@misc{9808, abstract = {Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).}, author = {Higareda Almaraz, Juan and Karbiener, Michael and Giroud, Maude and Pauler, Florian and Gerhalter, Teresa and Herzig, Stephan and Scheideler, Marcel}, publisher = {Springer Nature}, title = {{Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes}}, doi = {10.6084/m9.figshare.7295369.v1}, year = {2018}, } @inproceedings{193, abstract = {We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.}, author = {Alwen, Joel F and Gazi, Peter and Kamath Hosdurg, Chethan and Klein, Karen and Osang, Georg F and Pietrzak, Krzysztof Z and Reyzin, Lenoid and Rolinek, Michal and Rybar, Michal}, booktitle = {Proceedings of the 2018 on Asia Conference on Computer and Communication Security}, location = {Incheon, Republic of Korea}, pages = {51 -- 65}, publisher = {ACM}, title = {{On the memory hardness of data independent password hashing functions}}, doi = {10.1145/3196494.3196534}, year = {2018}, } @inproceedings{300, abstract = {We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems.}, author = {Micciancio, Daniele and Walter, Michael}, location = {Tel Aviv, Israel}, pages = {3 -- 28}, publisher = {Springer}, title = {{On the bit security of cryptographic primitives}}, doi = {10.1007/978-3-319-78381-9_1}, volume = {10820}, year = {2018}, } @article{312, abstract = {Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice.}, author = {Edelsbrunner, Herbert and Iglesias Ham, Mabel}, issn = {08954801}, journal = {SIAM J Discrete Math}, number = {1}, pages = {750 -- 782}, publisher = {Society for Industrial and Applied Mathematics }, title = {{On the optimality of the FCC lattice for soft sphere packing}}, doi = {10.1137/16M1097201}, volume = {32}, year = {2018}, } @article{409, abstract = {We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons.}, author = {Akopyan, Arseniy}, issn = {1631073X}, journal = {Comptes Rendus Mathematique}, number = {4}, pages = {412--414}, publisher = {Elsevier}, title = {{On the number of non-hexagons in a planar tiling}}, doi = {10.1016/j.crma.2018.03.005}, volume = {356}, year = {2018}, } @article{419, abstract = {Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.}, author = {Hilbe, Christian and Chatterjee, Krishnendu and Nowak, Martin}, journal = {Nature Human Behaviour}, pages = {469–477}, publisher = {Nature Publishing Group}, title = {{Partners and rivals in direct reciprocity}}, doi = {10.1038/s41562-018-0320-9}, volume = {2}, year = {2018}, } @inproceedings{78, abstract = {We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.}, author = {Bakhirkin, Alexey and Ferrere, Thomas and Nickovic, Dejan and Maler, Oded and Asarin, Eugene}, isbn = {978-3-030-00150-6}, location = {Bejing, China}, pages = {215 -- 232}, publisher = {Springer}, title = {{Online timed pattern matching using automata}}, doi = {10.1007/978-3-030-00151-3_13}, volume = {11022}, year = {2018}, } @article{317, abstract = {We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack.}, author = {Brauns, Matthias and Amitonov, Sergey and Spruijtenburg, Paul and Zwanenburg, Floris}, journal = {Scientific Reports}, number = {1}, publisher = {Nature Publishing Group}, title = {{Palladium gates for reproducible quantum dots in silicon}}, doi = {10.1038/s41598-018-24004-y}, volume = {8}, year = {2018}, } @article{194, abstract = {Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.}, author = {Liutkeviciute, Zita and Gil Mansilla, Esther and Eder, Thomas and Casillas Perez, Barbara E and Giulia Di Giglio, Maria and Muratspahić, Edin and Grebien, Florian and Rattei, Thomas and Muttenthaler, Markus and Cremer, Sylvia and Gruber, Christian}, issn = {08926638}, journal = {The FASEB Journal}, number = {12}, pages = {6808--6821}, publisher = {FASEB}, title = {{Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity}}, doi = {10.1096/fj.201800443}, volume = {32}, year = {2018}, } @article{159, abstract = {L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control.}, author = {Fehrentz, Timm and Huber, Florian and Hartrampf, Nina and Bruegmann, Tobias and Frank, James and Fine, Nicholas and Malan, Daniela and Danzl, Johann G and Tikhonov, Denis and Sumser, Maritn and Sasse, Philipp and Hodson, David and Zhorov, Boris and Klocker, Nikolaj and Trauner, Dirk}, journal = {Nature Chemical Biology}, number = {8}, pages = {764 -- 767}, publisher = {Nature Publishing Group}, title = {{Optical control of L-type Ca2+ channels using a diltiazem photoswitch}}, doi = {10.1038/s41589-018-0090-8}, volume = {14}, year = {2018}, } @inproceedings{79, abstract = {Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol.}, author = {Arming, Sebastian and Bartocci, Ezio and Chatterjee, Krishnendu and Katoen, Joost P and Sokolova, Ana}, location = {Beijing, China}, pages = {53--70}, publisher = {Springer}, title = {{Parameter-independent strategies for pMDPs via POMDPs}}, doi = {10.1007/978-3-319-99154-2_4}, volume = {11024}, year = {2018}, } @article{400, abstract = {We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case.}, author = {Deuchert, Andreas and Geisinge, Alissa and Hainzl, Christian and Loss, Michael}, journal = {Annales Henri Poincare}, number = {5}, pages = {1507 -- 1527}, publisher = {Springer}, title = {{Persistence of translational symmetry in the BCS model with radial pair interaction}}, doi = {10.1007/s00023-018-0665-7}, volume = {19}, year = {2018}, } @article{406, abstract = {Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. }, author = {Bod’Ová, Katarína and Mitchell, Gabriel and Harpaz, Roy and Schneidman, Elad and Tkacik, Gasper}, journal = {PLoS One}, number = {3}, publisher = {Public Library of Science}, title = {{Probabilistic models of individual and collective animal behavior}}, doi = {10.1371/journal.pone.0193049}, volume = {13}, year = {2018}, } @article{457, abstract = {Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages}, author = {Pleska, Maros and Lang, Moritz and Refardt, Dominik and Levin, Bruce and Guet, Calin C}, journal = {Nature Ecology and Evolution}, number = {2}, pages = {359 -- 366}, publisher = {Springer Nature}, title = {{Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity}}, doi = {10.1038/s41559-017-0424-z}, volume = {2}, year = {2018}, } @article{55, abstract = {Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.}, author = {Pull, Christopher and Metzler, Sina and Naderlinger, Elisabeth and Cremer, Sylvia}, journal = {Current Biology}, number = {19}, pages = {R1139 -- R1140}, publisher = {Cell Press}, title = {{Protection against the lethal side effects of social immunity in ants}}, doi = {10.1016/j.cub.2018.08.063}, volume = {28}, year = {2018}, } @article{181, abstract = {We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2.}, author = {Erdös, László and Krüger, Torben H and Renfrew, David T}, journal = {SIAM Journal on Mathematical Analysis}, number = {3}, pages = {3271 -- 3290}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Power law decay for systems of randomly coupled differential equations}}, doi = {10.1137/17M1143125}, volume = {50}, year = {2018}, } @article{322, abstract = {We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework.}, author = {Ganev, Iordan V}, journal = {Journal of Algebra}, pages = {92 -- 128}, publisher = {World Scientific Publishing}, title = {{Quantizations of multiplicative hypertoric varieties at a root of unity}}, doi = {10.1016/j.jalgebra.2018.03.015}, volume = {506}, year = {2018}, } @misc{9831, abstract = {Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.}, author = {Bod’Ová, Katarína and Mitchell, Gabriel and Harpaz, Roy and Schneidman, Elad and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Implementation of the inference method in Matlab}}, doi = {10.1371/journal.pone.0193049.s001}, year = {2018}, } @inproceedings{142, abstract = {We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.}, author = {Kong, Hui and Bartocci, Ezio and Henzinger, Thomas A}, location = {Oxford, United Kingdom}, pages = {449 -- 467}, publisher = {Springer}, title = {{Reachable set over-approximation for nonlinear systems using piecewise barrier tubes}}, doi = {10.1007/978-3-319-96145-3_24}, volume = {10981}, year = {2018}, } @article{427, abstract = {We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements.}, author = {Amaro, Pedro and Loureiro, Ulisses and Safari, Laleh and Fratini, Filippo and Indelicato, Paul and Stöhlker, Thomas and Santos, José}, journal = { Physical Review A - Atomic, Molecular, and Optical Physics}, number = {2}, publisher = {American Physical Society}, title = {{Quantum interference in laser spectroscopy of highly charged lithiumlike ions}}, doi = {10.1103/PhysRevA.97.022510}, volume = {97}, year = {2018}, }