@article{878,
abstract = {Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.
},
author = {Fyodor Kondrashov},
journal = {Nature Genetics},
number = {1},
pages = {9 -- 10},
publisher = {Nature Publishing Group},
title = {{In search of the limits of evolution}},
doi = {10.1038/ng0105-9},
volume = {37},
year = {2005},
}
@article{880,
abstract = {Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution.},
author = {Kondrashov, Fyodor},
journal = {Biofizika},
number = {3},
pages = {396 -- 403},
publisher = {Pleiades Publishing},
title = {{The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus}},
volume = {50},
year = {2005},
}
@article{882,
abstract = {Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively.},
author = {Fyodor Kondrashov},
journal = {Human Molecular Genetics},
number = {16},
pages = {2415 -- 2419},
publisher = {Oxford University Press},
title = {{Prediction of pathogenic mutations in mitochondrially encoded human tRNAs}},
doi = {10.1093/hmg/ddi243},
volume = {14},
year = {2005},
}
@article{893,
abstract = {Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.},
author = {Jordan, Ingo K and Fyodor Kondrashov and Adzhubeǐ, Ivan A and Wolf, Yuri I and Koonin, Eugene V and Kondrashov, Alexey S and Sunyaev, Shamil R},
journal = {Nature},
number = {7026},
pages = {633 -- 638},
publisher = {Nature Publishing Group},
title = {{A universal trend of amino acid gain and loss in protein evolution}},
doi = {10.1038/nature03306},
volume = {433},
year = {2005},
}
@article{1298,
abstract = {Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest fluorescence changes. However, GCaMP1.6 suffered from photobleaching, whereas the fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible, with TN-L15 showing the fastest rise of the signals at lower activity rates. We show for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR). The expression level of the indicator biased the signal kinetics and SNR, whereas the signal amplitude was independent. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of the optical signals.},
author = {Reiff, Dierk F and Ihring, Alexandra and Guerrero, Giovanna and Isacoff, Ehud Y and Maximilian Jösch and Nakai, Junichi and Borst, Alexander},
journal = {Journal of Neuroscience},
number = {19},
pages = {4766 -- 4778},
publisher = {Society for Neuroscience},
title = {{In vivo performance of genetically encoded indicators of neural activity in flies}},
doi = {10.1523/JNEUROSCI.4900-04.2005},
volume = {25},
year = {2005},
}
@inbook{1444,
abstract = {The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat connections and character varieties for curves, respectively. Several new results and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman and Earl-Kirwan are explained. These use the representation theory of finite groups of Lie-type via the arithmetic of character varieties and lead to an unexpected conjecture for a Hard Lefschetz theorem for their cohomology.},
author = {Tamas Hausel},
booktitle = {Geometric Methods in Algebra and Number Theory},
pages = {193 -- 217},
publisher = {Springer},
title = {{Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a curve}},
doi = {10.1007/0-8176-4417-2_9},
volume = {235},
year = {2005},
}
@article{1447,
abstract = {Building on a recent paper [8], here we argue that the combinatorics of matroids are intimately related to the geometry and topology of toric hyperkähler varieties. We show that just like toric varieties occupy a central role in Stanley’s proof for the necessity of McMullen’s conjecture (or g-inequalities) about the classification of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties leads to new restrictions on face vectors of matroid complexes. Namely in this paper we will give two proofs that the injectivity part of the Hard Lefschetz theorem survives for toric hyperkähler varieties. We explain how this implies the g-inequalities for rationally representable matroids. We show how the geometrical intuition in the first proof, coupled with results of Chari [3], leads to a proof of the g-inequalities for general matroid complexes, which is a recent result of Swartz [20]. The geometrical idea in the second proof will show that a pure O-sequence should satisfy the g-inequalities, thus showing that our result is in fact a consequence of a long-standing conjecture of Stanley.},
author = {Tamas Hausel},
journal = {Open Mathematics},
number = {1},
pages = {26 -- 38},
publisher = {Central European Science Journals},
title = {{Quaternionic geometry of matroids}},
doi = {10.2478/BF02475653},
volume = {3},
year = {2005},
}
@article{1463,
abstract = {We study an integration theory in circle equivariant cohomology in order to prove a theorem relating the cohomology ring of a hyperkähler quotient to the cohomology ring of the quotient by a maximal abelian subgroup, analogous to a theorem of Martin for symplectic quotients. We discuss applications of this theorem to quiver varieties, and compute as an example the ordinary and equivariant cohomology rings of a hyperpolygon space.},
author = {Tamas Hausel and Proudfoot, Nicholas J},
journal = {Topology},
number = {1},
pages = {231 -- 248},
publisher = {Elsevier},
title = {{Abelianization for hyperkähler quotients}},
doi = {10.1016/j.top.2004.04.002},
volume = {44},
year = {2005},
}
@inproceedings{3175,
abstract = {This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov Random Field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with "almost" metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented.},
author = {Rother, Carsten and Kumar, Sanjiv and Vladimir Kolmogorov and Blake, Andrew},
pages = {589 -- 596},
publisher = {IEEE},
title = {{Digital tapestry}},
doi = {10.1109/CVPR.2005.130},
volume = {1},
year = {2005},
}
@inproceedings{3176,
abstract = {This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.
},
author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten},
pages = {1186 -- 1186},
publisher = {IEEE},
title = {{Bi-layer segmentation of binocular stereo video}},
doi = {10.1109/CVPR.2005.90},
year = {2005},
}
@inproceedings{3181,
abstract = {Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method.},
author = {Vladimir Kolmogorov and Wainwright, Martin J},
pages = {316 -- 323},
publisher = {AUAI Press},
title = {{On the optimality of tree reweighted max product message passing}},
year = {2005},
}
@inproceedings{3182,
abstract = {In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such "submodular" metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the "shrinking" problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints.},
author = {Vladimir Kolmogorov and Boykov, Yuri},
pages = {564 -- 571},
publisher = {IEEE},
title = {{What metrics can be approximated by geo cuts or global optimization of length area and flux}},
doi = {10.1109/ICCV.2005.252},
volume = {1},
year = {2005},
}
@inproceedings{3183,
abstract = {This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar perfomance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.},
author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten},
pages = {407 -- 414},
publisher = {IEEE},
title = {{Bi-layer segmentation of binocular stereo video}},
doi = {10.1109/CVPR.2005.91},
volume = {2},
year = {2005},
}
@inproceedings{3211,
abstract = {We present an improved bound on the advantage of any q-query adversary at distinguishing between the CBC MAC over a random n-bit permutation and a random function outputting n bits. The result assumes that no message queried is a prefix of any other, as is the case when all messages to be MACed have the same length. We go on to give an improved analysis of the encrypted CBC MAC, where there is no restriction on queried messages. Letting m be the block length of the longest query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate into improved guarantees on the probability of forging these MACs.},
author = {Bellare, Mihir and Krzysztof Pietrzak and Rogaway, Phillip},
pages = {527 -- 545},
publisher = {Springer},
title = {{Improved security analyses for CBC MACs}},
doi = {10.1007/11535218_32},
volume = {3621},
year = {2005},
}
@inproceedings{3212,
abstract = {The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use.
In this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model.},
author = {Dodis, Yevgeniy and Oliveira, Roberto and Krzysztof Pietrzak},
pages = {449 -- 466},
publisher = {Springer},
title = {{On the generic insecurity of the full domain hash}},
doi = {10.1007/11535218_27},
volume = {3621},
year = {2005},
}
@inproceedings{3213,
abstract = {We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case.
In this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.},
author = {Krzysztof Pietrzak},
pages = {55 -- 65},
publisher = {Springer},
title = {{Composition does not imply adaptive security}},
doi = {10.1007/11535218_4},
volume = {3621},
year = {2005},
}
@article{3416,
abstract = {In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins.},
author = {Harald Janovjak and Sapra, Tanuj K and Mueller, Daniel J},
journal = {Biophysical Journal},
number = {5},
pages = {37 -- 39},
publisher = {Biophysical Society},
title = {{Complex stability of single proteins explored by forced unfolding experiments}},
doi = {10.1529/biophysj.105.059774},
volume = {88},
year = {2005},
}
@article{3417,
abstract = {Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.},
author = {Kuhn, Michael and Harald Janovjak and Hubain, Maurice and Mueller, Daniel J},
journal = {Journal of Microscopy},
number = {2},
pages = {125 -- 132},
publisher = {Wiley-Blackwell},
title = {{Automated alignment and pattern recognition of single-molecule force spectroscopy data}},
doi = {10.1111/j.1365-2818.2005.01478.x},
volume = {218},
year = {2005},
}
@article{3418,
abstract = {Atomic force microscopy (AFM) allows the critical forces that unfold single proteins and rupture individual receptor–ligand bonds to be measured. To derive the shape of the energy landscape, the dynamic strength of the system is probed at different force loading rates. This is usually achieved by varying the pulling speed between a few nm/s and a few mgrm/s, although for a more complete investigation of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic drag force acting on the AFM cantilever reaches the same order of magnitude as the molecular forces. This has limited the maximum pulling speed in AFM single-molecule force spectroscopy experiments. Here, we present an approach for considering these hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements recorded over an extended range of pulling speeds (and thus loading rates). To support and illustrate our theoretical considerations, we experimentally evaluated the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling speed.},
author = {Harald Janovjak and Struckmeier, Jens and Mueller, Daniel J},
journal = {European Biophysics Journal},
number = {1},
pages = {91 -- 96},
publisher = {Springer},
title = {{Hydrodynamic effects in fast AFM single molecule force measurements}},
doi = {10.1007/s00249-004-0430-3},
volume = {34},
year = {2005},
}
@inbook{3433,
author = {Jonathan Bollback},
booktitle = {Statistical methods in Molecular Evolution},
editor = {Nielsen, Rasmus},
pages = {439 -- 462},
publisher = {Springer},
title = {{Posterior mapping and posterior predictive distributions}},
doi = {10.1007/0-387-27733-1},
year = {2005},
}
@article{3443,
abstract = {In the hippocampal CA1 area, a relatively homogenous population of pyramidal cells is accompanied by a diversity of GABAergic interneurons. Previously, we found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum moleculare cells, innervating different domains of pyramidal cells, have distinct firing patterns during network oscillations in vivo. A second family of interneurons, expressing cholecystokinin but not parvalbumin, is known to target the same domains of pyramidal cells as do the parvalbumin cells. To test the temporal activity of these independent and parallel GABAergic inputs, we recorded the precise spike timing of identified cholecystokinin interneurons during hippocampal network oscillations in anesthetized rats and determined their molecular expression profiles and synaptic targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz during high-frequency ripple oscillations in an episode-dependent manner. During theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3 Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°), when place cells start firing in freely moving animals. The firing patterns of some interneurons recorded in drug-free behaving rats were similar to cholecystokinin cells in anesthetized animals. Our results demonstrate that cholecystokinin- and parvalbumin-expressing interneurons make different contributions to network oscillations and play distinct roles in different brain states. We suggest that the specific spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids might contribute to differentiate subgroups of pyramidal cells forming neuronal assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire network. Copyright © 2005 Society for Neuroscience.},
author = {Klausberger,Thomas and Marton,Laszlo F and Joseph O'Neill and Huck, Jojanneke H and Dalezios, Yannis and Fuentealba,Pablo and Suen, Wai Yee and Papp, Edit Cs and Kaneko, Takeshi and Watanabe, Masahiko and Jozsef Csicsvari and Somogyi, Péter},
journal = {Journal of Neuroscience},
number = {42},
pages = {9782 -- 9793},
publisher = {Society for Neuroscience},
title = {{Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations}},
doi = {10.1523/JNEUROSCI.3269-05.2005},
volume = {25},
year = {2005},
}
@misc{3509,
abstract = {Methods, apparatus and computer program products can generate light weight but highly realistic and accurate colored models of three-dimensional colored objects. The colored model may be generated from a second plurality of points that define a coarse digital representation of the surface and at least one texture map containing information derived from a first plurality of colored points that define a fine digital representation of the surface. This derivation is achieved by mapping points within the texture map to the fine digital representation of the three-dimensional surface. Colored scan data may be used to construct the fine digital representation as a triangulated surface (i.e., triangulation) using a wrapping operation.},
author = {Williams, Steven P and Herbert Edelsbrunner and Fu, Ping},
publisher = {Elsevier},
title = {{Methods, apparatus and computer program products for modeling three-dimensional colored objects}},
doi = {US 6,853,373 B2},
year = {2005},
}
@inproceedings{3557,
abstract = {A challenging problem in computer-aided geometric design is the decomposition of a surface into four-sided regions that are then represented by NURBS patches. There are various approaches published in the literature and implemented as commercially available software, but all fall short in either automation or quality of the result. At Raindrop Geomagic, we have recently taken a fresh approach based on concepts from Morse theory. This by itself is not a new idea, but we have some novel ingredients that make this work, one being a rational notion of hierarchy that guides the construction of a simplified decomposition sensitive to only the major critical points.},
author = {Herbert Edelsbrunner},
pages = {9 -- 11},
publisher = {ACM},
title = {{Surface tiling with differential topology}},
doi = {http://dx.doi.org/10.2312/SGP/SGP05/009-011},
year = {2005},
}
@inproceedings{3558,
abstract = {The tandem algorithm combines the marching cube algorithm for surface extraction and the edge contraction algorithm for surface simplification in lock-step to avoid the costly intermediate step of storing the entire extracted surface triangulation. Beyond this basic strategy, we introduce refinements to prevent artifacts in the resulting triangulation, first, by carefully monitoring the amount of simplification during the process and, second, by driving the simplification toward a compromise between shape approximation and mesh quality. We have implemented the algorithm and used extensive computational experiments to document the effects of various design options and to further fine-tune the algorithm.},
author = {Attali, Dominique and Cohen-Steiner, David and Herbert Edelsbrunner},
pages = {139 -- 148},
publisher = {ACM},
title = {{Extraction and simplification of iso-surfaces in tandem}},
year = {2005},
}
@inbook{3576,
abstract = {ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes.
Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics.
In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.},
author = {Herbert Edelsbrunner and Koehl, Patrice},
booktitle = {Combinatorial and Computational Geometry},
pages = {243 -- 275},
publisher = {Cambridge University Press},
title = {{The geometry of biomolecular solvation}},
volume = {52},
year = {2005},
}
@article{3611,
abstract = {We present two novel methods to infer mating patterns from genetic data. They differ from existing statistical methods of parentage inference in that they apply to populations that deviate from Hardy–Weinberg and linkage equilibrium, and so are suited for the study of assortative mating in hybrid zones. The core data set consists of genotypes at several loci for a number of full-sib clutches of unknown parentage. Our inference is based throughout on estimates of allelic associations within and across loci, such as heterozygote deficit and pairwise linkage disequilibrium. In the first method, the most likely parents of a given clutch are determined from the genotypic distribution of the associated adult population, given an explicit model of nonrandom mating. This leads to estimates of the strength of assortment. The second approach is based solely on the offspring genotypes and relies on the fact that a linear relation exists between associations among the offspring and those in the population of breeding pairs. We apply both methods to a sample from the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both approaches provide no evidence for a departure from random mating, despite adequate statistical power. Instead, B. variegata-like individuals among the adults contributed disproportionately to the offspring cohort, consistent with their preference for the type of breeding habitat in which this study was conducted.},
author = {Nürnberger, Beate and Nicholas Barton and Kruuk, Loeske E and Vines, Timothy H},
journal = {Heredity},
number = {2},
pages = {247 -- 257},
publisher = {Nature Publishing Group},
title = {{Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes}},
doi = {10.1038/sj.hdy.6800607},
volume = {94},
year = {2005},
}
@article{3612,
abstract = {Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent “single-gene speciation” or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be necessary to investigate populations in which both chiral morphs coexist.},
author = {Davison, Angus and Chiba, Satoshi and Nicholas Barton and Clarke, Bernard},
journal = {PLoS Biology},
number = {9},
publisher = {Public Library of Science},
title = {{Speciation and gene flow between snails of opposing chirality}},
doi = {10.1371/journal.pbio.0030282},
volume = {3},
year = {2005},
}
@article{3613,
abstract = {The extent of genetic variation in fitness is a crucial issue in evolutionary biology and yet remains largely unresolved. In Drosophila melanogaster, we have devised a method that allows the net effects on fitness of heterozygous wild-type chromosomes to be measured, by competing them against two different “balancer” chromosomes. We have applied the method to a large sample of 40 wild-type third chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes bearing recessive lethals. The measurements were made in the environment to which the population was adapted and did not involve inbreeding. The results show an extraordinary similarity in the behavior of replicates of the same chromosome, indicating consistent genetic effects on total fitness. Some invading chromosomes increased rapidly and some slowly, and some rose to appreciable frequency after several months, but then declined again: in every case, the same pattern was seen in each replicate. We estimated relative fitnesses, rates of change of fitness, and relative viabilities, for each chromosome. There were significant fluctuations around the fitted model, which were also highly replicable. Wild-type chromosomes varied substantially in their effects on heterozygous fitness, and these effects vary through time, most likely as a result of genotype × environment interactions.},
author = {Gardner, Michael P and Fowler, Kevin and Nicholas Barton and Patridge, Linda},
journal = {Genetics},
number = {3},
pages = {1553 -- 1571},
publisher = {Genetics Society of America},
title = {{Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns}},
doi = {10.1534/genetics.104.032367},
volume = {169},
year = {2005},
}
@inproceedings{3684,
abstract = {Ever since text processors became popular, users have
dreamt of handling documents printed on paper as comfortably
as electronic ones, with full text search typically
appearing very close to the top of the wish list.
This paper presents the design of a prototype system that
takes a step into this direction. The user’s desktop is continuously
monitored and of each detected document a high
resolution snapshot is taken using a digital camera. The
resulting image is processed using specially designed dewarping
and OCR algorithms, making a digital and fully
searchable version of the document available to the user in
real-time. These steps are performed without any user interaction.
This enables the system to run as a background
task without disturbing the user in her work, while at the
same time offering electronic access to all paper documents
that have been present on the desktop during the uptime of
the system.},
author = {Christoph Lampert and Braun,Tim and Ulges, Adrian and Keysers,Daniel and Breuel,Thomas M},
pages = {79 -- 86},
publisher = {CBDAR},
title = {{Oblivious document capture and real-time retrieval}},
year = {2005},
}
@inproceedings{3689,
abstract = {Digital cameras have become almost ubiquitous and their use for fast and casual capturing of natural images is unchallenged. For making images of documents, however, they have not caught up to flatbed scanners yet, mainly because camera images tend to suffer from distortion due to the perspective and are therefore limited in their further use for archival or OCR. For images of non-planar paper surfaces like books, page curl causes additional distortion, which poses an even greater problem due to its nonlinearity. This paper presents a new algorithm for removing both perspective and page curl distortion. It requires only a single camera image as input and relies on a priori layout information instead of additional hardware. Therefore, it is much more user friendly than most previous approaches, and allows for flexible ad hoc document capture. Results are presented showing that the algorithm produces visually pleasing output and increases OCR accuracy, thus having the potential to become a general purpose preprocessing tool for camera based document capture.},
author = {Ulges, Adrian and Christoph Lampert and Breuel,Thomas M},
pages = {1001 -- 1005},
publisher = {IEEE},
title = {{Document image dewarping using robust estimation of curled text lines}},
doi = { 10.1109/ICDAR.2005.90},
volume = {2},
year = {2005},
}
@article{3691,
abstract = {In strictly pseudoconvex domains with smooth boundary, we prove a commutator relationship between admissible integral operators, as introduced by Lieb and Range, and smooth vector fields which are tangential at boundary points. This makes it possible to gain estimates for admissible operators in function spaces which involve tangential derivatives. Examples are given under with circumstances these can be transformed into genuine Sobolev- and C k-estimates.},
author = {Christoph Lampert},
journal = {Publicacions Matemàtiques},
number = {1},
pages = {179 -- 195},
publisher = {Universitat Autònoma de Barcelona, Departament de Matemàtique},
title = {{Boundary regularity of admissible operators}},
doi = {10.5565/PUBLMAT_49105_08},
volume = {49},
year = {2005},
}
@article{3721,
abstract = {Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6–9nm) were supplied to the vertical displacement of the cantilever at a frequency of 3kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1μNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins.},
author = {Harald Janovjak and Mueller, Daniel J and Humphris, Andrew D},
journal = {Biophysical Journal},
number = {2},
pages = {1423 -- 1431},
publisher = {Biophysical Society},
title = {{Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins}},
doi = {10.1529/biophysj.104.052746},
volume = {88},
year = {2005},
}
@article{3741,
abstract = {In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster "prototype," does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures.},
author = {Slonim,N. and Atwal,G. and Gasper Tkacik and Bialek, William S},
journal = {PNAS},
number = {51},
pages = {18297 -- 18302},
publisher = {National Academy of Sciences},
title = {{Information-based clustering}},
doi = {10.1073/pnas.0507432102},
volume = {102},
year = {2005},
}
@unpublished{3746,
abstract = {We address the practical problems of estimating the information relations that characterize large networks. Building on methods developed for analysis of the neural code, we show that reliable estimates of mutual information can be obtained with manageable computational effort. The same methods allow estimation of higher order, multi-information terms. These ideas are illustrated by analyses of gene expression, financial markets, and consumer preferences. In each case, information theoretic measures correlate with independent, intuitive measures of the underlying structures in the system.},
author = {Slonim,Noam and Atwal,Gurinder S and Gasper Tkacik and Bialek, William S},
booktitle = {ArXiv},
pages = {1 -- 11},
publisher = {ArXiv},
title = {{Estimating mutual information and multi-information in large networks}},
year = {2005},
}
@article{3753,
abstract = {Characterizing the dynamics of specific RNA levels requires real-time RNA profiling in a single cell. We show that the combination of a synthetic modular genetic system with fluorescence correlation spectroscopy allows us to directly measure in real time the activity of any specific promoter in prokaryotes. Using a simple inducible gene expression system, we found that induced RNA levels within a single bacterium of Escherichia coli exhibited a pulsating profile in response to a steady input of inducer. The genetic deletion of an efflux pump system, a key determinant of antibiotic resistance, altered the pulsating transcriptional dynamics and caused overexpression of induced RNA. In contrast with population measurements, real-time RNA profiling permits identifying relationships between genotypes and transcriptional dynamics that are accessible only at the level of the single cell.},
author = {Le,Thuc T. and Harlepp, Sébastien and Calin Guet and Dittmar,Kimberly and Emonet,Thierry and Pan,Tao and Cluzel,Philippe},
journal = {PNAS},
number = {26},
pages = {9160 -- 9164},
publisher = {National Academy of Sciences},
title = {{Real-time RNA profiling within a single bacterium}},
doi = {10.1073/pnas.0503311102},
volume = {102},
year = {2005},
}
@article{3808,
abstract = {Action potentials in central neurons are initiated near the axon initial segment, propagate into the axon, and finally invade the presynaptic terminals, where they trigger transmitter release. Voltage-gated Na(+) channels are key determinants of excitability, but Na(+) channel density and properties in axons and presynaptic terminals of cortical neurons have not been examined yet. In hippocampal mossy fiber boutons, which emerge from parent axons en passant, Na(+) channels are very abundant, with an estimated number of approximately 2000 channels per bouton. Presynaptic Na(+) channels show faster inactivation kinetics than somatic channels, suggesting differences between subcellular compartments of the same cell. Computational analysis of action potential propagation in axon-multibouton structures reveals that Na(+) channels in boutons preferentially amplify the presynaptic action potential and enhance Ca(2+) inflow, whereas Na(+) channels in axons control the reliability and speed of propagation. Thus, presynaptic and axonal Na(+) channels contribute differentially to mossy fiber synaptic transmission.},
author = {Engel, Dominique and Peter Jonas},
journal = {Neuron},
number = {3},
pages = {405 -- 17},
publisher = {Elsevier},
title = {{Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons}},
doi = {10.1016/j.neuron.2004.12.048 },
volume = {45},
year = {2005},
}
@misc{3812,
abstract = {Hippocampal GABAergic interneurons show diverse molecular and morphological properties. The functional significance of this diversity for information processing is poorly understood. Here we show that cholecystokinin (CCK)-expressing interneurons in rat dentate gyrus release GABA in a highly asynchronous manner, in contrast to parvalbumin (PV) interneurons. With a gamma-frequency burst of ten action potentials, the ratio of asynchronous to synchronous release is 3:1 in CCK interneurons but is 1:5 in parvalbumin interneurons. N-type channels trigger synchronous and asynchronous release in CCK interneuron synapses, whereas P/Q-type Ca(2+) channels mediate release at PV interneuron synapses. Effects of Ca(2+) chelators suggest that both a long-lasting presynaptic Ca(2+) transient and a large distance between Ca(2+) source and sensor of exocytosis contribute to the higher ratio of asynchronous to synchronous release in CCK interneuron synapses. Asynchronous release occurs at physiological temperature and with behaviorally relevant stimulation patterns, thus generating long-lasting inhibition in the brain.},
author = {Hefft, Stefan and Peter Jonas},
booktitle = {Nature Neuroscience},
number = {10},
pages = {1319 -- 28},
publisher = {Nature Publishing Group},
title = {{Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review)}},
doi = {10.1038/nn1542},
volume = {8},
year = {2005},
}
@inproceedings{3892,
abstract = {In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent's payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it often suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of omega-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.},
author = {Krishnendu Chatterjee and Thomas Henzinger and Jurdziński, Marcin},
pages = {141 -- 161},
publisher = {Springer},
title = {{Games with secure equilibria}},
doi = {10.1007/11561163_7},
volume = {3657},
year = {2005},
}
@inproceedings{3893,
abstract = {We study infinite stochastic games played by two-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players' goals are not necessarily conflicting), and undiscounted. We show that if each player has an W-regular objective expressed as a paxity objective, then there exists an epsilon-Nash equilibrium, for every epsilon > 0. However, exact Nash equilibria need not exist. We study the complexity of finding values (payoff profile) of an epsilon-Nash equilibrium. We show that the values of an epsilon-Nash equilibrium in nonzero-sum concurrent parity games can be computed by solving the following two simpler problems: computing the values of zero-sum (the goals of the players axe strictly conflicting) concurrent parity games and computing epsilon-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives. As a consequence we establish that values of an epsilon-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME.},
author = {Krishnendu Chatterjee},
pages = {413 -- 427},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Two-player nonzero-sum ω-regular games}},
doi = {10.1007/11539452_32},
volume = {3653},
year = {2005},
}
@inproceedings{3896,
abstract = {Temporal Logic Model Checking is one of the most potent tools for the verification of finite state systems. Computation Tree Logic (CTL) has gained popularity because unlike most other logics, CTL model checking of a single transition system can be achieved in polynomial time. However, in most real-life problems, specially in distributed and parallel systems, the system consist of a set of concurrent processes and the verification problem translates to model check the composition of the component processes. Since explicit composition leads to state explosion, verifying the system without actually composing the components is attractive, even for possibly restrictive class of systems. We show that the problem of compositional CTL model checking is PSPACE complete for the class of systems composed of components that are tree-like transition structure and do not interact among themselves. For the simplest forms of existential and universal CTL formulas model checking turns out to be NP complete and coNP complete, respectively. The results hold for both synchronous and asynchronous composition.},
author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P},
pages = {89 -- 102},
publisher = {Springer},
title = {{Complexity of compositional model checking of computation tree logic on simple structures}},
doi = {10.1007/978-3-540-30536-1_13},
volume = {3326},
year = {2005},
}
@inproceedings{3902,
author = {Cremer, Sylvia and Boomsma, Jacobus},
publisher = {Elsevier},
title = {{The drawback of mobility: invasive species in a globalised world}},
year = {2005},
}
@article{3426,
abstract = {We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from the binding of ligands to receptors on the cell surface, incorporation into the cell, and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production.},
author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and González Gaitán, Marcos and Jülicher, Frank},
journal = {Physical Review Letters},
number = {1},
publisher = {American Physical Society},
title = {{Robust formation of morphogen gradients}},
doi = {10.1103/PhysRevLett.94.018103},
volume = {94},
year = {2005},
}
@inbook{3589,
abstract = {During zebrafish gastrulation, the interplay between patterning events and morphogenesis creates an embryo out of a seemingly unstructured blastula stage embryo, an embryo with distinct polarities along its anterior–posterior, dorsoventral and left–right axes at the end of gastrulation.},
author = {Köppen, Mathias and Heisenberg, Carl-Philipp J},
booktitle = {Encyclopedia of Life Sciences},
publisher = {Wiley-Blackwell},
title = {{Cleavage and gastrulation in zebrafish embryos}},
doi = {10.1038/npg.els.0001072},
year = {2005},
}
@inbook{3588,
author = {Castanon Ortega, Irinka and Heisenberg, Carl-Philipp J},
booktitle = {Cell Migration in Development and Disease},
editor = {Wedlich, Doris},
pages = {71 -- 105},
publisher = {Wiley-VCH},
title = {{Cell migration during zebrafish gastrulation}},
doi = {10.1002/3527604669},
year = {2005},
}
@article{3720,
author = {Guzmán, José and Gerevich, Zoltan and Hengstler, Jan and Illes, Peter and Kleemann, Werner},
journal = {Synapse},
number = {4},
pages = {235 -- 238},
publisher = {Wiley},
title = {{P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex.}},
doi = {10.1002/syn.20177},
volume = {57},
year = {2005},
}
@misc{3590,
author = {Castanon Ortega, Irinka and Heisenberg, Carl-Philipp J},
booktitle = {Nature Cell Biology},
number = {1},
pages = {19 -- 19},
publisher = {Nature Publishing Group},
title = {{A stern view of gastrulation}},
doi = {10.1038/ncb0105-19},
volume = {7},
year = {2005},
}
@article{3763,
abstract = {The generation of realistic motion satisfying user-defined requirements is one of the most important goals of computer animation. Our aim in this paper is the synthesis of realistic, controllable motion for lightweight natural objects in a gaseous medium. We formulate this problem as a large-scale spacetime optimization with user controls and fluid motion equations as constraints. We have devised novel and effective methods to make this large optimization tractable. Initial trajectories are generated with data-driven synthesis based on stylistic motion planning. Smoothed particle hydrodynamics (SPH) is used during optimization to produce fluid simulations at a reasonable computational cost, while interesting vortex-based fluid motion is generated by recording the presence of vortices in the initial trajectories and maintaining them through optimization. Object rotations are refined as a postprocess to enhance the visual quality of the results. We demonstrate our techniques on a number of animations involving single or multiple objects.},
author = {Shi, Lin and Yu, Yizhou and Wojtan, Christopher J and Chenney, Stephen},
journal = {The Visual Computer},
number = {7},
pages = {474 -- 487},
publisher = {Springer},
title = {{Controllable motion synthesis in a gaseous medium}},
doi = {10.1007/s00371-005-0296-0},
volume = {21},
year = {2005},
}
@article{4144,
abstract = {Wnt11 plays a central role in tissue morphogenesis during vertebrate gastrulation, but the molecular and cellular mechanisms by which Wnt11 exerts its effects remain poorly understood. Here, we show that Wnt11 functions during zebrafish gastrulation by regulating the cohesion of mesodermal and endodermal (mesendodermal) progenitor cells. Importantly, we demonstrate that Wnt11 activity in this process is mediated by the GTPase Rab5, a key regulator of early endocytosis, as blocking Rab5c activity in wild-type embryos phenocopies slb/wnt11 mutants, and enhancing Rab5c activity in slb/wnt11 mutant embryos rescues the mutant phenotype. In addition, we find that Wnt11 and Rab5c control the endocytosis of E-cadherin and are required in mesendodermal cells for E-cadherin-mediated cell cohesion. Together, our results suggest that Wnt11 controls tissue morphogenesis by modulating E-cadherin-mediated cell cohesion through Rab5c, a novel mechanism of Wnt signaling in gastrulation.},
author = {Ulrich, Florian and Krieg, Michael and Schötz, Eva and Link, Vinzenz and Castanon, Irinka and Schnabel, Viktor and Taubenberger, Anna and Müller, Daniel and Puech, Pierre and Heisenberg, Carl-Philipp J},
journal = {Developmental Cell},
number = {4},
pages = {555 -- 564},
publisher = {Cell Press},
title = {{Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin}},
doi = {10.1016/j.devcel.2005.08.011},
volume = {9},
year = {2005},
}
@article{4155,
abstract = {During vertebrate gastrulation, progenitor cells of different germ layers acquire specific adhesive properties that contribute to germ layer formation and separation. Wnt signals have been suggested to function in this process by modulating the different levels of adhesion between the germ layers, however, direct evidence for this is still lacking. Here we show that Wnt11, a key signal regulating gastrulation movements, is needed for the adhesion of zebrafish mesendodermal progenitor cells to fibronectin, an abundant extracellular matrix component during gastrulation. To measure this effect, we developed an assay to quantify the adhesion of single zebrafish primary mesendodermal progenitors using atomic-force microscopy (AFM). We observed significant differences in detachment force and work between cultured mesendodermal progenitors from wild-type embryos and from slb/wit11 mutant embryos, which carry a loss-of-function mutation in the wnt11 gene, when tested on fibronectin-coated substrates. These differences were probably due to reduced adhesion to the fibronectin substrate as neither the overall cell morphology nor the cell elasticity grossly differed between wild-type and mutant cells. Furthermore, in the presence of inhibitors of fibronectin-integrin binding, such as RGD peptides, the adhesion force and work were strongly decreased, indicating that integrins are involved in the binding of mesendodermal progenitors in our assay. These findings demonstrate that AFM can be used to quantitatively determine the substrate-adhesion of cultured primary gastrulating cells and provide insight into the role of Wnt11 signalling in modulating cell adhesion at the single cell scale.},
author = {Puech, Pierre and Taubenberger, Anna and Ulrich, Florian and Krieg, Michael and Mueller, Daniel and Heisenberg, Carl-Philipp J},
journal = {Journal of Cell Science},
number = {18},
pages = {4199 -- 4206},
publisher = {Company of Biologists},
title = {{Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy}},
doi = {10.1242/jcs.02547},
volume = {118},
year = {2005},
}
@article{4167,
abstract = {In this study, we elucidate the roles of the winged-helix transcription factor Foxa2 in ventral CNS development in zebrafish. Through cloning of monorail (mol), which we find encodes the transcription factor Foxa2, and phenotypic analysis of mol(-/-) embryos, we show that floorplate is induced in the absence of Foxa2 function but fails to further differentiate. In mol(-/-) mutants, expression of Foxa and Hh family genes is not maintained in floorplate cells and lateral expansion of the floorplate fails to occur. Our results suggest that this is due to defects both in the regulation of Hh activity in medial floorplate cells as well as cell-autonomous requirements for Foxa2 in the prospective laterally positioned floorplate cells themselves. Foxa2 is also required for induction and/or patterning of several distinct cell types in the ventral CNS. Serotonergic neurones of the raphe nucleus and the trochlear motor nucleus are absent in mol(-/-) embryos, and oculomotor and facial motoneurones ectopically occupy ventral CNS midline positions in the midbrain and hindbrain. There is also a severe reduction of prospective oligodendrocytes in the midbrain and hindbrain. Finally, in the absence of Foxa2, at least two likely Hh pathway target genes are ectopically expressed in more dorsal regions of the midbrain and hindbrain ventricular neuroepithelium, raising the possibility that Foxa2 activity may normally be required to limit the range of action of secreted Hh proteins.},
author = {Norton, Will and Mangoli, Maryam and Lele, Zsolt and Pogoda, Hans and Diamond, Brianne and Mercurio, Sara and Russell, Claire and Teraoka, Hiroki and Stickney, Heather and Rauch, Gerd and Heisenberg, Carl-Philipp J and Houart, Corinne and Schilling, Thomas and Frohnhoefer, Hans and Rastegar, Sepand and Neumann, Carl and Gardiner, R Mark and Strähle, Uwe and Geisler, Robert and Rees, Michelle and Talbot, William and Wilson, Stephen},
journal = {Development},
number = {4},
pages = {645 -- 658},
publisher = {Company of Biologists},
title = {{Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones}},
doi = {10.1242/dev.01611},
volume = {132},
year = {2005},
}
@article{4171,
abstract = {During vertebrate gastrulation, the three germ layers, ectoderm, mesoderm and endoderm are formed, and the resulting progenitor cells are brought into the positions from which they will later contribute more complex tissues and organs. A core element in this process is the internalization of mesodermal and endodermal progenitors at the onset of gastrulation. Although many of the molecules that induce mesendoderm have been identified, much less is known about the cellular mechanisms underlying mesendodermal cell internalization and germ layer formation. Here we show that at the onset of zebrafish gastrulation, mesendodermal progenitors in dorsal/axial regions of the germ ring internalize by single cell delamination. Once internalized, mesendodermal progenitors upregulate ECadherin (Cadherin 1) expression, become increasingly motile and eventually migrate along the overlying epiblast (ectodermal) cell layer towards the animal pole of the gastrula. When E-Cadherin function is compromised, mesendodermal progenitors still internalize, but, with gastrulation proceeding, fail to elongate and efficiently migrate along the epiblast, whereas epiblast cells themselves exhibit reduced radial cell intercalation movements. This indicates that cadherin-mediated cell-cell adhesion is needed within the forming shield for both epiblast cell intercalation, and mesendodermal progenitor cell elongation and migration during zebrafish gastrulation. Our data provide insight into the cellular mechanisms underlying mesendodermal progenitor cell internalization and subsequent migration during zebrafish gastrulation, and the role of cadherin-mediated cell-cell adhesion in these processes.},
author = {Montero, Juan and Carvalho, Lara and Wilsch Bräuninger, Michaela and Kilian, Beate and Mustafa, Chigdem and Heisenberg, Carl-Philipp J},
journal = {Development},
number = {6},
pages = {1187 -- 1198},
publisher = {Company of Biologists},
title = {{Shield formation at the onset of zebrafish gastrulation}},
doi = {10.1242/dev.01667},
volume = {132},
year = {2005},
}
@article{4183,
abstract = {The spreading of an epithelial cell sheet over a substrate is a common process during embryogenesis. Typical examples include epiboly during zebrafish gastrulation and Drosophila dorsal closure. We provide evidence that in both cases, actin-based contraction of the leading edge of the epithelium is of critical importance.},
author = {Köppen, Mathias and Fernández, Beatriz and Carvalho, Lara and Jacinto, António and Heisenberg, Carl-Philipp J},
journal = {Mechanisms of Development},
number = {Supplement 1},
pages = {S112 -- S113},
publisher = {Elsevier},
title = {{Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure}},
doi = {10.1016/j.mod.2005.06.010},
volume = {122},
year = {2005},
}
@article{8516,
abstract = {The purpose of this paper is to construct examples of diffusion for E-Hamiltonian perturbations
of completely integrable Hamiltonian systems in 2d-dimensional phase space, with d large.
In the first part of the paper, simple and explicit examples are constructed illustrating absence
of ‘long-time’ stability for size E Hamiltonian perturbations of quasi-convex integrable systems
already when the dimension 2d of phase space becomes as large as log 1/E . We first produce
the example in Gevrey class and then a real analytic one, with some additional work.
In the second part, we consider again E-Hamiltonian perturbations of completely integrable
Hamiltonian system in 2d-dimensional space with E-small but not too small, |E| > exp(−d), with
d the number of degrees of freedom assumed large. It is shown that for a class of analytic
time-periodic perturbations, there exist linearly diffusing trajectories. The underlying idea for
both examples is similar and consists in coupling a fixed degree of freedom with a large
number of them. The procedure and analytical details are however significantly different. As
mentioned, the construction in Part I is totally elementary while Part II is more involved, relying
in particular on the theory of normally hyperbolic invariant manifolds, methods of generating
functions, Aubry–Mather theory, and Mather’s variational methods.},
author = {Bourgain, Jean and Kaloshin, Vadim},
issn = {0022-1236},
journal = {Journal of Functional Analysis},
keywords = {Analysis},
number = {1},
pages = {1--61},
publisher = {Elsevier},
title = {{On diffusion in high-dimensional Hamiltonian systems}},
doi = {10.1016/j.jfa.2004.09.006},
volume = {229},
year = {2005},
}
@article{8491,
abstract = {Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H–15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H–15N and 1H−13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H–15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond 1H–13C and 1H–15N scalar and residual dipolar coupling constants.},
author = {Schanda, Paul and Kupče, Ēriks and Brutscher, Bernhard},
issn = {0925-2738},
journal = {Journal of Biomolecular NMR},
keywords = {Spectroscopy, Biochemistry},
number = {4},
pages = {199--211},
publisher = {Springer Nature},
title = {{SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds}},
doi = {10.1007/s10858-005-4425-x},
volume = {33},
year = {2005},
}
@article{8492,
abstract = {We demonstrate for different protein samples that 2D 1H−15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to measure fast hydrogen−deuterium exchange rate constants along the backbone of a small globular protein fragment by real-time 2D NMR.},
author = {Schanda, Paul and Brutscher, Bernhard},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
number = {22},
pages = {8014--8015},
publisher = {American Chemical Society},
title = {{Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds}},
doi = {10.1021/ja051306e},
volume = {127},
year = {2005},
}
@article{209,
author = {Timothy Browning and Heath-Brown, Roger},
journal = {Inventiones Mathematicae},
number = {3},
pages = {553 -- 573},
publisher = {Unknown},
title = {{Equal sums of three powers}},
doi = {10.1007/s00222-004-0360-9},
volume = {157},
year = {2004},
}
@article{2308,
abstract = {It is widely believed that the inflammatory events mediated by microglial activation contribute to several neurodegenerative processes. Alzheimer's disease, for example, is characterized by an accumulation of β-amyloid protein (Aβ) in neuritic plaques that are infiltrated by reactive microglia and astrocytes. Although Aβ and its fragment 25-35 exert a direct toxic effect on neurons, they also activate microglia. Microglial activation is accompanied by morphological changes, cell proliferation, and release of various cytokines and growth factors. A number of scientific reports suggest that the increased proliferation of microglial cells is dependent on ionic membrane currents and in particular on chloride conductances. An unusual chloride ion channel known to be associated with macrophage activation is the chloride intracellular channel-1 (CLIC1). Here we show that Aβ stimulation of neonatal rat microglia specifically leads to the increase in CLIC1 protein and to the functional expression of CLIC1 chloride conductance, both barely detectable on the plasma membrane of quiescent cells. CLIC1 protein expression in microglia increases after 24 hr of incubation with Aβ, simultaneously with the production of reactive nitrogen intermediates and of tumor necrosis factor-α (TNF-α). We demonstrate that reducing CLIC1 chloride conductance by a specific blocker [IAA-94 (R(+)-[(6,7-dichloro-2-cyclopentyl-2,3-dihydro-2-methyl-1-oxo-1H-inden-5yl)-oxy] acetic acid)] prevents neuronal apoptosis in neurons cocultured with Aβ-treated microglia. Furthermore, we show that small interfering RNAs used to knock down CLIC1 expression prevent TNF-α release induced by Aβ stimulation. These results provide a direct link between Aβ-induced microglial activation and CLIC1 functional expression.},
author = {Gaia Novarino and Fabrizi, Cinzia and Tonini, Raffaella and Denti, Michela A and Malchiodi, Albedi F and Lauro, Giuliana M and Sacchetti, Benedetto and Paradisi, Silvia and Ferroni, Arnaldo and Curmi, Paul M G and Breit, Samuel N and Mazzanti, Michele},
journal = {Journal of Neuroscience},
number = {23},
pages = {5322 -- 5330},
publisher = {Society for Neuroscience},
title = {{Involvement of the intracellular ion channel CLIC1 in microglia-mediated β-amyloid-induced neurotoxicity}},
doi = {10.1523/JNEUROSCI.1170-04.2004},
volume = {24},
year = {2004},
}
@article{2355,
abstract = {The BMV conjecture for traces, which states that Tr exp(A - λB) is the Laplace transform of a positive measure, is shown to be equivalent to two other statements: (i) The polynomial λ → Tr(A + λB) p has only non-negative coefficients for all A, B ≥ 0, p ∈ ℕ and (ii) λ → Tr(A + λB)-p is the Laplace transform of a positive measure for A, B ≥ 0, p > 0.},
author = {Lieb, Élliott H and Robert Seiringer},
journal = {Journal of Statistical Physics},
number = {1-2},
pages = {185 -- 190},
publisher = {Springer},
title = {{ Equivalent forms of the Bessis-Moussa-Villani conjecture}},
doi = {10.1023/B:JOSS.0000019811.15510.27},
volume = {115},
year = {2004},
}
@article{2356,
abstract = {Recent experimental and theoretical work has shown that there are conditions in which a trapped, low-density Bose gas behaves like the one-dimensional delta-function Bose gas solved years ago by Lieb and Liniger. This is an intrinsically quantum-mechanical phenomenon because it is not necessary to have a trap width that is the size of an atom - as might have been supposed - but it suffices merely to have a trap width such that the energy gap for motion in the transverse direction is large compared to the energy associated with the motion along the trap. Up to now the theoretical arguments have been based on variational - perturbative ideas or numerical investigations. In contrast, this paper gives a rigorous proof of the one-dimensional behavior as far as the ground state energy and particle density are concerned. There are four parameters involved: the particle number, N, transverse and longitudinal dimensions of the trap, r and L, and the scattering length a of the interaction potential. Our main result is that if r/L → 0 and N → ∞ the ground state energy and density can be obtained by minimizing a one-dimensional density functional involving the Lieb-Liniger energy density with coupling constant ∼ a/r 2. This density functional simplifies in various limiting cases and we identify five asymptotic parameter regions altogether. Three of these, corresponding to the weak coupling regime, can also be obtained as limits of a three-dimensional Gross-Pitaevskii theory. We also show that Bose-Einstein condensation in the ground state persists in a part of this regime. In the strong coupling regime the longitudinal motion of the particles is strongly correlated. The Gross-Pitaevskii description is not valid in this regime and new mathematical methods come into play.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {347 -- 393},
publisher = {Springer},
title = {{One-dimensional behavior of dilute, trapped Bose gases}},
doi = {10.1007/s00220-003-0993-3},
volume = {244},
year = {2004},
}
@article{2360,
abstract = {An optical lattice model developed that is similar to the Bose-Hubbard model to describe the transition between Bose-Einstein condensation (BEC) and a Mott insulator state was analyzed. It was found that the system was a hard core lattice gas at half of the maximum density and the optical lattice was modeled by a periodic potential of strength λ. It was also observed that the interparticle interaction was essential for this transition that occurred even in the ground state. The results show that all the essential features could be proved rigorously such as the existence of BEC for small λ and its suppression for a large λ.},
author = {Aizenman, Michael and Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {2},
pages = {023612 -- 1--0236121--2},
publisher = {American Physical Society},
title = {{Bose-Einstein quantum phase transition in an optical lattice model}},
doi = {10.1103/PhysRevA.70.023612},
volume = {70},
year = {2004},
}
@inbook{2417,
author = {Lovász, László and Vesztergombi, Katalin and Uli Wagner and Welzl, Emo},
booktitle = {Towards a Theory of Geometric Graphs},
editor = {Pach, János},
pages = {139 -- 148},
publisher = {American Mathematical Society},
title = {{Convex quadrilaterals and k-sets }},
doi = {10.1090/conm/342},
volume = {342},
year = {2004},
}
@article{2425,
abstract = {A finite set N ⊂ Rd is a weak ε-net for an n-point set X ⊂ Rd (with respect to convex sets) if N intersects every convex set K with |K ∩ X| ≥ εn. We give an alternative, and arguably simpler, proof of the fact, first shown by Chazelle et al., that every point set X in Rd admits a weak ε-net of cardinality O(ε-dpolylog(1/ε)). Moreover, for a number of special point sets (e.g., for points on the moment curve), our method gives substantially better bounds. The construction yields an algorithm to construct such weak ε-nets in time O(n ln(1/ε)).},
author = {Matoušek, Jiří and Uli Wagner},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {195 -- 206},
publisher = {Springer},
title = {{New constructions of weak ε-nets}},
doi = {10.1007/s00454-004-1116-4},
volume = {32},
year = {2004},
}
@article{2426,
abstract = {We introduce the adaptive neighborhood graph as a data structure for modeling a smooth manifold M embedded in some Euclidean space ℝ d. We assume that M is known to us only through a finite sample P ⊂ M, as is often the case in applications. The adaptive neighborhood graph is a geometric graph on P. Its complexity is at most min{2O(k)n, n2}, where n = P and k = dim M, as opposed to the n[d/2] complexity of the Delaunay triangulation, which is often used to model manifolds. We prove that we can correctly infer the connected components and the dimension of M from the adaptive neighborhood graph provided a certain standard sampling condition is fulfilled. The running time of the dimension detection algorithm is d20(k7 log k) for each connected component of M. If the dimension is considered constant, this is a constant-time operation, and the adaptive neighborhood graph is of linear size. Moreover, the exponential dependence of the constants is only on the intrinsic dimension k, not on the ambient dimension d. This is of particular interest if the co-dimension is high, i.e., if k is much smaller than d, as is the case in many applications. The adaptive neighborhood graph also allows us to approximate the geodesic distances between the points in P.},
author = {Giesen, Joachim and Uli Wagner},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {245 -- 267},
publisher = {Springer},
title = {{Shape dimension and intrinsic metric from samples of manifolds}},
doi = {10.1007/s00454-004-1120-8},
volume = {32},
year = {2004},
}
@misc{2461,
author = {Sauer, Michael and Friml, Jirí},
booktitle = {Development},
number = {23},
pages = {5774 -- 5775},
publisher = {Company of Biologists},
title = {{The Matryoshka dolls of plant polarity}},
doi = {10.1242/dev.01463},
volume = {131},
year = {2004},
}
@article{7333,
abstract = {The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system.},
author = {Santis, M. and Schmid, D. and Ruge, M. and Freunberger, Stefan Alexander and Büchi, F.N.},
issn = {1615-6846},
journal = {Fuel Cells},
number = {3},
pages = {214--218},
publisher = {Wiley},
title = {{Modular stack-internal air humidification concept-verification in a 1 kW stack}},
doi = {10.1002/fuce.200400028},
volume = {4},
year = {2004},
}
@article{7334,
abstract = {Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. },
author = {Mantzaras, John and Freunberger, Stefan Alexander and Büchi, Felix N. and Roos, Markus and Brandstätter, Wilhelm and Prestat, Michel and Gauckler, Ludwig J. and Andreaus, Bernhard and Hajbolouri, Faegheh and Senn, Stephan M. and Poulikakos, Dimos and Chaniotis, Andreas K. and Larrain, Diego and Autissier, Nordahl and Maréchal, François},
issn = {0009-4293},
journal = {CHIMIA International Journal for Chemistry},
number = {12},
pages = {857--868},
publisher = {Swiss Chemical Society},
title = {{Fuel cell modeling and simulations}},
doi = {10.2533/000942904777677029},
volume = {58},
year = {2004},
}
@article{7706,
abstract = {The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance.},
author = {Brunet, Anne and Sweeney, Lora Beatrice Jaeger and Sturgill, J Fitzhugh and Chua, Katrin and Greer, Paul and Lin, Yingxi and Tran, Hien and Ross, Sarah and Mostoslavsky, Raul and Cohen, Haim and Hu, Linda and Chen, Hwei-Ling and Jedrychowski, Mark and Gygi, Steven and Sinclair, David and Alt, Frederick and Greenberg, Michael},
issn = {0036-8075},
journal = {Science},
number = {5666},
pages = {2011--2015},
publisher = {American Association for the Advancement of Science},
title = {{Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase}},
doi = {10.1126/science.1094637},
volume = {303},
year = {2004},
}
@article{3918,
abstract = {Wingless (ergatoid) males of the tramp ant Cardiocondyla minutior attack and kill their young ergatoid rivals and thus attempt to monopolize mating with female sexuals reared in the colony. Because of the different strength of local mate competition in colonies with one or several reproductive queens, we expected the production of new ergatoid males to vary with queen number. Sex ratios were mostly female-biased, but in contrast to the sympatric species C. obscurior (Cremer and Heinze, 2002) neither the percentage of ergatoid males nor of female sexuals among the first 20 sexuals produced varied considerably with queen number. As in C. obscurior, experimental colony fragmentation led to the production of winged males, whereas in unfragmented control colonies only ergatoid males eclosed.},
author = {Heinze, Jürgen and Böttcher, A. and Cremer, Sylvia},
journal = {Insectes Sociaux},
number = {3},
pages = {275 -- 278},
publisher = {Springer},
title = {{Production of winged and wingless males in the ant, Cardiocondyla minutior}},
doi = {10.1007/s00040-004-0740-6},
volume = {51},
year = {2004},
}
@article{3929,
abstract = {The Nef protein of human and simian immunodeficiency virus (HIV/SIV) is believed to interfere with T cell activation signals by forming a signaling complex at the plasma membrane. Composition and function of the complex are not fully understood. Here we report that Nef recruits the Polycomb Group (PcG) protein Eed, so far known as a nuclear factor and repressor of transcription, to the membrane of cells. The Nef-induced translocation of Eed led to a potent stimulation of Tat-dependent HIV transcription, implying that Eed removal from the nucleus is required for optimal Tat function. Similar to Nef action, activation of integrin receptors recruited Eed to the plasma membrane, also leading to enhanced Tat/Nef-mediated transcription. Our results suggest a link between membrane-associated activation processes and transcriptional derepression and demonstrate how HIV exploits this mechanism.},
author = {Witte, Vanessa and Laffert, Bernd and Rosorius, Olaf and Lischka, Peter and Blume, Katja and Galler, Gunther and Stilper, Andrea and Willbold, Dieter and D'Aloja, Paola and Michael Sixt and Kolanus, Johanna and Ott, Melanie and Kolanus, Waldemar and Schuler, Gerold and Baur, Andreas S},
journal = {Molecular Cell},
number = {2},
pages = {179 -- 190},
publisher = {Cell Press},
title = {{HIV-1 Nef mimics an integrin receptor signal that recruits the polycomb group protein Eed to the plasma membrane}},
doi = {10.1016/S1097-2765(04)00004-8},
volume = {13},
year = {2004},
}
@article{3931,
abstract = {Hyaluronan is an unsulfated glycosaminoglycan (GAG) that is ubiquitously expressed in the extracellular matrix (ECM) of all vertebrates, where hyaluronan rich matrices constitute a particular permissive environment for the development of complex biological structures and also for tumor progression. Because of its conserved structure and ubiquitous expression, antibodies for its histochemical detection cannot be produced. We have engineered a fusion protein, neurocan-GFP, and expressed it as a secreted molecule in mammalian cells. Neurocan-GFP fusion protein specifically binds to hyaluronan and directly visualizes hyaluronan on tissue sections, revealing a very detailed picture of hyaluronan distribution. The fluorescent fusion protein can be used in combination with antibodies and nuclear markers for double or triple staining. In addition, it is suitable to visualize hyaluronan on living cells by time-lapse video microscopy. The successful production and application of the neurocan-GFP fusion protein opens up new perspectives for using GFP fusion proteins as detection tools in histological and cytological studies complementing conventional antibody and biotin/avidin techniques.},
author = {Zhang, Hui and Baader, Stephan L and Michael Sixt and Kappler, Joachim and Rauch, Uwe},
journal = {Journal of Histochemistry and Cytochemistry},
number = {7},
pages = {915 -- 922},
publisher = {Histochemical Society},
title = {{Neurocan-GFP fusion protein: a new approach to detect hyaluronan on tissue sections and living cells}},
doi = {10.1369/jhc.3A6221.2004},
volume = {52},
year = {2004},
}
@article{3984,
abstract = {We combine topological and geometric methods to construct a multiresolution representation for a function over a two-dimensional domain. In a preprocessing stage, we create the Morse-Smale complex of the function and progressively simplify its topology by cancelling pairs of critical points. Based on a simple notion of dependency among these cancellations, we construct a hierarchical data structure supporting traversal and reconstruction operations similarly to traditional geometry-based representations. We use this data structure to extract topologically valid approximations that satisfy error bounds provided at runtime.},
author = {Bremer, Peer-Timo and Herbert Edelsbrunner and Hamann, Bernd and Pascucci, Valerio},
journal = {IEEE Transactions on Visualization and Computer Graphics},
number = {4},
pages = {385 -- 396},
publisher = {IEEE},
title = {{A topological hierarchy for functions on triangulated surfaces}},
doi = {10.1109/TVCG.2004.3},
volume = {10},
year = {2004},
}
@article{3985,
abstract = {Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.},
author = {Cole-McLaughlin, Kree and Herbert Edelsbrunner and Harer, John and Natarajan, Vijay and Pascucci, Valerio},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {231 -- 244},
publisher = {Springer},
title = {{Loops in Reeb graphs of 2-manifolds}},
doi = {10.1007/s00454-004-1122-6},
volume = {32},
year = {2004},
}
@article{3986,
abstract = {The motion of a biomolecule greatly depends on the engulfing solution, which is mostly water. Instead of representing individual water molecules, it is desirable to develop implicit solvent models that nevertheless accurately represent the contribution of the solvent interaction to the motion. In such models, hydrophobicity is expressed as a weighted sum of atomic surface areas. The derivatives of these weighted areas contribute to the force that drives the motion. In this paper we give formulas for the weighted and unweighted area derivatives of a molecule modeled as a space-filling diagram made up of balls in motion. Other than the radii and the centers of the balls, the formulas are given in terms of the sizes of circular arcs of the boundary and edges of the power diagram. We also give inclusion-exclusion formulas for these sizes.},
author = {Bryant, Robert and Herbert Edelsbrunner and Koehl, Patrice and Levitt, Michael},
journal = {Discrete & Computational Geometry},
number = {3},
pages = {293 -- 308},
publisher = {Springer},
title = {{The area derivative of a space-filling diagram}},
doi = {10.1007/s00454-004-1099-1},
volume = {32},
year = {2004},
}
@article{3987,
abstract = {We consider scientific data sets that describe density functions over three-dimensional geometric domains. Such data sets are often large and coarsened representations are needed for visualization and analysis. Assuming a tetrahedral mesh representation, we construct such representations with a simplification algorithm that combines three goals: the approximation of the function, the preservation of the mesh topology, and the improvement of the mesh quality. The third goal is achieved with a novel extension of the well-known quadric error metric. We perform a number of computational experiments to understand the effect of mesh quality improvement on the density map approximation. In addition, we study the effect of geometric simplification on the topological features of the function by monitoring its critical points.},
author = {Natarajan, Vijay and Herbert Edelsbrunner},
journal = {IEEE Transactions on Visualization and Computer Graphics},
number = {5},
pages = {587 -- 597},
publisher = {IEEE},
title = {{Simplification of three-dimensional density maps}},
doi = {10.1109/TVCG.2004.32},
volume = {10},
year = {2004},
}
@inproceedings{3988,
abstract = {We give an algorithm that locally improves the fit between two proteins modeled as space-filling diagrams. The algorithm defines the fit in purely geometric terms and improves by applying a rigid motion to one of the two proteins. Our implementation of the algorithm takes between three and ten seconds and converges with high likelihood to the correct docked configuration, provided it starts at a position away from the correct one by at most 18 degrees of rotation and at most 3.0Angstrom of translation. The speed and convergence radius make this an attractive algorithm to use in combination with a coarse sampling of the six-dimensional space of rigid motions.},
author = {Choi, Vicky and Agarwal, Pankaj K and Herbert Edelsbrunner and Rudolph, Johannes},
pages = {218 -- 229},
publisher = {Springer},
title = {{Local search heuristic for rigid protein docking}},
doi = {10.1007/978-3-540-30219-3_19},
volume = {3240},
year = {2004},
}
@inproceedings{3989,
abstract = {We introduce local and global comparison measures for a collection of k less than or equal to d real-valued smooth functions on a common d-dimensional Riemannian manifold. For k = d = 2 we relate the measures to the set of critical points of one function restricted to the level sets of the other. The definition of the measures extends to piecewise linear functions for which they ace easy to compute. The computation of the measures forms the centerpiece of a software tool which we use to study scientific datasets.},
author = {Herbert Edelsbrunner and Harer, John and Natarajan, Vijay and Pascucci, Valerio},
pages = {275 -- 280},
publisher = {IEEE},
title = {{Local and global comparison of continuous functions}},
doi = {10.1109/VISUAL.2004.68},
year = {2004},
}
@article{3990,
abstract = {The writhing number measures the global geometry of a closed space curve or knot. We show that this measure is related to the average winding number of its Gauss map. Using this relationship, we give an algorithm for computing the writhing number for a polygonal knot with n edges in time roughly proportional to n(1.6). We also implement a different, simple algorithm and provide experimental evidence for its practical efficiency.},
author = {Agarwal, Pankaj K and Herbert Edelsbrunner and Wang, Yusu},
journal = {Discrete & Computational Geometry},
number = {1},
pages = {37 -- 53},
publisher = {Springer},
title = {{Computing the writhing number of a polygonal knot}},
doi = {10.1007/s00454-004-2864-x},
volume = {32},
year = {2004},
}
@inbook{4230,
author = {Harold Vladar and Cipriani, Roberto and Scharifker, Benjamin and Bubis, Jose},
booktitle = {Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds},
editor = {Hanslmeier,A. and Kempe,S. and Seckbach,J.},
pages = {83 -- 87},
publisher = {Springer},
title = {{A mechanism for the prebiotic emergence of proteins}},
year = {2004},
}
@inbook{4239,
author = {Harold Vladar and Cipriani, Roberto and Scharifker, Benjamin and Bubis, Jose},
booktitle = {Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds},
editor = {Seckbach,J. and Chela-Flores,J. and Owen,T. and Raulin,F.},
pages = {83 -- 87},
publisher = {Springer},
title = {{A Mechanism for the Prebiotic Emergence of Proteins}},
doi = {3807},
volume = {7},
year = {2004},
}
@article{4253,
abstract = {We consider a single genetic locus which carries two alleles, labelled P and Q. This locus experiences selection and mutation. It is linked to a second neutral locus with recombination rate r. If r = 0, this reduces to the study of a single selected locus. Assuming a Moran model for the population dynamics, we pass to a diffusion approximation and, assuming that the allele frequencies at the selected locus have reached stationarity, establish the joint generating function for the genealogy of a sample from the population and the frequency of the P allele. In essence this is the joint generating function for a coalescent and the random background in which it evolves. We use this to characterize, for the diffusion approximation, the probability of identity in state at the neutral locus of a sample of two individuals (whose type at the selected locus is known) as solutions to a system of ordinary differential equations. The only subtlety is to find the boundary conditions for this system. Finally, numerical examples are presented that illustrate the accuracy and predictions of the diffusion approximation. In particular, a comparison is made between this approach and one in which the frequencies at the selected locus are estimated by their value in the absence of fluctuations and a classical structured coalescent model is used.},
author = {Nicholas Barton and Etheridge, Alison M and Sturm, Anja K},
journal = {Annals of Applied Probability},
number = {2},
pages = {754 -- 785},
publisher = {Institute of Mathematical Statistics},
title = {{Coalescence in a Random Background}},
volume = {14},
year = {2004},
}
@inproceedings{4372,
author = {Maler, Oded and Dejan Nickovic},
pages = {152 -- 166},
publisher = {Springer},
title = {{Monitoring Temporal Properties of Continuous Signals}},
doi = {1572},
year = {2004},
}
@inproceedings{4445,
abstract = {We present a type system for E code, which is an assembly language that manages the release, interaction, and termination of real-time tasks. E code specifies a deadline for each task, and the type system ensures that the deadlines are path-insensitive. We show that typed E programs allow, for given worst-case execution times of tasks, a simple schedulability analysis. Moreover, the real-time programming language Giotto can be compiled into typed E~code. This shows that typed E~code identifies an easily schedulable yet expressive class of real-time programs. We have extended the Giotto compiler to generate typed E code, and enabled the run-time system for E code to perform a type and schedulability check before executing the code.},
author = {Thomas Henzinger and Kirsch, Christoph M},
pages = {104 -- 113},
publisher = {ACM},
title = {{A typed assembly language for real-time programs}},
doi = {10.1145/1017753.1017774},
year = {2004},
}
@inproceedings{4458,
abstract = {The success of model checking for large programs depends crucially on the ability to efficiently construct parsimonious abstractions. A predicate abstraction is parsimonious if at each control location, it specifies only relationships between current values of variables, and only those which are required for proving correctness. Previous methods for automatically refining predicate abstractions until sufficient precision is obtained do not systematically construct parsimonious abstractions: predicates usually contain symbolic variables, and are added heuristically and often uniformly to many or all control locations at once. We use Craig interpolation to efficiently construct, from a given abstract error trace which cannot be concretized, a parsominous abstraction that removes the trace. At each location of the trace, we infer the relevant predicates as an interpolant between the two formulas that define the past and the future segment of the trace. Each interpolant is a relationship between current values of program variables, and is relevant only at that particular program location. It can be found by a linear scan of the proof of infeasibility of the trace.We develop our method for programs with arithmetic and pointer expressions, and call-by-value function calls. For function calls, Craig interpolation offers a systematic way of generating relevant predicates that contain only the local variables of the function and the values of the formal parameters when the function was called. We have extended our model checker Blast with predicate discovery by Craig interpolation, and applied it successfully to C programs with more than 130,000 lines of code, which was not possible with approaches that build less parsimonious abstractions.},
author = {Thomas Henzinger and Jhala, Ranjit and Majumdar, Ritankar S and McMillan, Kenneth L},
pages = {232 -- 244},
publisher = {ACM},
title = {{Abstractions from proofs}},
doi = {10.1145/964001.964021},
year = {2004},
}
@inproceedings{4459,
abstract = {Software model checking has been successful for sequential programs, where predicate abstraction offers suitable models, and counterexample-guided abstraction refinement permits the automatic inference of models. When checking concurrent programs, we need to abstract threads as well as the contexts in which they execute. Stateless context models, such as predicates on global variables, prove insufficient for showing the absence of race conditions in many examples. We therefore use richer context models, which combine (1) predicates for abstracting data state, (2) control flow quotients for abstracting control state, and (3) counters for abstracting an unbounded number of threads. We infer suitable context models automatically by a combination of counterexample-guided abstraction refinement, bisimulation minimization, circular assume-guarantee reasoning, and parametric reasoning about an unbounded number of threads. This algorithm, called CIRC, has been implemented in BLAST and succeeds in checking many examples of NESC code for data races. In particular, BLAST proves the absence of races in several cases where previous race checkers give false positives.},
author = {Thomas Henzinger and Jhala, Ranjit and Majumdar, Ritankar S},
pages = {1 -- 13},
publisher = {ACM},
title = {{Race checking by context inference}},
doi = {10.1145/996841.996844},
year = {2004},
}
@inbook{4461,
abstract = {One of the central axioms of extreme programming is the disciplined use of regression testing during stepwise software development. Due to recent progress in software model checking, it has become possible to supplement this process with automatic checks for behavioral safety properties of programs, such as conformance with locking idioms and other programming protocols and patterns. For efficiency reasons, all checks must be incremental, i.e., they must reuse partial results from previous checks in order to avoid all unnecessary repetition of expensive verification tasks. We show that the lazy-abstraction algorithm, and its implementation in Blast, can be extended to support the fully automatic and incremental checking of temporal safety properties during software development.},
author = {Thomas Henzinger and Jhala, Ranjit and Majumdar, Ritankar S and Sanvido, Marco A},
booktitle = {Verification: Theory and Practice},
pages = {332 -- 358},
publisher = {Springer},
title = {{Extreme model checking}},
doi = {10.1007/978-3-540-39910-0_16},
volume = {2772},
year = {2004},
}
@inproceedings{4525,
abstract = {We present a new high-level programming language, called xGiotto, for programming applications with hard real-time constraints. Like its predecessor, xGiotto is based on the LET (logical execution time) assumption: the programmer specifies when the outputs of a task become available, and the compiler checks if the specification can be implemented on a given platform. However, while the predecessor language xGiotto was purely time-triggered, xGiotto accommodates also asynchronous events. Indeed, through a mechanism called event scoping, events are the main structuring principle of the new language. The xGiotto compiler and run-time system implement event scoping through a tree-based event filter. The compiler also checks programs for determinism (absence of race conditions).},
author = {Ghosal, Arkadeb and Thomas Henzinger and Kirsch, Christoph M and Sanvido, Marco A},
pages = {167 -- 170},
publisher = {Springer},
title = {{Event-driven programming with logical execution times}},
doi = {10.1007/978-3-540-24743-2_24},
volume = {2993},
year = {2004},
}
@inproceedings{4555,
abstract = {Strategies in repeated games can be classified as to whether or not they use memory and/or randomization. We consider Markov decision processes and 2-player graph games, both of the deterministic and probabilistic varieties. We characterize when memory and/or randomization are required for winning with respect to various classes of w-regular objectives, noting particularly when the use of memory can be traded for the use of randomization. In particular, we show that Markov decision processes allow randomized memoryless optimal strategies for all M?ller objectives. Furthermore, we show that 2-player probabilistic graph games allow randomized memoryless strategies for winning with probability 1 those M?ller objectives which are upward-closed. Upward-closure means that if a set α of infinitely repeating vertices is winning, then all supersets of α are also winning.},
author = {Krishnendu Chatterjee and de Alfaro, Luca and Thomas Henzinger},
pages = {206 -- 217},
publisher = {IEEE},
title = {{Trading memory for randomness}},
doi = {10.1109/QEST.2004.10051},
year = {2004},
}
@article{4556,
abstract = {We study the problem of determining stack boundedness and the exact maximum stack size for three classes of interrupt-driven programs. Interrupt-driven programs are used in many real-time applications that require responsive interrupt handling. In order to ensure responsiveness, programmers often enable interrupt processing in the body of lower-priority interrupt handlers. In such programs a programming error can allow interrupt handlers to be interrupted in a cyclic fashion to lead to an unbounded stack, causing the system to crash. For a restricted class of interrupt-driven programs, we show that there is a polynomial-time procedure to check stack boundedness, while determining the exact maximum stack size is PSPACE-complete. For a larger class of programs, the two problems are both PSPACE-complete, and for the largest class of programs we consider, the two problems are PSPACE-hard and can be solved in exponential time. While the complexities are high, our algorithms are exponential only in the number of handlers, and polynomial in the size of the program.},
author = {Krishnendu Chatterjee and Ma, Di and Majumdar, Ritankar S and Zhao, Tian and Thomas Henzinger and Palsberg, Jens},
journal = {Information and Computation},
number = {2},
pages = {144 -- 174},
publisher = {Elsevier},
title = {{Stack size analysis for interrupt-driven programs}},
doi = {10.1016/j.ic.2004.06.001},
volume = {194},
year = {2004},
}
@inproceedings{4558,
abstract = {We study perfect-information stochastic parity games. These are two-player nonterminating games which are played on a graph with turn-based probabilistic transitions. A play results in an infinite path and the conflicting goals of the two players are ω-regular path properties, formalized as parity winning conditions. The qualitative solution of such a game amounts to computing the set of vertices from which a player has a strategy to win with probability 1 (or with positive probability). The quantitative solution amounts to computing the value of the game in every vertex, i.e., the highest probability with which a player can guarantee satisfaction of his own objective in a play that starts from the vertex.For the important special case of one-player stochastic parity games (parity Markov decision processes) we give polynomial-time algorithms both for the qualitative and the quantitative solution. The running time of the qualitative solution is O(d · m3/2) for graphs with m edges and d priorities. The quantitative solution is based on a linear-programming formulation.For the two-player case, we establish the existence of optimal pure memoryless strategies. This has several important ramifications. First, it implies that the values of the games are rational. This is in contrast to the concurrent stochastic parity games of de Alfaro et al.; there, values are in general algebraic numbers, optimal strategies do not exist, and ε-optimal strategies have to be mixed and with infinite memory. Second, the existence of optimal pure memoryless strategies together with the polynomial-time solution forone-player case implies that the quantitative two-player stochastic parity game problem is in NP ∩ co-NP. This generalizes a result of Condon for stochastic games with reachability objectives. It also constitutes an exponential improvement over the best previous algorithm, which is based on a doubly exponential procedure of de Alfaro and Majumdar for concurrent stochastic parity games and provides only ε-approximations of the values.},
author = {Krishnendu Chatterjee and Jurdziński, Marcin and Thomas Henzinger},
pages = {121 -- 130},
publisher = {SIAM},
title = {{Quantitative stochastic parity games}},
year = {2004},
}
@inproceedings{4577,
abstract = {While model checking has been successful in uncovering subtle bugs in code, its adoption in software engineering practice has been hampered by the absence of a simple interface to the programmer in an integrated development environment. We describe an integration of the software model checker BLAST into the Eclipse development environment. We provide a verification interface for practical solutions for some typical program analysis problems - assertion checking, reachability analysis, dead code analysis, and test generation - directly on the source code. The analysis is completely automatic, and assumes no knowledge of model checking or formal notation. Moreover, the interface supports incremental program verification to support incremental design and evolution of code.},
author = {Beyer, Dirk and Thomas Henzinger and Jhala, Ranjit and Majumdar, Ritankar S},
pages = {251 -- 255},
publisher = {IEEE},
title = {{An eclipse plug-in for model checking}},
doi = {10.1109/WPC.2004.1311069 },
year = {2004},
}
@inproceedings{4578,
abstract = {BLAST is an automatic verification tool for checking temporal safety properties of C programs. Blast is based on lazy predicate abstraction driven by interpolation-based predicate discovery. In this paper, we present the Blast specification language. The language specifies program properties at two levels of precision. At the lower level, monitor automata are used to specify temporal safety properties of program executions (traces). At the higher level, relational reachability queries over program locations are used to combine lower-level trace properties. The two-level specification language can be used to break down a verification task into several independent calls of the model-checking engine. In this way, each call to the model checker may have to analyze only part of the program, or part of the specification, and may thus succeed in a reduction of the number of predicates needed for the analysis. In addition, the two-level specification language provides a means for structuring and maintaining specifications. },
author = {Beyer, Dirk and Chlipala, Adam J and Thomas Henzinger and Jhala, Ranjit and Majumdar, Ritankar S},
pages = {2 -- 18},
publisher = {Springer},
title = {{The BLAST query language for software verification}},
doi = {10.1007/978-3-540-27864-1_2},
volume = {3148},
year = {2004},
}
@inproceedings{4581,
abstract = {We have extended the software model checker BLAST to automatically generate test suites that guarantee full coverage with respect to a given predicate. More precisely, given a C program and a target predicate p, BLAST determines the set L of program locations which program execution can reach with p true, and automatically generates a set of test vectors that exhibit the truth of p at all locations in L. We have used BLAST to generate test suites and to detect dead code in C programs with up to 30 K lines of code. The analysis and test vector generation is fully automatic (no user intervention) and exact (no false positives).},
author = {Beyer, Dirk and Chlipala, Adam J and Thomas Henzinger and Jhala, Ranjit and Majumdar, Ritankar S},
pages = {326 -- 335},
publisher = {IEEE},
title = {{Generating tests from counterexamples}},
doi = {10.1109/ICSE.2004.1317455},
year = {2004},
}
@inproceedings{4629,
abstract = {Temporal logic is two-valued: a property is either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a generalization of the branching-time logic Ctl which achieves robustness with respect to model perturbations by giving a quantitative interpretation to predicates and logical operators, and by discounting the importance of events according to how late they occur. In every state, the value of a formula is a real number in the interval [0,1], where 1 corresponds to truth and 0 to falsehood. The boolean operators and and or are replaced by min and max, the path quantifiers ∃ and ∀ determine sup and inf over all paths from a given state, and the temporal operators and □ specify sup and inf over a given path; a new operator averages all values along a path. Furthermore, all path operators are discounted by a parameter that can be chosen to give more weight to states that are closer to the beginning of the path. We interpret the resulting logic Dctl over transition systems, Markov chains, and Markov decision processes. We present two semantics for Dctl: a path semantics, inspired by the standard interpretation of state and path formulas in CTL, and a fixpoint semantics, inspired by the μ-calculus evaluation of CTL formulas. We show that, while these semantics coincide for CTL, they differ for Dctl, and we provide model-checking algorithms for both semantics.},
author = {de Alfaro, Luca and Faella, Marco and Thomas Henzinger and Majumdar, Ritankar S and Stoelinga, Mariëlle},
pages = {77 -- 92},
publisher = {Springer},
title = {{Model checking discounted temporal properties}},
doi = {10.1007/978-3-540-24730-2_6},
volume = {2988},
year = {2004},
}
@article{6155,
abstract = {The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian β than α subunits [1]. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like and β-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid.},
author = {Cheung, Benny H.H and Arellano-Carbajal, Fausto and Rybicki, Irene and de Bono, Mario},
issn = {0960-9822},
journal = {Current Biology},
number = {12},
pages = {1105--1111},
publisher = {Elsevier},
title = {{Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior}},
doi = {10.1016/j.cub.2004.06.027},
volume = {14},
year = {2004},
}
@misc{2636,
author = {Momiyama, Akiko and Ryuichi Shigemoto},
booktitle = {Tanpakushitsu kakusan koso Protein nucleic acid enzyme},
number = {3 Suppl},
pages = {287 -- 294},
publisher = {Kyoritsu Shuppan},
title = {{Function and distribution of glutamate receptors in the central synapses}},
volume = {49},
year = {2004},
}
@article{2638,
abstract = {Among various types of low- and high-threshold calcium channels, the high voltage-activated P/Q-type channel is the most abundant in the cerebellum. These P/Q-type channels are involved in the regulation of neurotransmitter release and in the integration of dendritic inputs. We used an antibody specific for the α1A subunit of the P/Q-type channel in quantitative pre-embedding immunogold labelling combined with three-dimensional reconstruction to reveal the subcellular distribution of pre- and postsynaptic P/Q-type channels in the rat cerebellum. At the light microscopic level, immunoreactivity for the α1A protein was prevalent in the molecular layer, whereas immunostaining was moderate in the somata of Purkinje cells and weak in the granule cell layer. At the electron microscopic level, the most intense Immunoreactivity for the α1A subunit was found in the presynaptic active zone of parallel fibre varicosities. The dendritic spines of Purkinje cells were also strongly labelled with the highest density of immunoparticles detected within 180 nm from the edge of the asymmetrical parallel fibre-Purkinje cell synapses. By contrast, the immunolabelling was sparse in climbing fibre varicosities and axon terminals of GABAergic cells, and weak and diffuse in dendritic shafts of Purkinje cells. The association of the α1A subunit with the glutamatergic parallel fibre-Purkinje cell synapses suggests that presynaptic channels have a major role in the mediation of excitatory neurotransmission, whereas postsynaptic channels are likely to be involved in depolarization-induced generation of local calcium transients in Purkinje cells.},
author = {Kulik, Ákos and Nakadate, Kazuhiko and Hagiwara, Akari and Fukazawa, Yugo and Luján, Rafael and Saito, Hiromitsu and Suzuki, Noboru and Futatsugi, Akira and Mikoshiba, Katsuhiko and Frotscher, Michael and Ryuichi Shigemoto},
journal = {European Journal of Neuroscience},
number = {8},
pages = {2169 -- 2178},
publisher = {Wiley-Blackwell},
title = {{Immunocytochemical localization of the α1A subunit of the P/Q-type calcium channel in the rat cerebellum}},
doi = {10.1111/j.0953-816X.2004.03319.x},
volume = {19},
year = {2004},
}
@article{2639,
abstract = {Vesicular glutamate transporter type 3 (VGLUT3) containing neuronal elements were characterized using antibodies to VGLUT3 and molecular cell markers. All VGLUT3-positive somata were immunoreactive for CCK, and very rarely, also for calbindin; none was positive for parvalbumin, calretinin, VIP or somatostatin. In the CA1 area, 26.8 ± 0.7% of CCK-positive interneuron somata were VGLUT3-positive, a nonoverlapping 22.8 ± 1.9% were calbindin-positive, 10.7 ± 2.5% VIP-positive and the rest were only CCK-positive. The patterns of coexpression were similar in the CA3 area, the dentate gyrus and the isocortex. Immunoreactivity for VGLUT3 was undetectable in pyramidal and dentate granule cells. Boutons colabelled for VGLUT3, CCK and GAD were most abundant in the cellular layers of the hippocampus and in layers II-III of the isocortex. Large VGLUT3-labelled boutons at the border of strata radiatum and lacunosum-moleculare in the CA1 area were negative for GAD, but were labelled for vesicular monoamine transporter type 2, plasmalemmal serotonin transporter or serotonin. No colocalization was found in terminals between VGLUT3 and parvalbumin, vesicular acetylcholine transporter and group III (mGluR7a,b; mGluR8a,b) metabotropic glutamate receptors. In stratum radiatum and the isocortex, VGLUT3-positive but GAD-negative boutons heavily innervated the soma and proximal dendrites of some VGLUT3- or calbindin-positive interneurons. The results suggest that boutons coexpressing VGLUT3, CCK and GAD originate from CCK-positive basket cells, which are VIP-immunonegative. Other VGLUT3-positive boutons immunopositive for serotonergic markers but negative for GAD probably originate from the median raphe nucleus and innervate select interneurons. The presumed amino acid substrate of VGLUT3 may act on presynaptic kainate or group II metabotropic glutamate receptors.},
author = {Somogyi, Jozsef and Baude, Agnès and Omori, Yuko and Shimizu, Hidemi and El-Mestikawy, Salah and Fukaya, Masahiro and Ryuichi Shigemoto and Watanabe, Masahiko and Somogyi, Péter},
journal = {European Journal of Neuroscience},
number = {3},
pages = {552 -- 569},
publisher = {Wiley-Blackwell},
title = {{GABAergic basket cells expressing cholecystokinin contain vesicular glutamate transporter type 3 (VGLUT3) in their synaptic terminals in hippocampus and isocortex of the rat}},
doi = {10.1111/j.0953-816X.2003.03091.x},
volume = {19},
year = {2004},
}
@article{2640,
abstract = {Hyperpolarization-activated cation currents (Ih) contribute to various physiological properties and functions in the brain, including neuronal pacemaker activity, setting of resting membrane potential, and dendritic integration of synaptic input. Four subunits of the Hyperpolarization-activated and Cyclic-Nucleotide-gated nonselective cation channels (HCN1-4), which generate Ih, have been cloned recently. To better understand the functional diversity of Ih in the brain, we examined precise immunohistochemical localization of four HCNs in the rat brain. Immunoreactivity for HCN1 showed predominantly cortical distribution, being intense in the neocortex, hippocampus, superior colliculus, and cerebellum, whereas those for HCN3 and HCN4 exhibited subcortical distribution mainly concentrated in the hypothalamus and thalamus, respectively. Immunoreactivity for HCN2 had a widespread distribution throughout the brain. Double immunofluorescence revealed colocalization of immunoreactivity for HCN1 and HCN2 in distal dendrites of pyramidal cells in the hippocampus and neocortex. At the electron microscopic level, immunogold particles for HCN1 and HCN2 had similar distribution patterns along plasma membrane of dendritic shafts in layer I of the neocortex and stratum lacunosum moleculare of the hippocampal CA1 area, suggesting that these subunits could form heteromeric channels. Our results further indicate that HCNs are localized not only in somato-dendritic compartments but also in axonal compartments of neurons. Immunoreactivity for HCNs often occurred in preterminal rather than terminal portions of axons and in specific populations of myelinated axons. We also found HCN2-immunopositive oligodendrocytes including perineuronal oligodendrocytes throughout the brain. These results support previous electrophysiological findings and further suggest unexpected roles of Ih channels in the brain.},
author = {Notomi, Takuya and Ryuichi Shigemoto},
journal = {Journal of Comparative Neurology},
number = {3},
pages = {241 -- 276},
publisher = {Wiley-Blackwell},
title = {{Immunohistochemical localization of Ih channel subunits, HCN1-4, in the rat brain}},
doi = {10.1002/cne.11039},
volume = {471},
year = {2004},
}
@article{2641,
abstract = {The Na+-K+ pump current (Ip) and the h-current (Ih) flowing through hyperpolarization-activated channels (h-channels) participate in generating the resting potential. These two currents are thought to be produced independently. We show here bidirectional interactions between Na+-K+ pumps and h-channels in mesencephalic trigeminal neurons. Activation of Ih leads to the generation of two types of ouabain-sensitive Ip with temporal profiles similar to those of instantaneous and slow components of I h, presumably reflecting Na+ transients in a restricted cellular space. Moreover, the Ip activated by instantaneous I h can facilitate the subsequent activation of slow Ih. Such counteractive and cooperative interactions were also disclosed by replacing extracellular Na+ with Li+, which is permeant through h-channels but does not stimulate the Na+-K+ pump as strongly as Na+ ions. These observations indicate that the interactions are bidirectional and mediated by Na+ ions. Also after substitution of extracellular Na+ with Li+, the tail Ih was reduced markedly despite an enhancement of Ih itself, attributable to a negative shift of the reversal potential for I h presumably caused by intracellular accumulation of Li+ ions. This suggests the presence of a microdomain where the interactions can take place. Thus, the bidirectional interactions between Na+-K + pumps and h-channels are likely to be mediated by Na+ microdomain. Consistent with these findings, hyperpolarization-activated and cyclic nucleotide-modulated subunits (HCN1/2) and the Na+-K + pump α3 isoform were colocalized in plasma membrane of mesencephalic trigeminal neurons having numerous spines.},
author = {Kang, Youngnam and Notomi, Takuya and Saito, Mitsuru and Zhang, Wei and Ryuichi Shigemoto},
journal = {Journal of Neuroscience},
number = {14},
pages = {3694 -- 3702},
publisher = {Society for Neuroscience},
title = {{Bidirectional interactions between H-channels and Na+-K + pumps in mesencephalic trigeminal neurons}},
doi = {10.1523/JNEUROSCI.5641-03.2004},
volume = {24},
year = {2004},
}
@article{2642,
abstract = {In the hippocampal CA1 region, metabotropic glutamate subtype 1 (mGluR1) receptors have been implicated in a variety of physiological responses to glutamate, which include modulation of synaptic transmission and plasticity, as well as neuronal excitability and synchronization. The mGluR1α isoform is characteristically expressed only by nonprincipal cells, and it is particularly enriched in somatostatin (SS -containing interneurons in stratum oriens-alveus. Anatomical and physiological data have indicated the presence of mGluR1α in several distinct classes of interneurons with their somata located also in strata pyramidale, radiatum, and lacunosum moleculare. Each different interneuron subtype, as defined by functionally relevant criteria, including input/output characteristics and expression of selective molecular markers, subserves distinct functions in local hippocampal circuits. We have investigated which of the different CA1 interneuron classes express mGluR1α by immunofluorescent labeling, combining antibodies to mGluR1α, calcium-binding proteins, and neuropeptides, and by intracellular labeling in vitro. Several types of interneuron that are immunopositive for mGluR1α each targeted different domains of pyramidal cells and included (1) O-LM interneurons, found to coexpress both SS and parvalbumin (PV); (2) interneurons with target selectivity for other interneurons, expressing vasoactive intestinal polypeptide (VIP) and/or the calcium-binding protein calretinin; (3) procholecystokinin-immunopositive interneurons probably non-basket and dendrite-targeting; and (4) an as-yet unidentified SS-immunoreactive but PV-immunonegative interneuron class, possibly corresponding to oriensbistratified cells. Estimation of the relative proportion of mGluR1α-positive interneurons showed 43%, 46%, and 30% co-labeling with SS, VIP, or PV, respectively. The identification of the specific subclasses of CA1 interneurons expressing mGluR1α provides the network basis for assessing the contribution of this receptor to the excitability of the hippocampus.},
author = {Ferraguti, Francesco and Cobden, Philip M and Pollard, Marie and Cope, David W and Ryuichi Shigemoto and Watanabe, Masahiko and Somogyi, Péter},
journal = {Hippocampus},
number = {2},
pages = {193 -- 215},
publisher = {Wiley-Blackwell},
title = {{Immunolocalization of metabotropic glutamate receptor 1α (mGluR1α) in distinct classes of interneuron in the CA1 region of the rat hippocampus}},
doi = {10.1002/hipo.10163},
volume = {14},
year = {2004},
}