@article{1655, abstract = {Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration.}, author = {Martius, Georg S and Olbrich, Eckehard}, journal = {Entropy}, number = {10}, pages = {7266 -- 7297}, publisher = {MDPI}, title = {{Quantifying emergent behavior of autonomous robots}}, doi = {10.3390/e17107266}, volume = {17}, year = {2015}, } @article{1834, abstract = {Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks.}, author = {Chen, Chong and Wang, Chao and Zhao, Xuan and Zhou, Tao and Xu, Dao and Wang, Zhi and Wang, Ying}, journal = {ASN Neuro}, number = {2}, publisher = {SAGE Publications}, title = {{Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats}}, doi = {10.1177/1759091415575845}, volume = {7}, year = {2015}, } @article{1635, abstract = {We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters.}, author = {Erbar, Matthias and Maas, Jan and Tetali, Prasad}, journal = {Annales de la faculté des sciences de Toulouse}, number = {4}, pages = {781 -- 800}, publisher = {Faculté des sciences de Toulouse}, title = {{Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models}}, doi = {10.5802/afst.1464}, volume = {24}, year = {2015}, } @article{14303, abstract = {Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale.}, author = {Kick, B and Praetorius, Florian M and Dietz, H and Weuster-Botz, D}, issn = {1530-6992}, journal = {Nano Letters}, number = {7}, pages = {4672--4676}, publisher = {ACS Publications}, title = {{Efficient production of single-stranded phage DNA as scaffolds for DNA origami}}, doi = {10.1021/acs.nanolett.5b01461}, volume = {15}, year = {2015}, } @inproceedings{1603, abstract = {For deterministic systems, a counterexample to a property can simply be an error trace, whereas counterexamples in probabilistic systems are necessarily more complex. For instance, a set of erroneous traces with a sufficient cumulative probability mass can be used. Since these are too large objects to understand and manipulate, compact representations such as subchains have been considered. In the case of probabilistic systems with non-determinism, the situation is even more complex. While a subchain for a given strategy (or scheduler, resolving non-determinism) is a straightforward choice, we take a different approach. Instead, we focus on the strategy itself, and extract the most important decisions it makes, and present its succinct representation. The key tools we employ to achieve this are (1) introducing a concept of importance of a state w.r.t. the strategy, and (2) learning using decision trees. There are three main consequent advantages of our approach. Firstly, it exploits the quantitative information on states, stressing the more important decisions. Secondly, it leads to a greater variability and degree of freedom in representing the strategies. Thirdly, the representation uses a self-explanatory data structure. In summary, our approach produces more succinct and more explainable strategies, as opposed to e.g. binary decision diagrams. Finally, our experimental results show that we can extract several rules describing the strategy even for very large systems that do not fit in memory, and based on the rules explain the erroneous behaviour.}, author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Fellner, Andreas and Kretinsky, Jan}, location = {San Francisco, CA, United States}, pages = {158 -- 177}, publisher = {Springer}, title = {{Counterexample explanation by learning small strategies in Markov decision processes}}, doi = {10.1007/978-3-319-21690-4_10}, volume = {9206}, year = {2015}, } @misc{5549, abstract = {This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. We extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees. The archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library. To execute the program, please have a look at the README.txt, which provides instructions and further information on the archive. The archive contains scripts that (if run often enough) reproduces the data presented in the publication.}, author = {Fellner, Andreas}, keywords = {Markov Decision Process, Decision Tree, Probabilistic Verification, Counterexample Explanation}, publisher = {Institute of Science and Technology Austria}, title = {{Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes}}, doi = {10.15479/AT:ISTA:28}, year = {2015}, } @inproceedings{1512, abstract = {We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.}, author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, location = {Eindhoven, Netherlands}, pages = {507 -- 521}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Bounding Helly numbers via Betti numbers}}, doi = {10.4230/LIPIcs.SOCG.2015.507}, volume = {34}, year = {2015}, } @article{271, abstract = {We show that a non-singular integral form of degree d is soluble non-trivially over the integers if and only if it is soluble non-trivially over the reals and the p-adic numbers, provided that the form has at least (d-\sqrt{d}/2)2^d variables. This improves on a longstanding result of Birch.}, author = {Browning, Timothy D and Prendiville, Sean}, issn = {0075-4102}, journal = {Journal fur die Reine und Angewandte Mathematik}, number = {731}, pages = {203 -- 234}, publisher = {Walter de Gruyter}, title = {{Improvements in Birch's theorem on forms in many variables}}, doi = {10.1515/crelle-2014-0122}, volume = {2017}, year = {2015}, } @inproceedings{1675, abstract = {Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble).}, author = {Dziembowski, Stefan and Faust, Sebastian and Kolmogorov, Vladimir and Pietrzak, Krzysztof Z}, booktitle = {35th Annual Cryptology Conference}, isbn = {9783662479995}, issn = {0302-9743}, location = {Santa Barbara, CA, United States}, pages = {585 -- 605}, publisher = {Springer}, title = {{Proofs of space}}, doi = {10.1007/978-3-662-48000-7_29}, volume = {9216}, year = {2015}, } @article{15160, abstract = {The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms.}, author = {Michael, Alicia Kathleen and Harvey, Stacy L. and Sammons, Patrick J. and Anderson, Amanda P. and Kopalle, Hema M. and Banham, Alison H. and Partch, Carrie L.}, issn = {1097-2765}, journal = {Molecular Cell}, keywords = {Cell Biology, Molecular Biology}, number = {5}, pages = {743--754}, publisher = {Elsevier}, title = {{Cancer/Testis antigen PASD1 silences the circadian clock}}, doi = {10.1016/j.molcel.2015.03.031}, volume = {58}, year = {2015}, }