@article{43, abstract = {The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.}, author = {Rybicki, Joel and Kisdi, Eva and Anttila, Jani}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {42}, pages = {10690 -- 10695}, publisher = {National Academy of Sciences}, title = {{Model of bacterial toxin-dependent pathogenesis explains infective dose}}, doi = {10.1073/pnas.1721061115}, volume = {115}, year = {2018}, } @article{430, abstract = {In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly.}, author = {Novembre, John and Barton, Nicholas H}, journal = {Genetics}, number = {4}, pages = {1351 -- 1355}, publisher = {Genetics Society of America}, title = {{Tread lightly interpreting polygenic tests of selection}}, doi = {10.1534/genetics.118.300786}, volume = {208}, year = {2018}, } @inproceedings{433, abstract = {A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n.}, author = {Fulek, Radoslav and Pach, János}, location = {Boston, MA, United States}, pages = {160 -- 166}, publisher = {Springer}, title = {{Thrackles: An improved upper bound}}, doi = {10.1007/978-3-319-73915-1_14}, volume = {10692}, year = {2018}, } @article{434, abstract = {In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network.}, author = {Jiang, Yu and Liu, Han and Song, Huobing and Kong, Hui and Wang, Rui and Guan, Yong and Sha, Lui}, journal = {IEEE Transactions on Intelligent Transportation Systems}, number = {10}, pages = {3320 -- 3333}, publisher = {IEEE}, title = {{Safety-assured model-driven design of the multifunction vehicle bus controller}}, doi = {10.1109/TITS.2017.2778077}, volume = {19}, year = {2018}, } @article{18, abstract = {An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17].}, author = {Kolmogorov, Vladimir and Rolinek, Michal}, issn = {0381-7032}, journal = {Ars Combinatoria}, number = {10}, pages = {269 -- 304}, publisher = {Charles Babbage Research Centre}, title = {{Superconcentrators of density 25.3}}, volume = {141}, year = {2018}, } @article{180, abstract = {In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density.}, author = {Lewi, Mathieu and Lieb, Élliott and Seiringer, Robert}, issn = {2270-518X}, journal = {Journal de l'Ecole Polytechnique - Mathematiques}, pages = {79 -- 116}, publisher = {Ecole Polytechnique}, title = {{Statistical mechanics of the uniform electron gas}}, doi = {10.5802/jep.64}, volume = {5}, year = {2018}, } @inproceedings{182, abstract = {We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice.}, author = {Bakhirkin, Alexey and Ferrere, Thomas and Maler, Oded}, booktitle = {Proceedings of the 21st International Conference on Hybrid Systems}, isbn = {978-1-4503-5642-8 }, location = {Porto, Portugal}, pages = {177 -- 186}, publisher = {ACM}, title = {{Efficient parametric identification for STL}}, doi = {10.1145/3178126.3178132}, year = {2018}, } @inproceedings{183, abstract = {Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.}, author = {Bartocci, Ezio and Ferrere, Thomas and Manjunath, Niveditha and Nickovic, Dejan}, location = {Porto, Portugal}, pages = {197 -- 206}, publisher = {Association for Computing Machinery}, title = {{Localizing faults in simulink/stateflow models with STL}}, doi = {10.1145/3178126.3178131}, year = {2018}, } @inproceedings{184, abstract = {We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes.}, author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, location = {Budapest, Hungary}, pages = {41:1 -- 41:16}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Shellability is NP-complete}}, doi = {10.4230/LIPIcs.SoCG.2018.41}, volume = {99}, year = {2018}, } @article{5992, abstract = {Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow.}, author = {Dolati, Setareh and Kage, Frieda and Mueller, Jan and Müsken, Mathias and Kirchner, Marieluise and Dittmar, Gunnar and Sixt, Michael K and Rottner, Klemens and Falcke, Martin}, issn = {1939-4586}, journal = {Molecular Biology of the Cell}, number = {22}, pages = {2674--2686}, publisher = {American Society for Cell Biology}, title = {{On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility}}, doi = {10.1091/mbc.e18-02-0082}, volume = {29}, year = {2018}, } @unpublished{8547, abstract = {The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.}, author = {Llorca, Alfredo and Ciceri, Gabriele and Beattie, Robert J and Wong, Fong K. and Diana, Giovanni and Serafeimidou, Eleni and Fernández-Otero, Marian and Streicher, Carmen and Arnold, Sebastian J. and Meyer, Martin and Hippenmeyer, Simon and Maravall, Miguel and Marín, Oscar}, booktitle = {bioRxiv}, title = {{Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture}}, doi = {10.1101/494088}, year = {2018}, } @article{10286, abstract = {In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.}, author = {Allini, Elie Noumon and Skórski, Maciej and Petura, Oto and Bernard, Florent and Laban, Marek and Fischer, Viktor}, issn = {2569-2925}, journal = {IACR Transactions on Cryptographic Hardware and Embedded Systems}, number = {3}, pages = {214--242}, publisher = {International Association for Cryptologic Research}, title = {{Evaluation and monitoring of free running oscillators serving as source of randomness}}, doi = {10.13154/tches.v2018.i3.214-242}, volume = {2018}, year = {2018}, } @article{5995, abstract = {Motivation Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations. Results Here we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here.}, author = {Usmanova, Dinara R and Bogatyreva, Natalya S and Ariño Bernad, Joan and Eremina, Aleksandra A and Gorshkova, Anastasiya A and Kanevskiy, German M and Lonishin, Lyubov R and Meister, Alexander V and Yakupova, Alisa G and Kondrashov, Fyodor and Ivankov, Dmitry}, issn = {1367-4811}, journal = {Bioinformatics}, number = {21}, pages = {3653--3658}, publisher = {Oxford University Press}, title = {{Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation}}, doi = {10.1093/bioinformatics/bty340}, volume = {34}, year = {2018}, } @article{404, abstract = {We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence. }, author = {Fischer, Julian L and Grün, Günther}, journal = {SIAM Journal on Mathematical Analysis}, number = {1}, pages = {411 -- 455}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Existence of positive solutions to stochastic thin-film equations}}, doi = {10.1137/16M1098796}, volume = {50}, 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{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 = {0895-4801}, 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{22, abstract = {Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems.}, author = {Botello, Gabriel and Sedlmeir, Florian and Rueda Sanchez, Alfredo R and Abdalmalak, Kerlos and Brown, Elliott and Leuchs, Gerd and Preu, Sascha and Segovia Vargas, Daniel and Strekalov, Dmitry and Munoz, Luis and Schwefel, Harald}, issn = {2334-2536}, journal = {Optica}, number = {10}, pages = {1210--1219}, publisher = {Optica Publishing Group}, title = {{Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters}}, doi = {10.1364/OPTICA.5.001210}, volume = {5}, year = {2018}, } @techreport{5686, abstract = {In the working paper I describe in detail the approach for Open Access definitions which was presented in the Workshop "Open Access Monitoring - Approaches and Perspectives" in Vienna. It defines five criteria on which are the definitions build. Each criteria can be out of 4 classes. The minimum classes for the criteria which are used in a Open Access definition can be presented as the Classification of Open Access Tuples e.g. Open Access (Berlin Declaration) (1,1,1,1,3) this methods allows much easier to distinguish between different Open Access definitions. This is needed if the Open Access Universe should be measured in studies or monitoring approaches and the results should become more comparable. }, author = {Danowski, Patrick}, pages = {5}, publisher = {Zenodo}, title = {{An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors}}, doi = {10.5281/zenodo.1244154}, year = {2018}, } @article{58, abstract = {Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks.}, author = {Akopyan, Arseniy and Segal Halevi, Erel}, journal = {SIAM Journal on Discrete Mathematics}, number = {3}, pages = {2242 -- 2257}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Counting blanks in polygonal arrangements}}, doi = {10.1137/16M110407X}, volume = {32}, 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}, 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}, }