@article{3505,
abstract = {Cell migration on two-dimensional (2D) substrates follows entirely different rules than cell migration in three-dimensional (3D) environments. This is especially relevant for leukocytes that are able to migrate in the absence of adhesion receptors within the confined geometry of artificial 3D extracellular matrix scaffolds and within the interstitial space in vivo. Here, we describe in detail a simple and economical protocol to visualize dendritic cell migration in 3D collagen scaffolds along chemotactic gradients. This method can be adapted to other cell types and may serve as a physiologically relevant paradigm for the directed locomotion of most amoeboid cells.},
author = {Sixt, Michael K and Lämmermann, Tim},
journal = {Cell Migration},
pages = {149 -- 165},
publisher = {Springer},
title = {{In vitro analysis of chemotactic leukocyte migration in 3D environments}},
doi = {10.1007/978-1-61779-207-6_11},
volume = {769},
year = {2011},
}
@inbook{3311,
abstract = {Alpha shapes have been conceived in 1981 as an attempt to define the shape of a finite set of point in the plane. Since then, connections to diverse areas in the sciences and engineering have developed, including to pattern recognition, digital shape sampling and processing, and structural molecular biology. This survey begins with a historical account and discusses geometric, algorithmic, topological, and combinatorial aspects of alpha shapes in this sequence.},
author = {Herbert Edelsbrunner},
booktitle = {Tessellations in the Sciences},
publisher = {Springer},
title = {{Alpha shapes - a survey}},
year = {2011},
}
@inproceedings{3330,
abstract = {We consider the problem of approximating all real roots of a square-free polynomial f. Given isolating intervals, our algorithm refines each of them to a width at most 2-L, that is, each of the roots is approximated to L bits after the binary point. Our method provides a certified answer for arbitrary real polynomials, only requiring finite approximations of the polynomial coefficient and choosing a suitable working precision adaptively. In this way, we get a correct algorithm that is simple to implement and practically efficient. Our algorithm uses the quadratic interval refinement method; we adapt that method to be able to cope with inaccuracies when evaluating f, without sacrificing its quadratic convergence behavior. We prove a bound on the bit complexity of our algorithm in terms of degree, coefficient size and discriminant. Our bound improves previous work on integer polynomials by a factor of deg f and essentially matches best known theoretical bounds on root approximation which are obtained by very sophisticated algorithms.},
author = {Kerber, Michael and Sagraloff, Michael},
location = {California, USA},
pages = {209 -- 216},
publisher = {Springer},
title = {{Root refinement for real polynomials}},
doi = {10.1145/1993886.1993920 },
year = {2011},
}
@inbook{3335,
abstract = {We study the topology of the Megaparsec Cosmic Web in terms of the scale-dependent Betti numbers, which formalize the topological information content of the cosmic mass distribution. While the Betti numbers do not fully quantify topology, they extend the information beyond conventional cosmological studies of topology in terms of genus and Euler characteristic. The richer information content of Betti numbers goes along the availability of fast algorithms to compute them. For continuous density fields, we determine the scale-dependence of Betti numbers by invoking the cosmologically familiar filtration of sublevel or superlevel sets defined by density thresholds. For the discrete galaxy distribution, however, the analysis is based on the alpha shapes of the particles. These simplicial complexes constitute an ordered sequence of nested subsets of the Delaunay tessellation, a filtration defined by the scale parameter, α. As they are homotopy equivalent to the sublevel sets of the distance field, they are an excellent tool for assessing the topological structure of a discrete point distribution. In order to develop an intuitive understanding for the behavior of Betti numbers as a function of α, and their relation to the morphological patterns in the Cosmic Web, we first study them within the context of simple heuristic Voronoi clustering models. These can be tuned to consist of specific morphological elements of the Cosmic Web, i.e. clusters, filaments, or sheets. To elucidate the relative prominence of the various Betti numbers in different stages of morphological evolution, we introduce the concept of alpha tracks. Subsequently, we address the topology of structures emerging in the standard LCDM scenario and in cosmological scenarios with alternative dark energy content. The evolution of the Betti numbers is shown to reflect the hierarchical evolution of the Cosmic Web. We also demonstrate that the scale-dependence of the Betti numbers yields a promising measure of cosmological parameters, with a potential to help in determining the nature of dark energy and to probe primordial non-Gaussianities. We also discuss the expected Betti numbers as a function of the density threshold for superlevel sets of a Gaussian random field. Finally, we introduce the concept of persistent homology. It measures scale levels of the mass distribution and allows us to separate small from large scale features. Within the context of the hierarchical cosmic structure formation, persistence provides a natural formalism for a multiscale topology study of the Cosmic Web.},
author = {Van De Weygaert, Rien and Vegter, Gert and Edelsbrunner, Herbert and Jones, Bernard and Pranav, Pratyush and Park, Changbom and Hellwing, Wojciech and Eldering, Bob and Kruithof, Nico and Bos, Patrick and Hidding, Johan and Feldbrugge, Job and Ten Have, Eline and Van Engelen, Matti and Caroli, Manuel and Teillaud, Monique},
booktitle = {Transactions on Computational Science XIV},
editor = {Gavrilova, Marina and Tan, Kenneth and Mostafavi, Mir},
pages = {60 -- 101},
publisher = {Springer},
title = {{Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web}},
doi = {10.1007/978-3-642-25249-5_3},
volume = {6970},
year = {2011},
}
@inbook{3791,
abstract = {During the development of multicellular organisms, cell fate specification is followed by the sorting of different cell types into distinct domains from where the different tissues and organs are formed. Cell sorting involves both the segregation of a mixed population of cells with different fates and properties into distinct domains, and the active maintenance of their segregated state. Because of its biological importance and apparent resemblance to fluid segregation in physics, cell sorting was extensively studied by both biologists and physicists over the last decades. Different theories were developed that try to explain cell sorting on the basis of the physical properties of the constituent cells. However, only recently the molecular and cellular mechanisms that control the physical properties driving cell sorting, have begun to be unraveled. In this review, we will provide an overview of different cell-sorting processes in development and discuss how these processes can be explained by the different sorting theories, and how these theories in turn can be connected to the molecular and cellular mechanisms driving these processes.},
author = {Krens, Gabriel and Heisenberg, Carl-Philipp J},
booktitle = {Current Topics in Developmental Biology},
editor = {Labouesse, Michel},
pages = {189 -- 213},
publisher = {Elsevier},
title = {{Cell sorting in development}},
doi = {10.1016/B978-0-12-385065-2.00006-2},
volume = {95},
year = {2011},
}
@inbook{3796,
abstract = {We address the problem of covering ℝ n with congruent balls, while minimizing the number of balls that contain an average point. Considering the 1-parameter family of lattices defined by stretching or compressing the integer grid in diagonal direction, we give a closed formula for the covering density that depends on the distortion parameter. We observe that our family contains the thinnest lattice coverings in dimensions 2 to 5. We also consider the problem of packing congruent balls in ℝ n , for which we give a closed formula for the packing density as well. Again we observe that our family contains optimal configurations, this time densest packings in dimensions 2 and 3.},
author = {Edelsbrunner, Herbert and Kerber, Michael},
booktitle = {Rainbow of Computer Science},
editor = {Calude, Cristian and Rozenberg, Grzegorz and Salomaa, Arto},
pages = {20 -- 35},
publisher = {Springer},
title = {{Covering and packing with spheres by diagonal distortion in R^n}},
doi = {10.1007/978-3-642-19391-0_2},
volume = {6570},
year = {2011},
}
@article{3385,
author = {Sixt, Michael K},
journal = {Immunology Letters},
number = {1},
pages = {32 -- 34},
publisher = {Elsevier},
title = {{Interstitial locomotion of leukocytes}},
doi = {10.1016/j.imlet.2011.02.013},
volume = {138},
year = {2011},
}
@article{3392,
abstract = {Migrating lymphocytes acquire a polarized phenotype with a leading and a trailing edge, or uropod. Although in vitro experiments in cell lines or activated primary cell cultures have established that Rho-p160 coiled-coil kinase (ROCK)-myosin II-mediated uropod contractility is required for integrin de-adhesion on two-dimensional surfaces and nuclear propulsion through narrow pores in three-dimensional matrices, less is known about the role of these two events during the recirculation of primary, nonactivated lymphocytes. Using pharmacological antagonists of ROCK and myosin II, we report that inhibition of uropod contractility blocked integrin-independent mouse T cell migration through narrow, but not large, pores in vitro. T cell crawling on chemokine-coated endothelial cells under shear was severely impaired by ROCK inhibition, whereas transendothelial migration was only reduced through endothelial cells with high, but not low, barrier properties. Using three-dimensional thick-tissue imaging and dynamic two-photon microscopy of T cell motility in lymphoid tissue, we demonstrated a significant role for uropod contractility in intraluminal crawling and transendothelial migration through lymph node, but not bone marrow, endothelial cells. Finally, we demonstrated that ICAM-1, but not anatomical constraints or integrin-independent interactions, reduced parenchymal motility of inhibitor-treated T cells within the dense lymphoid microenvironment, thus assigning context-dependent roles for uropod contraction during lymphocyte recirculation.},
author = {Soriano, Silvia and Hons, Miroslav and Schumann, Kathrin and Kumar, Varsha and Dennier, Timo and Lyck, Ruth and Sixt, Michael K and Stein, Jens},
journal = {Journal of Immunology},
number = {5},
pages = {2356 -- 2364},
publisher = {American Association of Immunologists},
title = {{In vivo analysis of uropod function during physiological T cell trafficking}},
doi = {10.4049/jimmunol.1100935},
volume = {187},
year = {2011},
}
@article{3397,
abstract = {Recent advances in microscopy techniques and biophysical measurements have provided novel insight into the molecular, cellular and biophysical basis of cell adhesion. However, comparably little is known about a core element of cell–cell adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss approaches to understand the nature and regulation of adhesion energy, and propose strategies to determine adhesion energy between cells in vitro and in vivo.},
author = {Maître, Jean-Léon and Heisenberg, Carl-Philipp J},
journal = {Current Opinion in Cell Biology},
number = {5},
pages = {508 -- 514},
publisher = {Elsevier},
title = {{The role of adhesion energy in controlling cell-cell contacts}},
doi = {10.1016/j.ceb.2011.07.004},
volume = {23},
year = {2011},
}
@article{3405,
abstract = {Glutamate is the major excitatory neurotransmitter in the mammalian central nervous system and gates non-selective cation channels. The origins of glutamate receptors are not well understood as they differ structurally and functionally from simple bacterial ligand-gated ion channels. Here we report the discovery of an ionotropic glutamate receptor that combines the typical eukaryotic domain architecture with the 'TXVGYG' signature sequence of the selectivity filter found in K+ channels. This receptor exhibits functional properties intermediate between bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors.},
author = {Janovjak, Harald L and Sandoz, Guillaume and Isacoff, Ehud},
journal = {Nature Communications},
number = {232},
pages = {1 -- 6},
publisher = {Nature Publishing Group},
title = {{Modern ionotropic glutamate receptor with a K+ selectivity signature sequence}},
doi = {10.1038/ncomms1231},
volume = {2},
year = {2011},
}
@article{3429,
abstract = {Transcription factors are central to sustaining pluripotency, yet little is known about transcription factor dynamics in defining pluripotency in the early mammalian embryo. Here, we establish a fluorescence decay after photoactivation (FDAP) assay to quantitatively study the kinetic behaviour of Oct4, a key transcription factor controlling pre-implantation development in the mouse embryo. FDAP measurements reveal that each cell in a developing embryo shows one of two distinct Oct4 kinetics, before there are any morphologically distinguishable differences or outward signs of lineage patterning. The differences revealed by FDAP are due to differences in the accessibility of Oct4 to its DNA binding sites in the nucleus. Lineage tracing of the cells in the two distinct sub-populations demonstrates that the Oct4 kinetics predict lineages of the early embryo. Cells with slower Oct4 kinetics are more likely to give rise to the pluripotent cell lineage that contributes to the inner cell mass. Those with faster Oct4 kinetics contribute mostly to the extra-embryonic lineage. Our findings identify Oct4 kinetics, rather than differences in total transcription factor expression levels, as a predictive measure of developmental cell lineage patterning in the early mouse embryo.},
author = {Plachta, Nicolas and Bollenbach, Mark Tobias and Pease, Shirley and Fraser, Scott and Pantazis, Periklis},
journal = {Nature Cell Biology},
number = {2},
pages = {117 -- 123},
publisher = {Nature Publishing Group},
title = {{Oct4 kinetics predict cell lineage patterning in the early mammalian embryo}},
doi = {10.1038/ncb2154},
volume = {13},
year = {2011},
}
@article{3373,
abstract = {The use of optical traps to measure or apply forces on the molecular level requires a precise knowledge of the trapping force field. Close to the trap center, this field is typically approximated as linear in the displacement of the trapped microsphere. However, applications demanding high forces at low laser intensities can probe the light-microsphere interaction beyond the linear regime. Here, we measured the full nonlinear force and displacement response of an optical trap in two dimensions using a dual-beam optical trap setup with back-focal-plane photodetection. We observed a substantial stiffening of the trap beyond the linear regime that depends on microsphere size, in agreement with Mie theory calculations. Surprisingly, we found that the linear detection range for forces exceeds the one for displacement by far. Our approach allows for a complete calibration of an optical trap.},
author = {Jahnel, Marcus and Behrndt, Martin and Jannasch, Anita and Schaeffer, Erik and Grill, Stephan},
journal = {Optics Letters},
number = {7},
pages = {1260 -- 1262},
publisher = {OSA},
title = {{Measuring the complete force field of an optical trap}},
doi = {10.1364/OL.36.001260},
volume = {36},
year = {2011},
}
@article{3378,
abstract = {The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology.},
author = {Bendich, Paul and Harer, John},
journal = {Foundations of Computational Mathematics},
number = {3},
pages = {305 -- 336},
publisher = {Springer},
title = {{Persistent intersection homology}},
doi = {10.1007/s10208-010-9081-1},
volume = {11},
year = {2011},
}
@misc{5386,
abstract = {We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.},
author = {Chen, Chao and Freedman, Daniel and Lampert, Christoph},
issn = {2664-1690},
pages = {69},
publisher = {IST Austria},
title = {{Enforcing topological constraints in random field image segmentation}},
doi = {10.15479/AT:IST-2011-0002},
year = {2011},
}
@inproceedings{3323,
abstract = {We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.},
author = {Wies, Thomas and Muñiz, Marco and Kuncak, Viktor},
location = {Wrocław, Poland},
pages = {476 -- 491},
publisher = {Springer},
title = {{An efficient decision procedure for imperative tree data structures}},
doi = {10.1007/978-3-642-22438-6_36},
volume = {6803},
year = {2011},
}
@misc{5381,
abstract = {In two-player finite-state stochastic games of partial obser- vation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distri- bution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or pos- itively (i.e., with positive probability), no matter the strategy of the second player.
We classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two- sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization.
Our main results for pure strategies are as follows: (1) For one-sided games with player 2 perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strate- gies are not sufficient, and present an exponential upper bound on mem- ory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algo- rithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 perfect observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and posi- tive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence re- sult exhibit serious flaws in previous results in the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
issn = {2664-1690},
pages = {43},
publisher = {IST Austria},
title = {{Partial-observation stochastic games: How to win when belief fails}},
doi = {10.15479/AT:IST-2011-0007},
year = {2011},
}
@inproceedings{3366,
abstract = {We present an algorithmic method for the quantitative, performance-aware synthesis of concurrent programs. The input consists of a nondeterministic partial program and of a parametric performance model. The nondeterminism allows the programmer to omit which (if any) synchronization construct is used at a particular program location. The performance model, specified as a weighted automaton, can capture system architectures by assigning different costs to actions such as locking, context switching, and memory and cache accesses. The quantitative synthesis problem is to automatically resolve the nondeterminism of the partial program so that both correctness is guaranteed and performance is optimal. As is standard for shared memory concurrency, correctness is formalized "specification free", in particular as race freedom or deadlock freedom. For worst-case (average-case) performance, we show that the problem can be reduced to 2-player graph games (with probabilistic transitions) with quantitative objectives. While we show, using game-theoretic methods, that the synthesis problem is Nexp-complete, we present an algorithmic method and an implementation that works efficiently for concurrent programs and performance models of practical interest. We have implemented a prototype tool and used it to synthesize finite-state concurrent programs that exhibit different programming patterns, for several performance models representing different architectures. },
author = {Cerny, Pavol and Chatterjee, Krishnendu and Henzinger, Thomas A and Radhakrishna, Arjun and Singh, Rohit},
editor = {Gopalakrishnan, Ganesh and Qadeer, Shaz},
location = {Snowbird, USA},
pages = {243 -- 259},
publisher = {Springer},
title = {{Quantitative synthesis for concurrent programs}},
doi = {10.1007/978-3-642-22110-1_20 },
volume = {6806},
year = {2011},
}
@inproceedings{3359,
abstract = {Motivated by improvements in constraint-solving technology and by the increase of routinely available computational power, partial-program synthesis is emerging as an effective approach for increasing programmer productivity. The goal of the approach is to allow the programmer to specify a part of her intent imperatively (that is, give a partial program) and a part of her intent declaratively, by specifying which conditions need to be achieved or maintained. The task of the synthesizer is to construct a program that satisfies the specification. As an example, consider a partial program where threads access shared data without using any synchronization mechanism, and a declarative specification that excludes data races and deadlocks. The task of the synthesizer is then to place locks into the program code in order for the program to meet the specification.
In this paper, we argue that quantitative objectives are needed in partial-program synthesis in order to produce higher-quality programs, while enabling simpler specifications. Returning to the example, the synthesizer could construct a naive solution that uses one global lock for shared data. This can be prevented either by constraining the solution space further (which is error-prone and partly defeats the point of synthesis), or by optimizing a quantitative objective that models performance. Other quantitative notions useful in synthesis include fault tolerance, robustness, resource (memory, power) consumption, and information flow.},
author = {Cerny, Pavol and Henzinger, Thomas A},
location = {Taipei; Taiwan},
pages = {149 -- 154},
publisher = {ACM},
title = {{From boolean to quantitative synthesis}},
doi = {10.1145/2038642.2038666},
year = {2011},
}
@inproceedings{3361,
abstract = {In this paper, we investigate the computational complexity of quantitative information flow (QIF) problems. Information-theoretic quantitative relaxations of noninterference (based on Shannon entropy)have been introduced to enable more fine-grained reasoning about programs in situations where limited information flow is acceptable. The QIF bounding problem asks whether the information flow in a given program is bounded by a constant $d$. Our first result is that the QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem asks whether it is possible to resolve nondeterministic choices in a given partial program in such a way that in the resulting deterministic program, the quantitative information flow is bounded by a given constant $d$. Our second result is that the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless synthesis problem generalizes to QIF general synthesis problem which does not impose the memoryless requirement (that is, by allowing the synthesized program to have more variables then the original partial program). Our third result is that the QIF general synthesis problem is EXPTIME-hard.},
author = {Cerny, Pavol and Chatterjee, Krishnendu and Henzinger, Thomas A},
location = {Cernay-la-Ville, France},
pages = {205 -- 217},
publisher = {IEEE},
title = {{The complexity of quantitative information flow problems}},
doi = {10.1109/CSF.2011.21},
year = {2011},
}
@inproceedings{3347,
abstract = {The class of omega-regular languages provides a robust specification language in verification. Every omega-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens "eventually". Finitary liveness was proposed by Alur and Henzinger as a stronger formulation of liveness. It requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider automata with finitary acceptance conditions defined by finitary Buchi, parity and Streett languages. We study languages expressible by such automata: we give their topological complexity and present a regular-expression characterization. We compare the expressive power of finitary automata and give optimal algorithms for classical decisions questions. We show that the finitary languages are Sigma 2-complete; we present a complete picture of the expressive power of various classes of automata with finitary and infinitary acceptance conditions; we show that the languages defined by finitary parity automata exactly characterize the star-free fragment of omega B-regular languages; and we show that emptiness is NLOGSPACE-complete and universality as well as language inclusion are PSPACE-complete for finitary parity and Streett automata.},
author = {Chatterjee, Krishnendu and Fijalkow, Nathanaël},
location = {Tarragona, Spain},
pages = {216 -- 226},
publisher = {Springer},
title = {{Finitary languages}},
doi = {10.1007/978-3-642-21254-3_16},
volume = {6638},
year = {2011},
}