles outside of the condensate form a quasi-free state with finite kinetic energy, we show that in the large N limit, the fluctuations around the condensate can be effectively described using Bogoliubov approximation for all . The range of β is expected to be optimal for this large class of initial states.},
author = {Nam, Phan and Napiórkowski, Marcin M},
issn = {00217824},
journal = {Journal de Mathématiques Pures et Appliquées},
number = {5},
pages = {662 -- 688},
publisher = {Elsevier},
title = {{A note on the validity of Bogoliubov correction to mean field dynamics}},
doi = {10.1016/j.matpur.2017.05.013},
volume = {108},
year = {2017},
}
@article{740,
abstract = {Developments in bioengineering and molecular biology have introduced a palette of genetically encoded probes for identification of specific cell populations in electron microscopy. These probes can be targeted to distinct cellular compartments, rendering them electron dense through a subsequent chemical reaction. These electron densities strongly increase the local contrast in samples prepared for electron microscopy, allowing three major advances in ultrastructural mapping of circuits: genetic identification of circuit components, targeted imaging of regions of interest and automated analysis of the tagged circuits. Together, the gains from these advances can decrease the time required for the analysis of targeted circuit motifs by over two orders of magnitude. These genetic encoded tags for electron microscopy promise to simplify the analysis of circuit motifs and become a central tool for structure‐function studies of synaptic connections in the brain. We review the current state‐of‐the‐art with an emphasis on connectomics, the quantitative analysis of neuronal structures and motifs.},
author = {Shigemoto, Ryuichi and Jösch, Maximilian A},
issn = {17597684},
journal = {WIREs Developmental Biology},
number = {6},
publisher = {Wiley-Blackwell},
title = {{The genetic encoded toolbox for electron microscopy and connectomics}},
doi = {10.1002/wdev.288},
volume = {6},
year = {2017},
}
@article{736,
abstract = {The neurotransmitter receptor subtype, number, density, and distribution relative to the location of transmitter release sites are key determinants of signal transmission. AMPA-type ionotropic glutamate receptors (AMPARs) containing GluA3 and GluA4 subunits are prominently expressed in subsets of neurons capable of firing action potentials at high frequencies, such as auditory relay neurons. The auditory nerve (AN) forms glutamatergic synapses on two types of relay neurons, bushy cells (BCs) and fusiform cells (FCs) of the cochlear nucleus. AN-BC and AN-FC synapses have distinct kinetics; thus, we investigated whether the number, density, and localization of GluA3 and GluA4 subunits in these synapses are differentially organized using quantitative freeze-fracture replica immunogold labeling. We identify a positive correlation between the number of AMPARs and the size of AN-BC and AN-FC synapses. Both types of AN synapses have similar numbers of AMPARs; however, the AN-BC have a higher density of AMPARs than AN-FC synapses, because the AN-BC synapses are smaller. A higher number and density of GluA3 subunits are observed at AN-BC synapses, whereas a higher number and density of GluA4 subunits are observed at AN-FC synapses. The intrasynaptic distribution of immunogold labeling revealed that AMPAR subunits, particularly GluA3, are concentrated at the center of the AN-BC synapses. The central distribution of AMPARs is absent in GluA3-knockout mice, and gold particles are evenly distributed along the postsynaptic density. GluA4 gold labeling was homogenously distributed along both synapse types. Thus, GluA3 and GluA4 subunits are distributed at AN synapses in a target-cell-dependent manner.},
author = {Rubio, María and Matsui, Ko and Fukazawa, Yugo and Kamasawa, Naomi and Harada, Harumi and Itakura, Makoto and Molnár, Elek and Abe, Manabu and Sakimura, Kenji and Shigemoto, Ryuichi},
issn = {18632653},
journal = {Brain Structure and Function},
number = {8},
pages = {3375 -- 3393},
publisher = {Springer},
title = {{The number and distribution of AMPA receptor channels containing fast kinetic GluA3 and GluA4 subunits at auditory nerve synapses depend on the target cells}},
doi = {10.1007/s00429-017-1408-0},
volume = {222},
year = {2017},
}
@article{7360,
abstract = {Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.},
author = {Smole, Anže and Lainšček, Duško and Bezeljak, Urban and Horvat, Simon and Jerala, Roman},
issn = {1525-0016},
journal = {Molecular Therapy},
number = {1},
pages = {102--119},
publisher = {Elsevier},
title = {{A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation}},
doi = {10.1016/j.ymthe.2016.10.005},
volume = {25},
year = {2017},
}
@article{747,
abstract = {Bradykinin (BK), a component of the kallikrein-kininogen-kinin system exerts multiple effects via B1 and B2 receptor activation. In the cardiovascular system, bradykinin has cardioprotective and vasodilator properties. We investigated the effect of BK on cardiac-projecting neurons of nucleus ambiguus, a key site for the parasympathetic cardiac regulation. BK produced a dose-dependent increase in cytosolic Ca2+ concentration. Pretreatment with HOE140, a B2 receptor antagonist, but not with R715, a B1 receptor antagonist, abolished the response to BK. A selective B2 receptor agonist, but not a B1 receptor agonist, elicited an increase in cytosolic Ca2+ similarly to BK. Inhibition of N-type voltage-gated Ca2+ channels with ω-conotoxin GVIA had no effect on the Ca2+ signal produced by BK, while pretreatment with ω-conotoxin MVIIC, a blocker of P/Q-type of Ca2+ channels, significantly diminished the effect of BK. Pretreatment with xestospongin C and 2-aminoethoxydiphenyl borate, antagonists of inositol 1,4,5-trisphosphate receptors, abolished the response to BK. Inhibition of ryanodine receptors reduced the BK-induced Ca2+ increase, while disruption of lysosomal Ca2+ stores with bafilomycin A1 did not affect the response. BK produced a dose-dependent depolarization of nucleus ambiguus neurons, which was prevented by the B2 receptor antagonist. In vivo studies indicate that microinjection of BK into nucleus ambiguus elicited bradycardia in conscious rats via B2 receptors. In summary, in cardiac vagal neurons of nucleus ambiguus, BK activates B2 receptors promoting Ca2+ influx and Ca2+ release from endoplasmic reticulum, and membrane depolarization; these effects are translated in vivo by bradycardia.},
author = {Brǎiloiu, Eugen and Mcguire, Matthew and Shuler, Shadaria and Deliu, Elena and Barr, Jeffrey and Abood, Mary and Brailoiu, Gabriela},
issn = {03064522},
journal = {Neuroscience},
pages = {23 -- 32},
publisher = {Elsevier},
title = {{Modulation of cardiac vagal tone by bradykinin acting on nucleus ambiguus}},
doi = {10.1016/j.neuroscience.2017.09.034},
volume = {365},
year = {2017},
}
@article{744,
abstract = {In evolutionary game theory interactions between individuals are often assumed obligatory. However, in many real-life situations, individuals can decide to opt out of an interaction depending on the information they have about the opponent. We consider a simple evolutionary game theoretic model to study such a scenario, where at each encounter between two individuals the type of the opponent (cooperator/defector) is known with some probability, and where each individual either accepts or opts out of the interaction. If the type of the opponent is unknown, a trustful individual accepts the interaction, whereas a suspicious individual opts out of the interaction. If either of the two individuals opt out both individuals remain without an interaction. We show that in the prisoners dilemma optional interactions along with suspicious behaviour facilitates the emergence of trustful cooperation.},
author = {Priklopil, Tadeas and Chatterjee, Krishnendu and Nowak, Martin},
issn = {00225193},
journal = { Journal of Theoretical Biology},
pages = {64 -- 72},
publisher = {Elsevier},
title = {{Optional interactions and suspicious behaviour facilitates trustful cooperation in prisoners dilemma}},
doi = {10.1016/j.jtbi.2017.08.025},
volume = {433},
year = {2017},
}
@article{745,
abstract = {Fluid flows in nature and applications are frequently subject to periodic velocity modulations. Surprisingly, even for the generic case of flow through a straight pipe, there is little consensus regarding the influence of pulsation on the transition threshold to turbulence: while most studies predict a monotonically increasing threshold with pulsation frequency (i.e. Womersley number, ), others observe a decreasing threshold for identical parameters and only observe an increasing threshold at low . In the present study we apply recent advances in the understanding of transition in steady shear flows to pulsating pipe flow. For moderate pulsation amplitudes we find that the first instability encountered is subcritical (i.e. requiring finite amplitude disturbances) and gives rise to localized patches of turbulence ('puffs') analogous to steady pipe flow. By monitoring the impact of pulsation on the lifetime of turbulence we map the onset of turbulence in parameter space. Transition in pulsatile flow can be separated into three regimes. At small Womersley numbers the dynamics is dominated by the decay turbulence suffers during the slower part of the cycle and hence transition is delayed significantly. As shown in this regime thresholds closely agree with estimates based on a quasi-steady flow assumption only taking puff decay rates into account. The transition point predicted in the zero limit equals to the critical point for steady pipe flow offset by the oscillation Reynolds number (i.e. the dimensionless oscillation amplitude). In the high frequency limit on the other hand, puff lifetimes are identical to those in steady pipe flow and hence the transition threshold appears to be unaffected by flow pulsation. In the intermediate frequency regime the transition threshold sharply drops (with increasing ) from the decay dominated (quasi-steady) threshold to the steady pipe flow level.},
author = {Xu, Duo and Warnecke, Sascha and Song, Baofang and Ma, Xingyu and Hof, Björn},
issn = {00221120},
journal = {Journal of Fluid Mechanics},
pages = {418 -- 432},
publisher = {Cambridge University Press},
title = {{Transition to turbulence in pulsating pipe flow}},
doi = {10.1017/jfm.2017.620},
volume = {831},
year = {2017},
}
@article{746,
abstract = {Metabotropic glutamate receptor subtype 5 (mGluR5) is crucially implicated in the pathophysiology of Fragile X Syndrome (FXS); however, its dysfunction at the sub-cellular level, and related synaptic and cognitive phenotypes are unexplored. Here, we probed the consequences of mGluR5/Homer scaffold disruption for mGluR5 cell-surface mobility, synaptic N-methyl-D-Aspartate receptor (NMDAR) function, and behavioral phenotypes in the second-generation Fmr1 knockout (KO) mouse. Using single-molecule tracking, we found that mGluR5 was significantly more mobile at synapses in hippocampal Fmr1 KO neurons, causing an increased synaptic surface co-clustering of mGluR5 and NMDAR. This correlated with a reduced amplitude of synaptic NMDAR currents, a lack of their mGluR5-Activated long-Term depression, and NMDAR/hippocampus dependent cognitive deficits. These synaptic and behavioral phenomena were reversed by knocking down Homer1a in Fmr1 KO mice. Our study provides a mechanistic link between changes of mGluR5 dynamics and pathological phenotypes of FXS, unveiling novel targets for mGluR5-based therapeutics.},
author = {Aloisi, Elisabetta and Le Corf, Katy and Dupuis, Julien and Zhang, Pei and Ginger, Melanie and Labrousse, Virginie and Spatuzza, Michela and Georg Haberl, Matthias and Costa, Lara and Shigemoto, Ryuichi and Tappe Theodor, Anke and Drago, Fillippo and Vincenzo Piazza, Pier and Mulle, Christophe and Groc, Laurent and Ciranna, Lucia and Catania, Maria and Frick, Andreas},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Altered surface mGluR5 dynamics provoke synaptic NMDAR dysfunction and cognitive defects in Fmr1 knockout mice}},
doi = {10.1038/s41467-017-01191-2},
volume = {8},
year = {2017},
}
@article{741,
abstract = {We prove that a system of N fermions interacting with an additional particle via point interactions is stable if the ratio of the mass of the additional particle to the one of the fermions is larger than some critical m*. The value of m* is independent of N and turns out to be less than 1. This fact has important implications for the stability of the unitary Fermi gas. We also characterize the domain of the Hamiltonian of this model, and establish the validity of the Tan relations for all wave functions in the domain.},
author = {Moser, Thomas and Seiringer, Robert},
issn = {00103616},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {329 -- 355},
publisher = {Springer},
title = {{Stability of a fermionic N+1 particle system with point interactions}},
doi = {10.1007/s00220-017-2980-0},
volume = {356},
year = {2017},
}
@article{749,
abstract = {Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, Syt7 is strongly expressed in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. To resolve this apparent contradiction, we examined the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment, and facilitation. In combination, these three effects ensure efficient transmitter release during high-frequency activity and guarantee frequency independence of inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency of high-frequency inhibitory synaptic transmission},
author = {Chen, Chong and Satterfield, Rachel and Young, Samuel and Jonas, Peter M},
issn = {22111247},
journal = {Cell Reports},
number = {8},
pages = {2082 -- 2089},
publisher = {Cell Press},
title = {{Triple function of Synaptotagmin 7 ensures efficiency of high-frequency transmission at central GABAergic synapses}},
doi = {10.1016/j.celrep.2017.10.122},
volume = {21},
year = {2017},
}
@article{751,
abstract = {The basement membrane (BM) is a thin layer of extracellular matrix (ECM) beneath nearly all epithelial cell types that is critical for cellular and tissue function. It is composed of numerous components conserved among all bilaterians [1]; however, it is unknown how all of these components are generated and subsequently constructed to form a fully mature BM in the living animal. Although BM formation is thought to simply involve a process of self-assembly [2], this concept suffers from a number of logistical issues when considering its construction in vivo. First, incorporation of BM components appears to be hierarchical [3-5], yet it is unclear whether their production during embryogenesis must also be regulated in a temporal fashion. Second, many BM proteins are produced not only by the cells residing on the BM but also by surrounding cell types [6-9], and it is unclear how large, possibly insoluble protein complexes [10] are delivered into the matrix. Here we exploit our ability to live image and genetically dissect de novo BM formation during Drosophila development. This reveals that there is a temporal hierarchy of BM protein production that is essential for proper component incorporation. Furthermore, we show that BM components require secretion by migrating macrophages (hemocytes) during their developmental dispersal, which is critical for embryogenesis. Indeed, hemocyte migration is essential to deliver a subset of ECM components evenly throughout the embryo. This reveals that de novo BM construction requires a combination of both production and distribution logistics allowing for the timely delivery of core components.},
author = {Matsubayashi, Yutaka and Louani, Adam and Dragu, Anca and Sanchez Sanchez, Besaiz and Serna Morales, Eduardo and Yolland, Lawrence and György, Attila and Vizcay, Gema and Fleck, Roland and Heddleston, John and Chew, Teng and Siekhaus, Daria E and Stramer, Brian},
issn = {09609822},
journal = {Current Biology},
number = {22},
pages = {3526 -- 3534e.4},
publisher = {Cell Press},
title = {{A moving source of matrix components is essential for De Novo basement membrane formation}},
doi = {10.1016/j.cub.2017.10.001},
volume = {27},
year = {2017},
}
@inproceedings{787,
abstract = {Population protocols are a popular model of distributed computing, in which randomly-interacting agents with little computational power cooperate to jointly perform computational tasks. Inspired by developments in molecular computation, and in particular DNA computing, recent algorithmic work has focused on the complexity of solving simple yet fundamental tasks in the population model, such as leader election (which requires convergence to a single agent in a special "leader" state), and majority (in which agents must converge to a decision as to which of two possible initial states had higher initial count). Known results point towards an inherent trade-off between the time complexity of such algorithms, and the space complexity, i.e. size of the memory available to each agent. In this paper, we explore this trade-off and provide new upper and lower bounds for majority and leader election. First, we prove a unified lower bound, which relates the space available per node with the time complexity achievable by a protocol: for instance, our result implies that any protocol solving either of these tasks for n agents using O(log log n) states must take (n=polylogn) expected time. This is the first result to characterize time complexity for protocols which employ super-constant number of states per node, and proves that fast, poly-logarithmic running times require protocols to have relatively large space costs. On the positive side, we give algorithms showing that fast, poly-logarithmic convergence time can be achieved using O(log2 n) space per node, in the case of both tasks. Overall, our results highlight a time complexity separation between O(log log n) and (log2 n) state space size for both majority and leader election in population protocols, and introduce new techniques, which should be applicable more broadly.},
author = {Alistarh, Dan-Adrian and Aspnes, James and Eisenstat, David and Rivest, Ronald and Gelashvili, Rati},
pages = {2560 -- 2579},
publisher = {SIAM},
title = {{Time-space trade-offs in population protocols}},
doi = {doi.org/10.1137/1.9781611974782.169},
year = {2017},
}
@inproceedings{788,
abstract = {In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed with an appropriate error model in mind. Here we consider the model of chemical reaction networks that preserve molecular count (population protocols), and ask whether computation can be made robust to a natural model of unintended “leak” reactions. Our definition of leak is motivated by both the particular spurious behavior seen when implementing chemical reaction networks with DNA strand displacement cascades, as well as the unavoidable side reactions in any implementation due to the basic laws of chemistry. We develop a new “Robust Detection” algorithm for the problem of fast (logarithmic time) single molecule detection, and prove that it is robust to this general model of leaks. Besides potential applications in single molecule detection, the error-correction ideas developed here might enable a new class of robust-by-design chemical algorithms. Our analysis is based on a non-standard hybrid argument, combining ideas from discrete analysis of population protocols with classic Markov chain techniques.},
author = {Alistarh, Dan-Adrian and Dudek, Bartłomiej and Kosowski, Adrian and Soloveichik, David and Uznański, Przemysław},
pages = {155 -- 171},
publisher = {Springer},
title = {{Robust detection in leak-prone population protocols}},
doi = {10.1007/978-3-319-66799-7_11},
volume = {10467 LNCS},
year = {2017},
}
@inproceedings{791,
abstract = {Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between "heavily loaded" balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance.},
author = {Alistarh, Dan-Adrian and Kopinsky, Justin and Li, Jerry and Nadiradze, Giorgi},
booktitle = {Proceedings of the ACM Symposium on Principles of Distributed Computing},
isbn = {978-145034992-5},
location = {Washington, WA, USA},
pages = {283 -- 292},
publisher = {ACM},
title = {{The power of choice in priority scheduling}},
doi = {10.1145/3087801.3087810},
volume = {Part F129314},
year = {2017},
}
@article{792,
abstract = {The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics.},
author = {Budanur, Nazmi B and Short, Kimberly and Farazmand, Mohammad and Willis, Ashley and Cvitanović, Predrag},
issn = {00221120},
journal = {Journal of Fluid Mechanics},
pages = {274 -- 301},
publisher = {Cambridge University Press},
title = {{Relative periodic orbits form the backbone of turbulent pipe flow}},
doi = {10.1017/jfm.2017.699},
volume = {833},
year = {2017},
}
@article{793,
abstract = {Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c > 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). },
author = {Fulek, Radoslav and Mojarrad, Hossein and Naszódi, Márton and Solymosi, József and Stich, Sebastian and Szedlák, May},
issn = {09257721},
journal = {Computational Geometry: Theory and Applications},
pages = {28 -- 31},
publisher = {Elsevier},
title = {{On the existence of ordinary triangles}},
doi = {10.1016/j.comgeo.2017.07.002},
volume = {66},
year = {2017},
}
@article{8016,
abstract = {Long-term modifications of neuronal connections are critical for reliable memory storage in the brain. However, their locus of expression—pre- or postsynaptic—is highly variable. Here we introduce a theoretical framework in which long-term plasticity performs an optimization of the postsynaptic response statistics toward a given mean with minimal variance. Consequently, the state of the synapse at the time of plasticity induction determines the ratio of pre- and postsynaptic modifications. Our theory explains the experimentally observed expression loci of the hippocampal and neocortical synaptic potentiation studies we examined. Moreover, the theory predicts presynaptic expression of long-term depression, consistent with experimental observations. At inhibitory synapses, the theory suggests a statistically efficient excitatory-inhibitory balance in which changes in inhibitory postsynaptic response statistics specifically target the mean excitation. Our results provide a unifying theory for understanding the expression mechanisms and functions of long-term synaptic transmission plasticity.},
author = {Costa, Rui Ponte and Padamsey, Zahid and D’Amour, James A. and Emptage, Nigel J. and Froemke, Robert C. and Vogels, Tim P},
issn = {0896-6273},
journal = {Neuron},
number = {1},
pages = {177--189.e7},
publisher = {Elsevier},
title = {{Synaptic transmission optimization predicts expression loci of long-term plasticity}},
doi = {10.1016/j.neuron.2017.09.021},
volume = {96},
year = {2017},
}
@article{8018,
abstract = {Nervous systems use excitatory cell assemblies to encode and represent sensory percepts. Similarly, synaptically connected cell assemblies or "engrams" are thought to represent memories of past experience. Multiple lines of recent evidence indicate that brain systems create and use inhibitory replicas of excitatory representations for important cognitive functions. Such matched "inhibitory engrams" can form through homeostatic potentiation of inhibition onto postsynaptic cells that show increased levels of excitation. Inhibitory engrams can reduce behavioral responses to familiar stimuli, thereby resulting in behavioral habituation. In addition, by preventing inappropriate activation of excitatory memory engrams, inhibitory engrams can make memories quiescent, stored in a latent form that is available for context-relevant activation. In neural networks with balanced excitatory and inhibitory engrams, the release of innate responses and recall of associative memories can occur through focused disinhibition. Understanding mechanisms that regulate the formation and expression of inhibitory engrams in vivo may help not only to explain key features of cognition but also to provide insight into transdiagnostic traits associated with psychiatric conditions such as autism, schizophrenia, and posttraumatic stress disorder. },
author = {Barron, Helen C. and Vogels, Tim P and Behrens, Timothy E. and Ramaswami, Mani},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences},
number = {26},
pages = {6666--6674},
publisher = {Proceedings of the National Academy of Sciences},
title = {{Inhibitory engrams in perception and memory}},
doi = {10.1073/pnas.1701812114},
volume = {114},
year = {2017},
}
@article{803,
abstract = {Eukaryotic cells store their chromosomes in a single nucleus. This is important to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei) are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble their nucleus and release individualized chromosomes for segregation. How numerous chromosomes subsequently reform a single nucleus has remained unclear. Using image-based screening of human cells, we identified barrier-to-autointegration factor (BAF) as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear assembly does not require BAF?s association with inner nuclear membrane proteins but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging and in vitro reconstitution showed that BAF enriches around the mitotic chromosome ensemble to induce a densely cross-bridged chromatin layer that is mechanically stiff and limits membranes to the surface. Our study reveals that BAF-mediated changes in chromosome mechanics underlie nuclear assembly with broad implications for proper genome function.},
author = {Samwer, Matthias and Schneider, Maximilian and Hoefler, Rudolf and Schmalhorst, Philipp S and Jude, Julian and Zuber, Johannes and Gerlic, Daniel},
issn = {00928674},
journal = {Cell},
number = {5},
pages = {956 -- 972},
publisher = {Cell Press},
title = {{DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes}},
doi = {10.1016/j.cell.2017.07.038},
volume = {170},
year = {2017},
}
@article{800,
abstract = {Gamma oscillations (30–150 Hz) in neuronal networks are associated with the processing and recall of information. We measured local field potentials in the dentate gyrus of freely moving mice and found that gamma activity occurs in bursts, which are highly heterogeneous in their spatial extensions, ranging from focal to global coherent events. Synaptic communication among perisomatic-inhibitory interneurons (PIIs) is thought to play an important role in the generation of hippocampal gamma patterns. However, how neuronal circuits can generate synchronous oscillations at different spatial scales is unknown. We analyzed paired recordings in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron synapses is distance dependent. Synaptic strength declines whereas the duration of inhibitory signals increases with axonal distance among interconnected PIIs. Using neuronal network modeling, we show that distance-dependent inhibition generates multiple highly synchronous focal gamma bursts allowing the network to process complex inputs in parallel in flexibly organized neuronal centers.},
author = {Strüber, Michael and Sauer, Jonas and Jonas, Peter M and Bartos, Marlene},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Nature Publishing Group},
title = {{Distance-dependent inhibition facilitates focality of gamma oscillations in the dentate gyrus}},
doi = {10.1038/s41467-017-00936-3},
volume = {8},
year = {2017},
}
@inproceedings{8129,
abstract = {Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function.
Overall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts.},
author = {Costa, Rui Ponte and Assael, Yannis M. and Shillingford, Brendan and Freitas, Nando de and Vogels, Tim P},
booktitle = {Advances in Neural Information Processing Systems},
issn = {10495258},
location = {Long Beach, CA, United States},
pages = {272--283},
publisher = {Neural Information Processing Systems Foundation},
title = {{Cortical microcircuits as gated-recurrent neural networks}},
volume = {30},
year = {2017},
}
@phdthesis{820,
abstract = {The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.
In Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.
In Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.
To start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.},
author = {Jesse, Fabienne},
pages = {87},
publisher = {IST Austria},
title = {{The lac operon in the wild}},
doi = {10.15479/AT:ISTA:th_857},
year = {2017},
}
@phdthesis{819,
abstract = {Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. },
author = {Pull, Christopher},
pages = {122},
publisher = {IST Austria},
title = {{Disease defence in garden ants}},
doi = {10.15479/AT:ISTA:th_861},
year = {2017},
}
@article{732,
abstract = {Background: Social insects form densely crowded societies in environments with high pathogen loads, but have evolved collective defences that mitigate the impact of disease. However, colony-founding queens lack this protection and suffer high rates of mortality. The impact of pathogens may be exacerbated in species where queens found colonies together, as healthy individuals may contract pathogens from infectious co-founders. Therefore, we tested whether ant queens avoid founding colonies with pathogen-exposed conspecifics and how they might limit disease transmission from infectious individuals. Results: Using Lasius Niger queens and a naturally infecting fungal pathogen Metarhizium brunneum, we observed that queens were equally likely to found colonies with another pathogen-exposed or sham-treated queen. However, when one queen died, the surviving individual performed biting, burial and removal of the corpse. These undertaking behaviours were performed prophylactically, i.e. targeted equally towards non-infected and infected corpses, as well as carried out before infected corpses became infectious. Biting and burial reduced the risk of the queens contracting and dying from disease from an infectious corpse of a dead co-foundress. Conclusions: We show that co-founding ant queens express undertaking behaviours that, in mature colonies, are performed exclusively by workers. Such infection avoidance behaviours act before the queens can contract the disease and will therefore improve the overall chance of colony founding success in ant queens.},
author = {Pull, Christopher and Cremer, Sylvia},
issn = {14712148},
journal = {BMC Evolutionary Biology},
number = {1},
publisher = {BioMed Central},
title = {{Co-founding ant queens prevent disease by performing prophylactic undertaking behaviour}},
doi = {10.1186/s12862-017-1062-4},
volume = {17},
year = {2017},
}
@article{734,
abstract = {Social insect societies are long-standing models for understanding social behaviour and evolution. Unlike other advanced biological societies (such as the multicellular body), the component parts of social insect societies can be easily deconstructed and manipulated. Recent methodological and theoretical innovations have exploited this trait to address an expanded range of biological questions. We illustrate the broadening range of biological insight coming from social insect biology with four examples. These new frontiers promote open-minded, interdisciplinary exploration of one of the richest and most complex of biological phenomena: sociality.},
author = {Kennedy, Patrick and Baron, Gemma and Qiu, Bitao and Freitak, Dalial and Helantera, Heikki and Hunt, Edmund and Manfredini, Fabio and O'Shea Wheller, Thomas and Patalano, Solenn and Pull, Christopher and Sasaki, Takao and Taylor, Daisy and Wyatt, Christopher and Sumner, Seirian},
issn = {01695347},
journal = {Trends in Ecology and Evolution},
number = {11},
pages = {861 -- 872},
publisher = {Cell Press},
title = {{Deconstructing superorganisms and societies to address big questions in biology}},
doi = {10.1016/j.tree.2017.08.004},
volume = {32},
year = {2017},
}
@inproceedings{833,
abstract = {We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams.},
author = {Heiss, Teresa and Wagner, Hubert},
editor = {Felsberg, Michael and Heyden, Anders and Krüger, Norbert},
issn = {03029743},
location = {Ystad, Sweden},
pages = {397 -- 409},
publisher = {Springer},
title = {{Streaming algorithm for Euler characteristic curves of multidimensional images}},
doi = {10.1007/978-3-319-64689-3_32},
volume = {10424},
year = {2017},
}
@article{834,
abstract = {Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition.},
author = {Serbyn, Maksym and Zlatko, Papic and Abanin, Dmitry},
issn = {24699950},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {10},
publisher = {American Physical Society},
title = {{Thouless energy and multifractality across the many-body localization transition}},
doi = {10.1103/PhysRevB.96.104201},
volume = {96},
year = {2017},
}
@article{835,
abstract = {An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined.},
author = {Makhijani, Kalpana and Alexander, Brandy and Rao, Deepti and Petraki, Sophia and Herboso, Leire and Kukar, Katelyn and Batool, Itrat and Wachner, Stephanie and Gold, Katrina and Wong, Corinna and O'Connor, Michael and Brückner, Katja},
issn = {20411723},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons}},
doi = {10.1038/ncomms15990},
volume = {8},
year = {2017},
}