@article{4626, abstract = {We consider concurrent two-player games with reachability objectives. In such games, at each round, player 1 and player 2 independently and simultaneously choose moves, and the two choices determine the next state of the game. The objective of player 1 is to reach a set of target states; the objective of player 2 is to prevent this. These are zero-sum games, and the reachability objective is one of the most basic objectives: determining the set of states from which player 1 can win the game is a fundamental problem in control theory and system verification. There are three types of winning states, according to the degree of certainty with which player 1 can reach the target. From type-1 states, player 1 has a deterministic strategy to always reach the target. From type-2 states, player 1 has a randomized strategy to reach the target with probability 1. From type-3 states, player 1 has for every real ε>0 a randomized strategy to reach the target with probability greater than 1−ε. We show that for finite state spaces, all three sets of winning states can be computed in polynomial time: type-1 states in linear time, and type-2 and type-3 states in quadratic time. The algorithms to compute the three sets of winning states also enable the construction of the winning and spoiling strategies.}, author = {de Alfaro, Luca and Thomas Henzinger and Kupferman, Orna}, journal = {Theoretical Computer Science}, number = {3}, pages = {188 -- 217}, publisher = {Elsevier}, title = {{Concurrent reachability games}}, doi = {10.1016/j.tcs.2007.07.008}, volume = {386}, year = {2007}, } @inproceedings{582, abstract = {Using the techniques of "quantum weak-measurements" as a coherent amplification mechanism for small signals, for the first time we have measured the recently proposed "spin Hall effect" of light.}, author = {Onur Hosten and Kwiat, Paul G}, publisher = {OSA}, title = {{Observing the spin hall effect of light via quantum weak measurements}}, doi = {10.1364/FIO.2007.JTuA4}, year = {2007}, } @article{6150, author = {Gumienny, Tina L. and MacNeil, Lesley T. and Wang, Huang and de Bono, Mario and Wrana, Jeffrey L. and Padgett, Richard W.}, issn = {0960-9822}, journal = {Current Biology}, number = {2}, pages = {159--164}, publisher = {Elsevier}, title = {{Glypican LON-2 is a conserved negative regulator of BMP-like signaling in Caenorhabditis elegans}}, doi = {10.1016/j.cub.2006.11.065}, volume = {17}, year = {2007}, } @unpublished{6321, abstract = {These lecture notes describe the current state of affairs for Manin's conjecture in the context of del Pezzo surfaces.}, author = {Browning, Timothy D}, booktitle = {arXiv}, title = {{The Manin conjecture in dimension 2}}, doi = {10.48550/arXiv.0704.1217}, year = {2007}, } @inbook{6323, abstract = {This paper surveys recent progress towards the Manin conjecture for (singular and non-singular) del Pezzo surfaces. To illustrate some of the techniques available, an upper bound of the expected order of magnitude is established for a singular del Pezzo surface of degree four.}, author = {Browning, Timothy D}, booktitle = {A Tribute to Gauss and Dirichlet}, pages = {39--56}, publisher = {American Mathematical Society}, title = {{An overview of Manin's conjecture for del Pezzo surfaces}}, volume = {7}, year = {2007}, } @article{7323, abstract = {The main factors for reducing the consumption of a vehicle are reduction of curb weight, air drag and increase in the drivetrain efficiency. Highly efficient drivetrains can be developed based on PEFC technology and curb weight may be limited by an innovative vehicle construction. In this paper, data on consumption and efficiency of a four‐place passenger vehicle with a curb weight of 850 kg and an H2/O2 fed PEFC/Supercap hybrid electric powertrain are presented. Hydrogen consumption in the New European Driving Cycle is 0.67 kg H2/100 km, which corresponds to a gasoline equivalent consumption of 2.5 l/100 km. When including the energy needed to supply pure oxygen, the calculated consumption increases from 0.67 to 0.69–0.79 kg H2/100 km, depending on the method of oxygen production.}, author = {Büchi, F. N. and Paganelli, G. and Dietrich, P. and Laurent, D. and Tsukada, A. and Varenne, P. and Delfino, A. and Kötz, R. and Freunberger, Stefan Alexander and Magne, P.-A. and Walser, D. and Olsommer, D.}, issn = {1615-6846}, journal = {Fuel Cells}, number = {4}, pages = {329--335}, publisher = {Wiley}, title = {{Consumption and efficiency of a passenger car with a Hydrogen/Oxygen PEFC based hybrid electric drivetrain}}, doi = {10.1002/fuce.200600050}, volume = {7}, year = {2007}, } @article{7324, abstract = {Efficiency is the key parameter for the application of fuel cells in automotive applications. The efficiency of a hydrogen/oxygen polymer electrolyte fuel cell system is analyzed and compared to hydrogen/air systems. The analysis is performed for the tank to electric power chain. Furthermore, the additional energy required for using pure oxygen as a second fuel is analyzed and included in the calculation. The results show that if hydrogen is produced from primary fossil energy carriers, such as natural gas and pure oxygen needs to be obtained by a conventional process; the fuel to electric current efficiency is comparable for hydrogen/oxygen and hydrogen/air systems. However, if hydrogen and oxygen are produced by the splitting of water, i.e., by electrolysis or by a thermochemical process, the fuel to electric current efficiency for the hydrogen/oxygen system is clearly superior.}, author = {Büchi, F. N. and Freunberger, Stefan Alexander and Reum, M. and Paganelli, G. and Tsukada, A. and Dietrich, P. and Delfino, A.}, issn = {1615-6846}, journal = {Fuel Cells}, number = {2}, pages = {159--164}, publisher = {Wiley}, title = {{On the efficiency of an advanced automotive fuel cell system}}, doi = {10.1002/fuce.200500257}, volume = {7}, year = {2007}, } @article{7325, abstract = {Our experimental results shown here disprove that finite diffusion can generally be assumed in ac impedance models for H2/air-polymer electrolyte fuel cells (PEFCs) to account for the diffusive transport of oxygen through the gas diffusion layer (GDL) toward the air electrode. It is shown that the amplitude of the oxygen concentration oscillation created as a consequence of superimposed ac current at the air electrode is not zero at the channel/GDL interface but extends into the gas channels, at least below modulation frequencies of fmod=10 Hz . By this, sinusoidal oxygen-concentration oscillations within the cathode gas channels are excited locally along the flow field. Due to the forced air convection in the cathode flow-field channels, a coupling via the gas phase occurs downstream of the flow field. The coupling strongly affects the local and by this the overall impedance response of the cell and evokes the formation of a low-frequency arc in H2/air-PEFC impedance spectra. Based on the experimental results, a qualitative model is presented explaining the local impedance response of a segmented 200cm2H2/air PEFC.}, author = {Schneider, I. A. and Freunberger, Stefan Alexander and Kramer, D. and Wokaun, A. and Scherer, G. G.}, issn = {0013-4651}, journal = {Journal of The Electrochemical Society}, number = {4}, publisher = {The Electrochemical Society}, title = {{Oscillations in gas channels: Part I. The forgotten player in impedance spectroscopy in PEFCs}}, doi = {10.1149/1.2435706}, volume = {154}, year = {2007}, } @article{3427, abstract = {We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the wing disk of the fruit fly Drosophila. © 2007 The American Physical Society}, author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and Gonzalez Gaitan, Marcos and Julicher, Frank}, journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics}, number = {1}, publisher = {American Institute of Physics}, title = {{Morphogen transport in epithelia}}, doi = {10.1103/PhysRevE.75.011901}, volume = {75}, year = {2007}, } @inbook{3432, abstract = {Evolution has left its signature on the molecules and morphology of living organisms. Ancestral reconstruction offers an excellent tool for understanding the process of evolution using comparative information. Methods for ancestral reconstruction have generally focused on reconstructing the ancestral states at the internal nodes of a phylogeny. Often, we are not interested in particular nodes of the phylogeny but the whole history of a character. This chapter focuses on a Bayesian method for estimating these histories, or mutational paths, on phylogenies. Mutational path methods differ most notably from other approaches in their ability to estimate not only the ancestral states at the internal nodes of a phylogeny, but also the order and timing of mutational changes across the phylogeny. The chapter provides a concise introduction to the statistical tools needed for sampling mutational paths on a phylogeny.}, author = {Jonathan Bollback and Gardner, Paul P and Nielsen, Rasmus}, booktitle = {Ancestral Sequence Reconstruction}, editor = {Liberles, David A}, pages = {69 -- 79}, publisher = {Oxford University Press}, title = {{Estimating the history of mutations on a phylogeny}}, doi = {10.1093/acprof:oso/9780199299188.003.0006}, year = {2007}, } @article{3436, abstract = {he potential for di? erences between genetic paternity and paternity inferred from behavioral observation has long been recognized. These di? erences are associated with the challenge for females of seeking both genetic and material bene? ts; this challenge is less severe in species with polygynous, non-resource-based mating systems (such as leks) than in those with resource-based systems. We pres- ent the ? rst study of paternity patt erns in a non-resource-based species that does not form true leks. We compared paternity inferred from observed mating behavior to genetically assigned paternity in the Satin Bowerbird (Ptilonorhynchus violaceus) using eight microsatellite markers. Mating behavior was observed and recorded via automated video-cameras positioned at all bowers (29?34 bowers each year) in the study site throughout each mating season. We obtained blood samples and identi- ? ed mothers for 11 chicks in 9 nests. For all chicks, the most likely genetic father had been observed to mate with the mother in the year the chick was sampled. All most likely genetic fathers were assigned with high con? dence and all were bower- holding males. These results demonstrate that genetic paternity can be inferred from observed mating behavior with reasonable con? dence in Satin Bowerbirds. Observed male mating-success is therefore a reliable predictor of reproductive success, and this suggests that high skew in observed male mating-success translates directly to high skew in reproductive success. }, author = {Reynolds, Sheila M and Dryer, Katie and Jonathan Bollback and Uy, J Albert and Patricelli, Gail L and Robson, Timothy and Borgia, Gerald and Braun, Michael J}, journal = {The Auk}, number = {3}, pages = {857 -- 867}, publisher = {University of California Press}, title = {{Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system}}, doi = {10.1642/0004-8038(2007)124[857:BPPGPI]2.0.CO;2}, volume = {124}, year = {2007}, } @article{3450, author = {Peter Jonas and Buzsáki, György}, journal = {Scholarpedia}, publisher = {Scholarpedia}, title = {{Neural inhibition}}, doi = {10.4249/scholarpedia.3286}, volume = {2}, year = {2007}, } @article{3523, abstract = {On the linear track, the recent firing sequences of CA1 place cells recur during sharp wave/ripple patterns (SWRs) in a reverse temporal order [Foster & Wilson (2006) Nature, 440, 680-683]. We have found similar reverse-order reactivation during SWRs in open-field exploration where the firing sequence of cells varied before each SWR. Both the onset times and the firing patterns of cells showed a tendency for reversed sequences during SWRs. These effects were observed for SWRs that occurred during exploration, but not for those during longer immobility periods. Additionally, reverse reactivation was stronger when it was preceded by higher speed (> 5 cm/s) run periods. The trend for reverse-order SWR reactivation was not significantly different in familiar and novel environments, even though SWR-associated firing rates of both pyramidal cells and interneurons were reduced in novel environments as compared with familiar. During exploration-associated SWRs (eSWR) place cells retain place-selective firing [O'Neill et al. (2006) Neuron, 49, 143-155]. Here, we have shown that each cell's firing onset was more delayed and firing probability more reduced during eSWRs the further the rat was from the middle of the cell's place field; that is, cells receiving less momentary place-related excitatory drive fired later during SWR events. However, even controlling for place field distance, the recent firing of cells was still significantly correlated with SWR reactivation sequences. We therefore propose that both place-related drive and the firing history of cells contribute to reverse reactivation during eSWRs.}, author = {Jozsef Csicsvari and Joseph O'Neill and Allen, Kevin and Senior,Timothy}, journal = {European Journal of Neuroscience}, number = {3}, pages = {704 -- 716}, publisher = {Wiley-Blackwell}, title = {{Place-selective firing contributes to the reverse-order reactivation of CA1 pyramidal cells during sharp waves in open-field exploration}}, doi = {10.1111/j.1460-9568.2007.05684.x}, volume = {26}, year = {2007}, } @inproceedings{3561, abstract = {The main result of this paper is an extension of de Silva's Weak Delaunay Theorem to smoothly embedded curves and surfaces in Euclidean space. Assuming a sufficiently fine sampling, we prove that i + 1 points in the sample span an i-simplex in the restricted Delaunay triangulation iff every subset of the i + 1 points has a weak witness.}, author = {Attali, Dominique and Herbert Edelsbrunner and Mileyko, Yuriy}, pages = {143 -- 150}, publisher = {ACM}, title = {{Weak witnesses for Delaunay triangulations of submanifolds}}, doi = {10.1145/1236246.1236267}, year = {2007}, } @inproceedings{3601, abstract = {In this paper, the multiobjective optimal design of space-based reconfigurable sensor networks with novel adaptive MEMS antennas is investigated by using multiobjective evolutionary algorithms. The non-dominated sorting genetic algorithm II (NSGA-II) is employed to obtain multi-criteria Pareto-optimal solutions, which allows system designers to easily make a reasonable trade-off choice from the set of non-dominated solutions according to their preferences and system requirements. As a case study, a cluster-based satellite sensing network is simulated under multiple objectives. Most importantly, this paper also presents the application of our newly designed adaptive MEMS antennas together with the NSGA-II to the multiobjective optimal design of space-based reconfigurable sensor networks.}, author = {Yang, Erfu and Haridas, Nakul and El-Rayis, Ahmed O and Erdogan, Ahmet T and Arslan, Tughrul and Nicholas Barton}, pages = {27 -- 34}, publisher = {IEEE}, title = {{Multiobjective optimal design of MEMS-based reconfigurable and evolvable sensor networks for space applications}}, doi = {10.1109/AHS.2007.76}, year = {2007}, } @book{3674, abstract = {Evolution permeates all of biology. But researchers in molecular and cellular biology, genetics, developmental biology, microbiology, and neuroscience have only recently begun to think seriously in terms of evolution. The chief reasons for this shift are the growing list of organisms with sequenced genomes; the increasingly sophisticated ways of interpreting those sequences; and the ever more powerful experimental techniques (and wider range of model organisms) with which to ask questions about evolution as well as mechanism. Evolution serves as a primary text for undergraduate and graduate courses in evolution. It is also a text working scientists can use to educate themselves on how evolution affects their fields. It differs from currently available alternatives in containing more molecular biology than is traditionally the case. But this is not at the expense of traditional evolutionary theory. Indeed, a glance at the Table of Contents and the authors' interests reveals the range of material covered in this book. The authors are world-renowned in population genetics, bacterial genomics, paleontology, human genetics, and developmental biology. The integration of molecular biology and evolutionary biology reflects the current direction of much research among evolutionary scientists.}, author = {Barton, Nicholas H and Briggs, Derek and Eisen, Jonathan and Goldstein, David and Patel, Nipam}, isbn = {978-087969684-9}, pages = {XIV, 833}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Evolution}}, year = {2007}, } @inproceedings{3681, abstract = {The extraction of a parametric global motion from a motion field is a task with several applications in video processing. We present two probabilistic formulations of the problem and carry out optimization using the RAST algorithm, a geometric matching method novel to motion estimation in video. RAST uses an exhaustive and adaptive search of transformation space and thus gives – in contrast to local sampling optimization techniques used in the past – a globally optimal solution. Among other applications, our framework can thus be used as a source of ground truth for benchmarking motion estimation algorithms. Our main contributions are: first, the novel combination of a state-of-the-art MAP criterion for dominant motion estimation with a search procedure that guarantees global optimality. Second, experimental results that illustrate the superior performance of our approach on synthetic flow fields as well as real-world video streams. Third, a significant speedup of the search achieved by extending the model with an additional smoothness prior.}, author = {Ulges, Adrian and Christoph Lampert and Keysers,Daniel and Breuel,Thomas M}, pages = {204 -- 213}, publisher = {Springer}, title = {{Optimal dominant motion estimation using adaptive search of transformation space}}, doi = {10.1007/978-3-540-74936-3_21}, volume = {4713}, year = {2007}, } @techreport{3687, abstract = {Recent years have seen huge advances in object recognition from images. Recognition rates beyond 95% are the rule rather than the exception on many datasets. However, most state-of-the-art methods can only decide if an object is present or not. They are not able to provide information on the object location or extent within in the image. We report on a simple yet powerful scheme that extends many existing recognition methods to also perform localization of object bounding boxes. This is achieved by maximizing the classification score over all possible subrectangles in the image. Despite the impression that this would be computationally intractable, we show that in many situations efficient algorithms exist which solve a generalized maximum subrectangle problem. We show how our method is applicable to a variety object detection frameworks and demonstrate its performance by applying it to the popular bag of visual words model, achieving competitive results on the PASCAL VOC 2006 dataset.}, author = {Blaschko,Matthew B and Hofmann,Thomas and Christoph Lampert}, booktitle = {Unknown}, number = {164}, publisher = {Max-Planck-Institute for Biological Cybernetics}, title = {{Efficient subwindow search for object localization}}, year = {2007}, } @article{3723, abstract = {The folding and function of proteins is guided by their multidimensional energy landscapes. Local corrugations on rugged energy surfaces determine the dynamics of functionally related conformational changes and molecular flexibilities. By varying the temperature during the force-induced unfolding of the membrane protein bacteriorhodopsin, we directly determined the energy roughness of individual transmembrane α-helices. All helices have rugged energy surfaces with an overall roughness scale of 4−6 kBT, in line with the vital roles of transmembrane helices as functional and structural building blocks. Interestingly, the mechanical unfolding of misfolded membrane proteins in vivo is likely to occur on similarly energy rugged surfaces, which may also provide an energetic framework for small vertical motions of functionally relevant helices. Finally, our results also indicate that transmembrane protein structures can have rough energy surfaces despite their highly restricted conformational spaces in confining lipid bilayer environments. }, author = {Harald Janovjak and Knaus, Helene and Mueller, Daniel J}, journal = {Journal of the American Chemical Society}, number = {2}, pages = {246 -- 247}, publisher = {ACS}, title = {{Transmembrane helices have rough energy surfaces}}, doi = {10.1021/ja065684a}, volume = {129}, year = {2007}, } @article{3727, abstract = {Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand–receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.}, author = {Bippes, Christian A and Harald Janovjak and Kedrov, Alexej and Mueller, Daniel J}, journal = {Nanotechnology}, number = {4}, publisher = {IOP Publishing Ltd.}, title = {{Digital force-feedback for protein unfolding experiments using atomic force microscopy}}, doi = {10.1088/0957-4484/18/4/044022}, volume = {18}, year = {2007}, }