@article{1522,
abstract = {We classify smooth Brunnian (i.e., unknotted on both components) embeddings (S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to an explicitly constructed embedding fk,m,n for some integers k, m, n such that m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2 × S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such that the componentwise embedded connected sum f # g is isotopic to f # g′ but g is not isotopic to g′.},
author = {Avvakumov, Serhii},
journal = {Moscow Mathematical Journal},
number = {1},
pages = {1 -- 25},
publisher = {Independent University of Moscow},
title = {{The classification of certain linked 3-manifolds in 6-space}},
volume = {16},
year = {2016},
}
@article{1523,
abstract = {For random graphs, the containment problem considers the probability that a binomial random graph G(n, p) contains a given graph as a substructure. When asking for the graph as a topological minor, i.e., for a copy of a subdivision of the given graph, it is well known that the (sharp) threshold is at p = 1/n. We consider a natural analogue of this question for higher-dimensional random complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k = 2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold for containing a subdivision of any fixed complete 2-complex. For higher dimensions k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability of containing a subdivision of a fixed k-dimensional complex.},
author = {Gundert, Anna and Wagner, Uli},
journal = {Proceedings of the American Mathematical Society},
number = {4},
pages = {1815 -- 1828},
publisher = {American Mathematical Society},
title = {{On topological minors in random simplicial complexes}},
doi = {10.1090/proc/12824},
volume = {144},
year = {2016},
}
@inproceedings{1524,
abstract = {When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.
Our algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude.},
author = {Beica, Andreea and Guet, Calin C and Petrov, Tatjana},
location = {Madrid, Spain},
pages = {173 -- 191},
publisher = {Springer},
title = {{Efficient reduction of kappa models by static inspection of the rule-set}},
doi = {10.1007/978-3-319-26916-0_10},
volume = {9271},
year = {2016},
}
@inproceedings{1526,
abstract = {We present the first study of robustness of systems that are both timed as well as reactive (I/O). We study the behavior of such timed I/O systems in the presence of uncertain inputs and formalize their robustness using the analytic notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions over timed words such as the timed version of the Manhattan distance and the Skorokhod distance. We consider two models of timed I/O systems — timed transducers and asynchronous sequential circuits. We show that K-robustness of timed transducers can be decided in polynomial space under certain conditions. For asynchronous sequential circuits, we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete letter-to-letter transducers and show PSpace-completeness of the problem.},
author = {Henzinger, Thomas A and Otop, Jan and Samanta, Roopsha},
location = {St. Petersburg, FL, USA},
pages = {250 -- 267},
publisher = {Springer},
title = {{Lipschitz robustness of timed I/O systems}},
doi = {10.1007/978-3-662-49122-5_12},
volume = {9583},
year = {2016},
}
@article{1529,
abstract = {We consider partially observable Markov decision processes (POMDPs) with a set of target states and an integer cost associated with every transition. The optimization objective we study asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest.},
author = {Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Raghav and Kanodia, Ayush},
journal = {Artificial Intelligence},
pages = {26 -- 48},
publisher = {Elsevier},
title = {{Optimal cost almost-sure reachability in POMDPs}},
doi = {10.1016/j.artint.2016.01.007},
volume = {234},
year = {2016},
}
@article{1545,
abstract = {We provide general conditions for which bosonic quadratic Hamiltonians on Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover the case when quantum systems have infinite degrees of freedom and the associated one-body kinetic and paring operators are unbounded. Our sufficient conditions are optimal in the sense that they become necessary when the relevant one-body operators commute.},
author = {Nam, Phan and Napiórkowski, Marcin M and Solovej, Jan},
journal = {Journal of Functional Analysis},
number = {11},
pages = {4340 -- 4368},
publisher = {Academic Press},
title = {{Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations}},
doi = {10.1016/j.jfa.2015.12.007},
volume = {270},
year = {2016},
}
@article{1552,
abstract = {Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.},
author = {Qi, Qin and Toll Riera, Macarena and Heilbron, Karl and Preston, Gail and Maclean, R Craig},
journal = {Proceedings of the Royal Society of London Series B Biological Sciences},
number = {1822},
publisher = {Royal Society, The},
title = {{The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa}},
doi = {10.1098/rspb.2015.2452},
volume = {283},
year = {2016},
}
@article{1599,
abstract = {The addition of polysialic acid to N- and/or O-linked glycans, referred to as polysialylation, is a rare posttranslational modification that is mainly known to control the developmental plasticity of the nervous system. Here we show that CCR7, the central chemokine receptor controlling immune cell trafficking to secondary lymphatic organs, carries polysialic acid. This modification is essential for the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited conformation, which is released upon interaction with polysialic acid. Thus, we describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic basis.
},
author = {Kiermaier, Eva and Moussion, Christine and Veldkamp, Christopher and Gerardy Schahn, Rita and De Vries, Ingrid and Williams, Larry and Chaffee, Gary and Phillips, Andrew and Freiberger, Friedrich and Imre, Richard and Taleski, Deni and Payne, Richard and Braun, Asolina and Förster, Reinhold and Mechtler, Karl and Mühlenhoff, Martina and Volkman, Brian and Sixt, Michael K},
journal = {Science},
number = {6269},
pages = {186 -- 190},
publisher = {American Association for the Advancement of Science},
title = {{Polysialylation controls dendritic cell trafficking by regulating chemokine recognition}},
doi = {10.1126/science.aad0512},
volume = {351},
year = {2016},
}
@article{1608,
abstract = {We show that the Anderson model has a transition from localization to delocalization at exactly 2 dimensional growth rate on antitrees with normalized edge weights which are certain discrete graphs. The kinetic part has a one-dimensional structure allowing a description through transfer matrices which involve some Schur complement. For such operators we introduce the notion of having one propagating channel and extend theorems from the theory of one-dimensional Jacobi operators that relate the behavior of transfer matrices with the spectrum. These theorems are then applied to the considered model. In essence, in a certain energy region the kinetic part averages the random potentials along shells and the transfer matrices behave similar as for a one-dimensional operator with random potential of decaying variance. At d dimensional growth for d>2 this effective decay is strong enough to obtain absolutely continuous spectrum, whereas for some uniform d dimensional growth with d<2 one has pure point spectrum in this energy region. At exactly uniform 2 dimensional growth also some singular continuous spectrum appears, at least at small disorder. As a corollary we also obtain a change from singular spectrum (d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete adjacency operator (Laplacian) on ℤd and λ a random potential. },
author = {Sadel, Christian},
journal = {Annales Henri Poincare},
number = {7},
pages = {1631 -- 1675},
publisher = {Birkhäuser},
title = {{Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel}},
doi = {10.1007/s00023-015-0456-3},
volume = {17},
year = {2016},
}
@article{1612,
abstract = {We prove that whenever A is a 3-conservative relational structure with only binary and unary relations,then the algebra of polymorphisms of A either has no Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety (i.e.,CSP(A)has bounded width).},
author = {Kazda, Alexandr},
journal = {Algebra Universalis},
number = {1},
pages = {75 -- 84},
publisher = {Springer},
title = {{CSP for binary conservative relational structures}},
doi = {10.1007/s00012-015-0358-8},
volume = {75},
year = {2016},
}