@article{518,
abstract = {Cancer stem cells or cancer initiating cells are believed to contribute to cancer recurrence after therapy. MicroRNAs (miRNAs) are short RNA molecules with fundamental roles in gene regulation. The role of miRNAs in cancer stem cells is only poorly understood. Here, we report miRNA expression profiles of glioblastoma stem cell-containing CD133 + cell populations. We find that miR-9, miR-9 * (referred to as miR-9/9 *), miR-17 and miR-106b are highly abundant in CD133 + cells. Furthermore, inhibition of miR-9/9 * or miR-17 leads to reduced neurosphere formation and stimulates cell differentiation. Calmodulin-binding transcription activator 1 (CAMTA1) is a putative transcription factor, which induces the expression of the anti-proliferative cardiac hormone natriuretic peptide A (NPPA). We identify CAMTA1 as an miR-9/9 * and miR-17 target. CAMTA1 expression leads to reduced neurosphere formation and tumour growth in nude mice, suggesting that CAMTA1 can function as tumour suppressor. Consistently, CAMTA1 and NPPA expression correlate with patient survival. Our findings could provide a basis for novel strategies of glioblastoma therapy.},
author = {Schraivogel, Daniel and Weinmann, Lasse and Beier, Dagmar and Tabatabai, Ghazaleh and Eichner, Alexander and Zhu, Jia and Anton, Martina and Sixt, Michael K and Weller, Michael and Beier, Christoph and Meister, Gunter},
journal = {EMBO Journal},
number = {20},
pages = {4309 -- 4322},
publisher = {Wiley-Blackwell},
title = {{CAMTA1 is a novel tumour suppressor regulated by miR-9/9 * in glioblastoma stem cells}},
doi = {10.1038/emboj.2011.301},
volume = {30},
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},
}
@misc{5379,
abstract = {Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is ̃O(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the ̃O(n·m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of O(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m > n4/3 an earlier bound of O(min(m1.5, m·n2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n2), which is an improvement over earlier bounds for m > n4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.},
author = {Chatterjee, Krishnendu and Henzinger, Monika},
issn = {2664-1690},
pages = {20},
publisher = {IST Austria},
title = {{An O(n2) time algorithm for alternating Büchi games}},
doi = {10.15479/AT:IST-2011-0009},
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},
}
@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},
}
@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{3266,
abstract = {We present a joint image segmentation and labeling model (JSL) which, given a bag of figure-ground segment hypotheses extracted at multiple image locations and scales, constructs a joint probability distribution over both the compatible image interpretations (tilings or image segmentations) composed from those segments, and over their labeling into categories. The process of drawing samples from the joint distribution can be interpreted as first sampling tilings, modeled as maximal cliques, from a graph connecting spatially non-overlapping segments in the bag [1], followed by sampling labels for those segments, conditioned on the choice of a particular tiling. We learn the segmentation and labeling parameters jointly, based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure. The partition function over tilings and labelings is increasingly more accurately approximated by including incorrect configurations that a not-yet-competent model rates probable during learning. We show that the proposed methodologymatches the current state of the art in the Stanford dataset [2], as well as in VOC2010, where 41.7% accuracy on the test set is achieved.},
author = {Ion, Adrian and Carreira, Joao and Sminchisescu, Cristian},
booktitle = {NIPS Proceedings},
location = {Granada, Spain},
pages = {1827 -- 1835},
publisher = {Neural Information Processing Systems Foundation},
title = {{Probabilistic joint image segmentation and labeling}},
volume = {24},
year = {2011},
}
@phdthesis{3273,
author = {Maître, Jean-Léon},
publisher = {IST Austria},
title = {{Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors}},
year = {2011},
}
@inproceedings{3297,
abstract = {Animating detailed liquid surfaces has always been a challenge for computer graphics researchers and visual effects artists. Over the past few years, researchers in this field have focused on mesh-based surface tracking to synthesize extremely detailed liquid surfaces as efficiently as possible. This course provides a solid understanding of the steps required to create a fluid simulator with a mesh-based liquid surface.
The course begins with an overview of several existing liquid-surface-tracking techniques and the pros and cons of each method. Then it explains how to embed a triangle mesh into a finite-difference-based fluid simulator and describes several methods for allowing the liquid surface to merge together or break apart. The final section showcases the benefits and further applications of a mesh-based liquid surface, highlighting state-of-the-art methods for tracking colors and textures, maintaining liquid volume, preserving small surface features, and simulating realistic surface-tension waves.},
author = {Wojtan, Christopher J and Müller Fischer, Matthias and Brochu, Tyson},
location = {Vancouver, BC, Canada},
publisher = {ACM},
title = {{Liquid simulation with mesh-based surface tracking}},
doi = {10.1145/2037636.2037644},
year = {2011},
}
@misc{3312,
abstract = {We study the 3D reconstruction of plant roots from multiple 2D images. To meet the challenge caused by the delicate nature of thin branches, we make three innovations to cope with the sensitivity to image quality and calibration. First, we model the background as a harmonic function to improve the segmentation of the root in each 2D image. Second, we develop the concept of the regularized visual hull which reduces the effect of jittering and refraction by ensuring consistency with one 2D image. Third, we guarantee connectedness through adjustments to the 3D reconstruction that minimize global error. Our software is part of a biological phenotype/genotype study of agricultural root systems. It has been tested on more than 40 plant roots and results are promising in terms of reconstruction quality and efficiency.},
author = {Zheng, Ying and Gu, Steve and Edelsbrunner, Herbert and Tomasi, Carlo and Benfey, Philip},
booktitle = {Proceedings of the IEEE International Conference on Computer Vision},
location = {Barcelona, Spain},
publisher = {IEEE},
title = {{ Detailed reconstruction of 3D plant root shape}},
doi = {10.1109/ICCV.2011.6126475},
year = {2011},
}
@inproceedings{3329,
abstract = {We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance µ in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution shape P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(n log n)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. An alternative algorithm, based purely on rational arithmetic, answers the same deconstruction problem, up to an uncertainty parameter, and its running time depends on the parameter δ (in addition to the other input parameters: n, δ and the radius of the disk). If the input shape is found to be approximable, the rational-arithmetic algorithm also computes an approximate solution shape for the problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution shape P with at most one more vertex than a vertex-minimal one. Our study is motivated by applications from two different domains. However, since the offset operation has numerous uses, we anticipate that the reverse question that we study here will be still more broadly applicable. We present results obtained with our implementation of the rational-arithmetic algorithm.},
author = {Berberich, Eric and Halperin, Dan and Kerber, Michael and Pogalnikova, Roza},
booktitle = {Proceedings of the twenty-seventh annual symposium on Computational geometry},
location = {Paris, France},
pages = {187 -- 196},
publisher = {ACM},
title = {{Deconstructing approximate offsets}},
doi = {10.1145/1998196.1998225},
year = {2011},
}
@inproceedings{3343,
abstract = {We present faster and dynamic algorithms for the following problems arising in probabilistic verification: Computation of the maximal end-component (mec) decomposition of Markov decision processes (MDPs), and of the almost sure winning set for reachability and parity objectives in MDPs. We achieve the following running time for static algorithms in MDPs with graphs of n vertices and m edges: (1) O(m · min{ √m, n2/3 }) for the mec decomposition, improving the longstanding O(m·n) bound; (2) O(m·n2/3) for reachability objectives, improving the previous O(m · √m) bound for m > n4/3; and (3) O(m · min{ √m, n2/3 } · log(d)) for parity objectives with d priorities, improving the previous O(m · √m · d) bound. We also give incremental and decremental algorithms in linear time for mec decomposition and reachability objectives and O(m · log d) time for parity ob jectives.},
author = {Chatterjee, Krishnendu and Henzinger, Monika},
location = {San Francisco, USA},
pages = {1318 -- 1336},
publisher = {SIAM},
title = {{Faster and dynamic algorithms for maximal end component decomposition and related graph problems in probabilistic verification}},
doi = {10.1137/1.9781611973082.101},
year = {2011},
}
@inproceedings{3324,
abstract = {Automated termination provers often use the following schema to prove that a program terminates: construct a relational abstraction of the program's transition relation and then show that the relational abstraction is well-founded. The focus of current tools has been on developing sophisticated techniques for constructing the abstractions while relying on known decidable logics (such as linear arithmetic) to express them. We believe we can significantly increase the class of programs that are amenable to automated termination proofs by identifying more expressive decidable logics for reasoning about well-founded relations. We therefore present a new decision procedure for reasoning about multiset orderings, which are among the most powerful orderings used to prove termination. We show that, using our decision procedure, one can automatically prove termination of natural abstractions of programs.},
author = {Piskac, Ruzica and Wies, Thomas},
editor = {Jhala, Ranjit and Schmidt, David},
location = {Texas, USA},
pages = {371 -- 386},
publisher = {Springer},
title = {{Decision procedures for automating termination proofs}},
doi = {10.1007/978-3-642-18275-4_26},
volume = {6538},
year = {2011},
}
@article{3386,
abstract = {Evolutionary theories of ageing predict that life span increases with decreasing extrinsic mortality, and life span variation among queens in ant species seems to corroborate this prediction: queens, which are the only reproductive in a colony, live much longer than queens in multi-queen colonies. The latter often inhabit ephemeral nest sites and accordingly are assumed to experience a higher mortality risk. Yet, all prior studies compared queens from different single- and multi-queen species. Here, we demonstrate an effect of queen number on longevity and fecundity within a single, socially plastic species, where queens experience the similar level of extrinsic mortality. Queens from single- and two-queen colonies had significantly longer lifespan and higher fecundity than queens living in associations of eight queens. As queens also differ neither in morphology nor the mode of colony foundation, our study shows that the social environment itself strongly affects ageing rate.},
author = {Schrempf, Alexandra and Cremer, Sylvia and Heinze, Jürgen},
journal = {Journal of Evolutionary Biology},
number = {7},
pages = {1455 -- 1461},
publisher = {Wiley-Blackwell},
title = {{Social influence on age and reproduction reduced lifespan and fecundity in multi queen ant colonies}},
doi = {10.1111/j.1420-9101.2011.02278.x},
volume = {24},
year = {2011},
}
@article{3393,
abstract = {Unlike unconditionally advantageous “Fisherian” variants that tend to spread throughout a species range once introduced anywhere, “bistable” variants, such as chromosome translocations, have two alternative stable frequencies, absence and (near) fixation. Analogous to populations with Allee effects, bistable variants tend to increase locally only once they become sufficiently common, and their spread depends on their rate of increase averaged over all frequencies. Several proposed manipulations of insect populations, such as using Wolbachia or “engineered underdominance” to suppress vector-borne diseases, produce bistable rather than Fisherian dynamics. We synthesize and extend theoretical analyses concerning three features of their spatial behavior: rate of spread, conditions to initiate spread from a localized introduction, and wave stopping caused by variation in population densities or dispersal rates. Unlike Fisherian variants, bistable variants tend to spread spatially only for particular parameter combinations and initial conditions. Wave initiation requires introduction over an extended region, while subsequent spatial spread is slower than for Fisherian waves and can easily be halted by local spatial inhomogeneities. We present several new results, including robust sufficient conditions to initiate (and stop) spread, using a one-parameter cubic approximation applicable to several models. The results have both basic and applied implications.},
author = {Barton, Nicholas H and Turelli, Michael},
journal = {American Naturalist},
number = {3},
pages = {E48 -- E75},
publisher = {University of Chicago Press},
title = {{Spatial waves of advance with bistable dynamics: Cytoplasmic and genetic analogues of Allee effects}},
doi = {10.1086/661246},
volume = {178},
year = {2011},
}
@article{3374,
abstract = {Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'.},
author = {Tkacik, Gasper and Walczak, Aleksandra},
journal = {Journal of Physics: Condensed Matter},
number = {15},
publisher = {IOP Publishing Ltd.},
title = {{Information transmission in genetic regulatory networks a review}},
doi = {10.1088/0953-8984/23/15/153102},
volume = {23},
year = {2011},
}
@article{3379,
abstract = {The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion.},
author = {Row, Richard and Maître, Jean-Léon and Martin, Benjamin and Stockinger, Petra and Heisenberg, Carl-Philipp J and Kimelman, David},
journal = {Developmental Biology},
number = {1},
pages = {102 -- 110},
publisher = {Elsevier},
title = {{Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail}},
doi = {10.1016/j.ydbio.2011.03.025},
volume = {354},
year = {2011},
}
@inproceedings{3348,
abstract = {We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two-player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a linear (in the number of clocks) number of memory bits. Precisely, we show that for safety objectives, a memory of size (3 · |C|+lg(|C|+1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential bound. We also settle the open question of whether winning region controller strategies require memory for safety objectives by showing with an example the necessity of memory for region strategies to win for safety objectives.},
author = {Chatterjee, Krishnendu and Prabhu, Vinayak},
location = {Chicago, USA},
pages = {221 -- 230},
publisher = {Springer},
title = {{Synthesis of memory efficient real time controllers for safety objectives}},
doi = {10.1145/1967701.1967734},
year = {2011},
}
@inproceedings{3350,
abstract = {A controller for a discrete game with ω-regular objectives requires attention if, intuitively, it requires measuring the state and switching from the current control action. Minimum attention controllers are preferable in modern shared implementations of cyber-physical systems because they produce the least burden on system resources such as processor time or communication bandwidth. We give algorithms to compute minimum attention controllers for ω-regular objectives in imperfect information discrete two-player games. We show a polynomial-time reduction from minimum attention controller synthesis to synthesis of controllers for mean-payoff parity objectives in games of incomplete information. This gives an optimal EXPTIME-complete synthesis algorithm. We show that the minimum attention controller problem is decidable for infinite state systems with finite bisimulation quotients. In particular, the problem is decidable for timed and rectangular automata.},
author = {Chatterjee, Krishnendu and Majumdar, Ritankar},
editor = {Fahrenberg, Uli and Tripakis, Stavros},
location = {Aalborg, Denmark},
pages = {145 -- 159},
publisher = {Springer},
title = {{Minimum attention controller synthesis for omega regular objectives}},
doi = {10.1007/978-3-642-24310-3_11},
volume = {6919},
year = {2011},
}
@inproceedings{3355,
abstract = {Byzantine Fault Tolerant (BFT) protocols aim to improve the reliability of distributed systems. They enable systems to tolerate arbitrary failures in a bounded number of nodes. BFT protocols are usually proven correct for certain safety and liveness properties. However, recent studies have shown that the performance of state-of-the-art BFT protocols decreases drastically in the presence of even a single malicious node. This motivates a formal quantitative analysis of BFT protocols to investigate their performance characteristics under different scenarios. We present HyPerf, a new hybrid methodology based on model checking and simulation techniques for evaluating the performance of BFT protocols. We build a transition system corresponding to a BFT protocol and systematically explore the set of behaviors allowed by the protocol. We associate certain timing information with different operations in the protocol, like cryptographic operations and message transmission. After an elaborate state exploration, we use the time information to evaluate the performance characteristics of the protocol using simulation techniques. We integrate our framework in Mace, a tool for building and verifying distributed systems. We evaluate the performance of PBFT using our framework. We describe two different use-cases of our methodology. For the benign operation of the protocol, we use the time information as random variables to compute the probability distribution of the execution times. In the presence of faults, we estimate the worst-case performance of the protocol for various attacks that can be employed by malicious nodes. Our results show the importance of hybrid techniques in systematically analyzing the performance of large-scale systems.},
author = {Halalai, Raluca and Henzinger, Thomas A and Singh, Vasu},
location = {Aachen, Germany},
pages = {255 -- 264},
publisher = {IEEE},
title = {{Quantitative evaluation of BFT protocols}},
doi = {10.1109/QEST.2011.40},
year = {2011},
}