@inproceedings{81, abstract = {We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,}, author = {Elgyütt, Adrian and Ferrere, Thomas and Henzinger, Thomas A}, location = {Beijing, China}, pages = {53 -- 70}, publisher = {Springer}, title = {{Monitoring temporal logic with clock variables}}, doi = {10.1007/978-3-030-00151-3_4}, volume = {11022}, year = {2018}, } @article{76, abstract = {Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.}, author = {Lenzen, Christoph and Rybicki, Joel}, journal = {Distributed Computing}, publisher = {Springer}, title = {{Near-optimal self-stabilising counting and firing squads}}, doi = {10.1007/s00446-018-0342-6}, year = {2018}, } @article{530, abstract = {Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software.}, author = {Edelsbrunner, Herbert and Iglesias Ham, Mabel}, journal = {Computational Geometry: Theory and Applications}, pages = {119 -- 133}, publisher = {Elsevier}, title = {{Multiple covers with balls I: Inclusion–exclusion}}, doi = {10.1016/j.comgeo.2017.06.014}, volume = {68}, year = {2018}, } @article{307, abstract = {Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. }, author = {Redchenko, Elena and Makarov, Alexander and Yudson, Vladimir}, journal = { Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Nanoscopy of pairs of atoms by fluorescence in a magnetic field}}, doi = {10.1103/PhysRevA.97.043812}, volume = {97}, year = {2018}, } @article{279, abstract = {Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.}, author = {Zapata, Luis and Pich, Oriol and Serrano, Luis and Kondrashov, Fyodor and Ossowski, Stephan and Schaefer, Martin}, journal = {Genome Biology}, publisher = {BioMed Central}, title = {{Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome}}, doi = {10.1186/s13059-018-1434-0}, volume = {19}, year = {2018}, } @article{145, abstract = {Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.}, author = {Truckenbrodt, Sven M and Viplav, Abhiyan and Jähne, Sebsatian and Vogts, Angela and Denker, Annette and Wildhagen, Hanna and Fornasiero, Eugenio and Rizzoli, Silvio}, issn = {0261-4189}, journal = {The EMBO Journal}, number = {15}, publisher = {Wiley}, title = {{Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission}}, doi = {10.15252/embj.201798044}, volume = {37}, year = {2018}, } @article{462, abstract = {AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. }, author = {Fan, Ligang and Zhao, Lei and Hu, Wei and Li, Weina and Novák, Ondřej and Strnad, Miroslav and Simon, Sibu and Friml, Jirí and Shen, Jinbo and Jiang, Liwen and Qiu, Quan}, journal = {Plant, Cell and Environment}, pages = {850 -- 864}, publisher = {Wiley-Blackwell}, title = {{NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development}}, doi = {10.1111/pce.13153}, volume = {41}, year = {2018}, } @article{519, abstract = {This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. }, author = {Altmeyer, Sebastian}, journal = {Journal of Magnetism and Magnetic Materials}, pages = {427 -- 441}, publisher = {Elsevier}, title = {{Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow}}, doi = {10.1016/j.jmmm.2017.12.073}, volume = {452}, year = {2018}, } @inproceedings{5679, abstract = {We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs.}, author = {Huang, Mingzhang and Fu, Hongfei and Chatterjee, Krishnendu}, editor = {Ryu, Sukyoung}, isbn = {9783030027674}, issn = {03029743}, location = {Wellington, New Zealand}, pages = {181--201}, publisher = {Springer}, title = {{New approaches for almost-sure termination of probabilistic programs}}, doi = {10.1007/978-3-030-02768-1_11}, volume = {11275}, year = {2018}, } @misc{9812, abstract = {This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)}, author = {Zapata, Luis and Pich, Oriol and Serrano, Luis and Kondrashov, Fyodor and Ossowski, Stephan and Schaefer, Martin}, publisher = {Springer Nature}, title = {{Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome}}, doi = {10.6084/m9.figshare.6401414.v1}, year = {2018}, }