@article{624, abstract = {Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein.}, author = {Nikolic, Nela and Didara, Zrinka and Moll, Isabella}, issn = {21678359}, journal = {PeerJ}, number = {9}, publisher = {PeerJ}, title = {{MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations}}, doi = {10.7717/peerj.3830}, volume = {2017}, year = {2017}, } @inproceedings{628, abstract = {We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. The motivation is that several classical textbook algorithms have quite efficient expected-runtime complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since the main focus of expected-runtime analysis is to obtain efficient bounds, we consider bounds that are either logarithmic, linear or almost-linear (O(log n), O(n), O(n · log n), respectively, where n represents the input size). Our main contribution is an efficient (simple linear-time algorithm) sound approach for deriving such expected-runtime bounds for the analysis of recurrence relations induced by randomized algorithms. The experimental results show that our approach can efficiently derive asymptotically optimal expected-runtime bounds for recurrences of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select, Coupon-Collector, where the worst-case bounds are either inefficient (such as linear as compared to logarithmic expected-runtime complexity, or quadratic as compared to linear or almost-linear expected-runtime complexity), or ineffective.}, author = {Chatterjee, Krishnendu and Fu, Hongfei and Murhekar, Aniket}, editor = {Majumdar, Rupak and Kunčak, Viktor}, isbn = {978-331963386-2}, location = {Heidelberg, Germany}, pages = {118 -- 139}, publisher = {Springer}, title = {{Automated recurrence analysis for almost linear expected runtime bounds}}, doi = {10.1007/978-3-319-63387-9_6}, volume = {10426}, year = {2017}, } @inbook{629, abstract = {Even simple cells like bacteria have precisely regulated cellular anatomies, which allow them to grow, divide and to respond to internal or external cues with high fidelity. How spatial and temporal intracellular organization in prokaryotic cells is achieved and maintained on the basis of locally interacting proteins still remains largely a mystery. Bulk biochemical assays with purified components and in vivo experiments help us to approach key cellular processes from two opposite ends, in terms of minimal and maximal complexity. However, to understand how cellular phenomena emerge, that are more than the sum of their parts, we have to assemble cellular subsystems step by step from the bottom up. Here, we review recent in vitro reconstitution experiments with proteins of the bacterial cell division machinery and illustrate how they help to shed light on fundamental cellular mechanisms that constitute spatiotemporal order and regulate cell division.}, author = {Loose, Martin and Zieske, Katja and Schwille, Petra}, booktitle = {Prokaryotic Cytoskeletons}, pages = {419 -- 444}, publisher = {Springer}, title = {{Reconstitution of protein dynamics involved in bacterial cell division}}, doi = {10.1007/978-3-319-53047-5_15}, volume = {84}, year = {2017}, } @inproceedings{630, abstract = {Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.}, author = {Sauermann, Stefan and David, Veronika and Schlögl, Alois and Egelkraut, Reinhard and Frohner, Matthias and Pohn, Birgit and Urbauer, Philipp and Mense, Alexander}, isbn = {978-161499758-0}, location = {Vienna, Austria}, pages = {356 -- 362}, publisher = {IOS Press}, title = {{Biosignals standards and FHIR: The way to go}}, doi = {10.3233/978-1-61499-759-7-356}, volume = {236}, year = {2017}, } @article{632, abstract = {We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. }, author = {Lewin, Mathieu and Nam, Phan and Rougerie, Nicolas}, journal = {Proceedings of the American Mathematical Society}, number = {6}, pages = {2441 -- 2454}, publisher = {American Mathematical Society}, title = {{A note on 2D focusing many boson systems}}, doi = {10.1090/proc/13468}, volume = {145}, year = {2017}, } @inbook{634, abstract = {As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental condition, long-time consensus was that its hallmark features are irreversible. However, several studies from recent years using defined mouse models of ASD have provided clear evidence that in mice neurobiological and behavioural alterations can be ameliorated or even reversed by genetic restoration or pharmacological treatment either before or after symptom onset. Here, we review findings on genetic and pharmacological reversibility of phenotypes in mouse models of ASD. Our review should give a comprehensive overview on both aspects and encourage future studies to better understand the underlying molecular mechanisms that might be translatable from animals to humans.}, author = {Schroeder, Jan and Deliu, Elena and Novarino, Gaia and Schmeisser, Michael}, booktitle = {Translational Anatomy and Cell Biology of Autism Spectrum Disorder}, editor = {Schmeisser, Michael and Boekers, Tobias}, pages = {189 -- 211}, publisher = {Springer}, title = {{Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder}}, doi = {10.1007/978-3-319-52498-6_10}, volume = {224}, year = {2017}, } @inproceedings{633, abstract = {A Rapidly-exploring Random Tree (RRT) is an algorithm which can search a non-convex region of space by incrementally building a space-filling tree. The tree is constructed from random points drawn from system’s state space and is biased to grow towards large unexplored areas in the system. RRT can provide better coverage of a system’s possible behaviors compared with random simulations, but is more lightweight than full reachability analysis. In this paper, we explore some of the design decisions encountered while implementing a hybrid extension of the RRT algorithm, which have not been elaborated on before. In particular, we focus on handling non-determinism, which arises due to discrete transitions. We introduce the notion of important points to account for this phenomena. We showcase our ideas using heater and navigation benchmarks.}, author = {Bak, Stanley and Bogomolov, Sergiy and Henzinger, Thomas A and Kumar, Aviral}, editor = {Abate, Alessandro and Bodo, Sylvie}, isbn = {978-331963500-2}, location = {Heidelberg, Germany}, pages = {83 -- 89}, publisher = {Springer}, title = {{Challenges and tool implementation of hybrid rapidly exploring random trees}}, doi = {10.1007/978-3-319-63501-9_6}, volume = {10381}, year = {2017}, } @inproceedings{635, abstract = {Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is dominated by memory cost. As memory, unlike computation, costs about the same across different platforms, MHFs cannot be evaluated at significantly lower cost on dedicated hardware like ASICs. MHFs have found widespread applications including password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt, a simple candidate MHF designed by Percival, and described in RFC 7914. It has been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and has been an inspiration for Argon2d, one of the winners of the recent password-hashing competition. Despite its popularity, no rigorous lower bounds on its memory complexity are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w and n are the output length and number of invocations of the underlying hash function, respectively. High cmc is a strong security target for MHFs introduced by Alwen and Serbinenko (STOC’15) which implies high memory cost even for adversaries who can amortize the cost over many evaluations and evaluate the underlying hash functions many times in parallel. Our proof is the first showing optimal memory-hardness for any MHF. Our result improves both quantitatively and qualitatively upon the recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of Ω(n2w/ log2 n) for a restricted class of adversaries.}, author = {Alwen, Joel F and Chen, Binchi and Pietrzak, Krzysztof Z and Reyzin, Leonid and Tessaro, Stefano}, editor = {Coron, Jean-Sébastien and Buus Nielsen, Jesper}, isbn = {978-331956616-0}, location = {Paris, France}, pages = {33 -- 62}, publisher = {Springer}, title = {{Scrypt is maximally memory hard}}, doi = {10.1007/978-3-319-56617-7_2}, volume = {10212}, year = {2017}, } @inproceedings{636, abstract = {Signal regular expressions can specify sequential properties of real-valued signals based on threshold conditions, regular operations, and duration constraints. In this paper we endow them with a quantitative semantics which indicates how robustly a signal matches or does not match a given expression. First, we show that this semantics is a safe approximation of a distance between the signal and the language defined by the expression. Then, we consider the robust matching problem, that is, computing the quantitative semantics of every segment of a given signal relative to an expression. We present an algorithm that solves this problem for piecewise-constant and piecewise-linear signals and show that for such signals the robustness map is a piecewise-linear function. The availability of an indicator describing how robustly a signal segment matches some regular pattern provides a general framework for quantitative monitoring of cyber-physical systems.}, author = {Bakhirkin, Alexey and Ferrere, Thomas and Maler, Oded and Ulus, Dogan}, editor = {Abate, Alessandro and Geeraerts, Gilles}, isbn = {978-331965764-6}, location = {Berlin, Germany}, pages = {189 -- 206}, publisher = {Springer}, title = {{On the quantitative semantics of regular expressions over real-valued signals}}, doi = {10.1007/978-3-319-65765-3_11}, volume = {10419}, year = {2017}, } @proceedings{638, abstract = {This book constitutes the refereed proceedings of the 9th InternationalWorkshop on Numerical Software Verification, NSV 2016, held in Toronto, ON, Canada in July 2011 - colocated with CAV 2016, the 28th International Conference on Computer Aided Verification. The NSV workshop is dedicated to the development of logical and mathematical techniques for the reasoning about programmability and reliability.}, editor = {Bogomolov, Sergiy and Martel, Matthieu and Prabhakar, Pavithra}, issn = {0302-9743}, location = {Toronto, ON, Canada}, publisher = {Springer}, title = {{Numerical Software Verification}}, doi = {10.1007/978-3-319-54292-8}, volume = {10152}, year = {2017}, }