@article{1866, author = {Henzinger, Thomas A and Raskin, Jean}, journal = {Communications of the ACM}, number = {2}, pages = {86--86}, publisher = {ACM}, title = {{The equivalence problem for finite automata: Technical perspective}}, doi = {10.1145/2701001}, volume = {58}, year = {2015}, } @article{1871, abstract = {The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.}, author = {Grones, Peter and Friml, Jirí}, journal = {Journal of Cell Science}, number = {1}, pages = {1 -- 7}, publisher = {Company of Biologists}, title = {{Auxin transporters and binding proteins at a glance}}, doi = {10.1242/jcs.159418}, volume = {128}, year = {2015}, } @article{1874, abstract = {The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource.}, author = {Boccara, Charlotte and Kjønigsen, Lisa and Hammer, Ingvild and Bjaalie, Jan and Leergaard, Trygve and Witter, Menno}, journal = {Hippocampus}, number = {7}, pages = {838 -- 857}, publisher = {Wiley}, title = {{A three-plane architectonic atlas of the rat hippocampal region}}, doi = {10.1002/hipo.22407}, volume = {25}, year = {2015}, } @article{1873, abstract = {We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.}, author = {Chatterjee, Krishnendu and Chmelik, Martin}, journal = {Artificial Intelligence}, pages = {46 -- 72}, publisher = {Elsevier}, title = {{POMDPs under probabilistic semantics}}, doi = {10.1016/j.artint.2014.12.009}, volume = {221}, year = {2015}, } @article{1879, abstract = {When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.}, author = {Kremer, A and Lippens, Stefaan and Bartunkova, Sonia and Asselbergh, Bob and Blanpain, Cendric and Fendrych, Matyas and Goossens, A and Holt, Matthew and Janssens, Sophie and Krols, Michiel and Larsimont, Jean and Mc Guire, Conor and Nowack, Moritz and Saelens, Xavier and Schertel, Andreas and Schepens, B and Slezak, M and Timmerman, Vincent and Theunis, Clara and Van Brempt, Ronald and Visser, Y and Guérin, Christophe}, journal = {Journal of Microscopy}, number = {2}, pages = {80 -- 96}, publisher = {Wiley-Blackwell}, title = {{Developing 3D SEM in a broad biological context}}, doi = {10.1111/jmi.12211}, volume = {259}, year = {2015}, } @article{1880, abstract = {We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder}, author = {Könenberg, Martin and Moser, Thomas and Seiringer, Robert and Yngvason, Jakob}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Superfluid behavior of a Bose-Einstein condensate in a random potential}}, doi = {10.1088/1367-2630/17/1/013022}, volume = {17}, year = {2015}, } @inproceedings{1882, abstract = {We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations.}, author = {Fahrenberg, Uli and Kretinsky, Jan and Legay, Axel and Traonouez, Louis}, location = {Bertinoro, Italy}, pages = {306 -- 324}, publisher = {Springer}, title = {{Compositionality for quantitative specifications}}, doi = {10.1007/978-3-319-15317-9_19}, volume = {8997}, year = {2015}, } @article{1883, abstract = {We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point. }, author = {Keller-Schmidt, Stephanie and Tugrul, Murat and Eguíluz, Víctor and Hernandez Garcia, Emilio and Klemm, Konstantin}, journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics}, number = {2}, publisher = {American Institute of Physics}, title = {{Anomalous scaling in an age-dependent branching model}}, doi = {10.1103/PhysRevE.91.022803}, volume = {91}, year = {2015}, } @article{1878, abstract = {Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron).}, author = {Cires Rodriguez, Eduardo and Prieto, José}, journal = {Journal of Plant Research}, number = {2}, pages = {223 -- 238}, publisher = {Springer}, title = {{Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula}}, doi = {10.1007/s10265-014-0691-6}, volume = {128}, year = {2015}, } @article{1885, abstract = {The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. }, author = {Tkacik, Gasper and Dubuis, Julien and Petkova, Mariela and Gregor, Thomas}, journal = {Genetics}, number = {1}, pages = {39 -- 59}, publisher = {Genetics Society of America}, title = {{Positional information, positional error, and readout precision in morphogenesis: A mathematical framework}}, doi = {10.1534/genetics.114.171850}, volume = {199}, year = {2015}, }