@misc{4291,
author = {Nicholas Barton},
booktitle = {Genetical Research},
number = {2},
pages = {180 -- 181},
publisher = {Cambridge University Press},
title = {{The ccological detective: Confronting models with data}},
volume = {70},
year = {1997},
}
@inbook{4293,
abstract = {Natural populations differ from the simplest models in ways which can significantly affect their evolution. Real populations are rarely all of the same size; the rates of migration into and out of populations vary in space and time; some populations go extinct, and new ones are established, while all populations fluctuate in size. Furthermore, the genetic properties of real species are not like those assumed in simple models. Alleles are exposed to a wide variety of selection mutation rarely creates novel genotypes with each mutation event, generations overlap, and environments vary from place to place. Evolution in a metapopulation can be substantially different from the predictions of single-population models and, indeed, very different from the simplest models of subdivided species.},
author = {Nicholas Barton and Whitlock, Michael},
booktitle = {Metapopulation Biology},
pages = {183 -- 210},
publisher = {Academic Press},
title = {{The evolution of metapopulations}},
doi = {10.1016/B978-012323445-2/50012-2},
year = {1997},
}
@inproceedings{4438,
abstract = {In temporal-logic model checking, we verify the correctness of a program with respect to a desired behavior by checking whether a structure that models the program satisfies a temporal-logic formula that specifies the behavior. The model-checking problem for the branching-time temporal logic CTL can be solved in linear running time, and model-checking tools for CTL are used successfully in industrial applications. The development of programs that must meet rigid real-time constraints has brought with it a need for real-time temporal logics that enable quantitative reference to time. Early research on real-time temporal logics uses the discrete domain of the integers to model time. Present research on real-time temporal logics focuses on continuous time and uses the dense domain of the reals to model time. There, model checking becomes significantly more complicated. For example, the model-checking problem for TCTL, a continuous-time extension of the logic CTL, is PSPACE-complete.
In this paper we suggest a reduction from TCTL model checking to CTL model checking. The contribution of such a reduction is twofold. Theoretically, while it has long been known that model-checking methods for untimed temporal logics can be extended quite easily to handle discrete time, it was not clear whether and how untimed methods can handle the reset quantifier of TCTL, which resets a realvalued clock. Practically, our reduction enables anyone who has a tool for CTL model checking to use it for TCTL model checking. The TCTL model-checking algorithm that follows from our reduction is in PSPACE, matching the known bound for this problem. In addition, it enjoys the wide distribution of CTL model-checking tools and the extensive and fruitful research efforts and heuristics that have been put into these tools.},
author = {Thomas Henzinger and Kupferman, Orna},
pages = {48 -- 62},
publisher = {Springer},
title = {{From quantity to quality}},
doi = { 10.1007/BFb0014712},
volume = {1201},
year = {1997},
}
@inproceedings{4441,
abstract = {Rectangular hybrid automata model digital control programs of analog plant environments. We study rectangular hybrid automata where the plant state evolves continuously in real-numbered time, and the controller samples the plant state and changes the control state discretely, only at the integer points in time. We prove that rectangular hybrid automata have finite bisimilarity quotients when all control transitions happen at integer times, even if the constraints on the derivatives of the variables vary between control states. This is sharply in contrast with the conventional model where control transitions may happen at any real time, and already the reachability problem is undecidable. Based on the finite bisimilarity quotients, we give an exponential algorithm for the symbolic sampling-controller synthesis of rectangular automata. We show our algorithm to be optimal by proving the problem to be EXPTIME-hard. We also show that rectangular automata form a maximal class of systems for which the sampling-controller synthesis problem can be solved algorithmically.},
author = {Thomas Henzinger and Kopke, Peter W},
pages = {582 -- 593},
publisher = {Springer},
title = {{Discrete-time control for rectangular hybrid automata}},
doi = {10.1007/3-540-63165-8_213},
volume = {1256},
year = {1997},
}
@article{4493,
author = {Thomas Henzinger and Ho, Pei-Hsin and Wong-Toi, Howard},
journal = {Software Tools For Technology Transfer},
number = {1-2},
pages = {110 -- 122},
publisher = {Springer},
title = {{HyTech: A model checker for hybrid systems}},
doi = {10.1007/s100090050008},
volume = {1},
year = {1997},
}
@inproceedings{4494,
abstract = {A hybrid system consists of a collection of digital programs that interact with each other and with an analog environment. Examples of hybrid systems include medical equipment, manufacturing controllers, automotive controllers, and robots. The formal analysis of the mixed digital-analog nature of these systems requires a model that incorporates the discrete behavior of computer programs with the continuous behavior of environment variables, such as temperature and pressure. Hybrid automata capture both types of behavior by combining finite automata with differential inclusions (i.e. differential inequalities). HyTech is a symbolic model checker for linear hybrid automata, an expressive, yet automatically analyzable, subclass of hybrid automata. A key feature of HyTech is its ability to perform parametric analysis, i.e. to determine the values of design parameters for which a linear hybrid automaton satisfies a temporal requirement.},
author = {Thomas Henzinger and Ho, Pei-Hsin and Wong-Toi, Howard},
pages = {460 -- 463},
publisher = {Springer},
title = {{HyTech: A model checker for hybrid systems}},
doi = {10.1007/3-540-63166-6_48},
volume = {1254},
year = {1997},
}
@inproceedings{4496,
abstract = {The simulation preorder for labeled transition systems is defined locally as a game that relates states with their immediate successor states. Liveness assumptions about transition systems are typically modeled using fairness constraints. Existing notions of simulation for fair transition systems, however, are not local, and as a result, many appealing properties of the simulation preorder are lost. We extend the local definition of simulation to account for fairness: system S fairly simulates system I iff in the simulation game, there is a strategy that matches with each fair computation of I a fair computation of S. Our definition enjoys a fully abstract semantics and has a logical characterization: S fairly simulates I iff every fair computation tree embedded in the unrolling of I can be embedded also in the unrolling of S or, equivalently, iff every Fair-AFMC formula satisfied by I is satisfied also by S (AFMC is the universal fragment of the alternation-free -calculus). The locality of the definition leads us to a polynomial-time algorithm for checking fair simulation for finite-state systems with weak and strong fairness constraints. Finally, fair simulation implies fair trace-containment, and is therefore useful as an efficientlycomputable local criterion for proving linear-time abstraction hierarchies.},
author = {Thomas Henzinger and Kupferman, Orna and Rajamani, Sriram K},
pages = {273 -- 287},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Fair simulation}},
doi = {10.1007/3-540-63141-0_19},
volume = {1243},
year = {1997},
}
@inproceedings{4520,
abstract = {We define robust timed automata, which are timed automata that accept all trajectories robustly: if a robust timed automaton accepts a trajectory, then it must accept neighboring trajectories also; and if a robust timed automaton rejects a trajectory, then it must reject neighboring trajectories also. We show that the emptiness problem for robust timed automata is still decidable, by modifying the region construction for timed automata. We then show that, like timed automata, robust timed automata cannot be determinized. This result is somewhat unexpected, given that in temporal logic, the removal of realtime equality constraints is known to lead to a decidable theory that is closed under all boolean operations.},
author = {Gupta, Vineet and Thomas Henzinger and Jagadeesan, Radha},
pages = {331 -- 345},
publisher = {Springer},
title = {{Robust timed automata}},
doi = {10.1007/BFb0014736},
volume = {1201},
year = {1997},
}
@article{4201,
abstract = {In zebrafish, as in other vertebrates, an initially singular eye held within the neural plate has to split during morphogenesis to allow the development of two separated eyes. It has been suggested that anterior progression of midline tissue within the neural plate is involved in the bilateralization of the eye held. Mutations in the recently identified silberblick (slb) gene cause an incomplete separation of the eyes. During gastrulation and early somitogenesis, the ventral midline of the central nervous system (CNS) together with the underlying axial mesendoderm is shortened and broadened in slb embryos. While in wild-type embryos the ventral CNS midline extends to the anterior limit of the neural plate at the end of gastrulation, there is a gap between the anterior tip of the ventral CNS midline and the anterior edge of the neural plate in slb. To investigate the cause for the shortening of the ventral CNS midline in slb we determined the fate of labeled ventral CNS midline cells in wild-type and slb embryos at different stages of development. In slb, anterior migration of ventral CNS midline cells is impaired, which indicates that migration of these cells is needed for elongation of the ventral CNS midline. The anterior shortening of the ventral CNS midline in slb leads to medial instead of bilateral induction of optic stalks followed by a partial fusion of the eyes at later developmental stages. The analysis of the sIb phenotype indicates that anterior migration of midline cells within the neural plate is required for proper induction and subsequent bilateralization of an initially singular eye field. These findings may therefore provide a starting point in elucidating the role of neural plate morphogenesis in positioning of the eyes. (C) 1997 Academic Press.},
author = {Heisenberg, Carl-Philipp and Nüsslein-Volhard, Christiane N},
journal = {Developmental Biology},
number = {1},
pages = {85 -- 94},
publisher = {Elsevier},
title = {{The function of silberblick in the positioning of the eye anlage in the zebrafish embryo}},
doi = {10.1006/dbio.1997.8511},
volume = {184},
year = {1997},
}
@inproceedings{4583,
abstract = {In a trace-based world, the modular specification, verification, and control of live systems require each module to be receptive; that is, each module must be able to meet its liveness assumptions no matter how the other modules behave. In a real-time world, liveness is automatically present in the form of diverging time. The receptiveness condition, then, translates to the requirement that a module must be able to let time diverge no matter how the environment behaves. We study the receptiveness condition for real-time systems by extending the model of reactive modules to timed and hybrid modules. We define the receptiveness of such a module as the existence of a winning strategy in a game of the module against its environment. By solving the game on region graphs, we present an (optimal) Exptime algorithm for checking the receptiveness of prepositional timed modules. By giving a fixpoint characterization of the game, we present a symbolic procedure for checking the receptiveness of linear hybrid modules. Finally, we present an assume-guarantee principle for reasoning about timed and hybrid modules, and a method for synthesizing receptive controllers of timed and hybrid modules.},
author = {Alur, Rajeev and Thomas Henzinger},
pages = {74 -- 88},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Modularity for timed and hybrid systems}},
doi = {10.1007/3-540-63141-0_6},
volume = {1243},
year = {1997},
}
@article{4584,
abstract = {This paper introduces, gently but rigorously, the clock approach to real-time programming. We present with mathematical precision, assuming no prerequisites other than familiarity with logical and programming notations, the concepts that are necessary for understanding, writing, and executing clock programs. In keeping with an expository style, all references are clustered in bibliographic remarks at the end of each section. The first appendix presents proof rules for verifying temporal properties of clock programs. The second appendix points to selected literature on formal methods and tools for programming with clocks. In particular, the timed automaton, which is a finite-state machine equipped with clocks, has become a standard paradigm for real-time model checking; it underlies the tools HyTech, Kronos, and Uppaal, which are discussed elsewhere in this volume.},
author = {Alur, Rajeev and Thomas Henzinger},
journal = {Software Tools For Technology Transfer},
number = {1-2},
pages = {86 -- 109},
publisher = {Springer},
title = {{Real-time system = discrete system + clock variables}},
doi = {10.1007/s100090050007},
volume = {1},
year = {1997},
}
@inproceedings{4605,
abstract = {A hybrid system is a dynamical system whose behavior exhibits both discrete and continuous change. A hybrid automaton is a mathematical model for hybrid systems, which combines, in a single formalism, automaton transitions for capturing discrete change with differential equations for capturing continuous change. In this survey, we demonstrate symbolic algorithms for the verification of and controller synthesis for linear hybrid automata, a subclass of hybrid automata that can be analyzed automatically},
author = {Alur, Rajeev and Thomas Henzinger and Wong-Toi, Howard},
pages = {702 -- 707},
publisher = {IEEE},
title = {{Symbolic analysis of hybrid systems}},
doi = {10.1109/CDC.1997.650717 },
year = {1997},
}
@article{4607,
abstract = {We present a verification algorithm for duration properties of real-time systems. While simple real-time properties constrain the total elapsed time between events, duration properties constrain the accumulated satisfaction time of state predicates. We formalize the concept of durations by introducing duration measures for timed automata. A duration measure assigns to each finite run of a timed automaton a real number —the duration of the run— which may be the accumulated satisfaction time of a state predicate along the run. Given a timed automaton with a duration measure, an initial and a final state, and an arithmetic constraint, the duration-bounded reachability problem asks if there is a run of the automaton from the initial state to the final state such that the duration of the run satisfies the constraint. Our main result is an (optimal) PSPACE decision procedure for the duration-bounded reachability problem.},
author = {Alur, Rajeev and Courcoubetis, Costas and Thomas Henzinger},
journal = {Formal Methods in System Design},
number = {2},
pages = {137 -- 156},
publisher = {Springer},
title = {{Computing accumulated delays in real-time systems}},
doi = {10.1023/A:1008626013578},
volume = {11},
year = {1997},
}
@inproceedings{4608,
abstract = {State space explosion is a fundamental obstacle in formal verification of designs and protocols. Several techniques for combating this problem have emerged in the past few years, among which two are significant: partial-order reductions and symbolic state space search. In asynchronous systems, interleavings of independent concurrent events are equivalent, and only a representative interleaving needs to be explored to verify local properties. Partial-order methods exploit this redundancy and visit only a subset of the reachable states. Symbolic techniques, on the other hand, capture the transition relation of a system and the set of reachable states as boolean functions. In many cases, these functions can be represented compactly using binary decision diagrams (BDDs). Traditionally, the two techniques have been practiced by two different schools—partial-order methods with enumerative depth-first search for the analysis of asynchronous network protocols, and symbolic breadth-first search for the analysis of synchronous hardware designs. We combine both approaches and develop a method for using partial-order reduction techniques in symbolic BDD-based invariant checking. We present theoretical results to prove the correctness of the method, and experimental results to demonstrate its efficacy.},
author = {Alur, Rajeev and Brayton, Robert K and Thomas Henzinger and Qadeer,Shaz and Rajamani, Sriram K},
pages = {340 -- 351},
publisher = {Springer},
title = {{Partial-order reduction in symbolic state-space exploration}},
doi = {10.1007/3-540-63166-6_34},
volume = {1254},
year = {1997},
}
@inproceedings{4609,
abstract = {Temporal logic comes in two varieties: linear-time temporal logic assumes implicit universal quantification over all paths that are generated by system moves; branching-time temporal logic allows explicit existential and universal quantification over all paths. We introduce a third, more general variety of temporal logic: alternating-time temporal logic offers selective quantification over those paths that are possible outcomes of games, such as the game in which the system and the environment alternate moves. While linear-time and branching-time logics are natural specification languages for closed systems, alternating-time logics are natural specification languages for open systems. For example, by preceding the temporal operator “eventually” with a selective path quantifier, we can specify that in the game between the system and the environment, the system has a strategy to reach a certain state. Also the problems of receptiveness, realizability, and controllability can be formulated as model-checking problems for alternating-time formulas},
author = {Alur, Rajeev and Thomas Henzinger and Kupferman, Orna},
pages = {100 -- 109},
publisher = {IEEE},
title = {{Alternating-time temporal logic}},
doi = { 10.1109/SFCS.1997.646098 },
year = {1997},
}
@inproceedings{1942,
author = {Leonid Sazanov and Burrows, P and Nixon, P J},
pages = {705 -- 708},
publisher = {Kluwer},
title = {{Presence of a large protein complex containing the ndhK gene product and possessing NADH-specific dehydrogenase activity in thylakoid membranes of higher plant chloroplasts}},
volume = {2},
year = {1996},
}
@article{1951,
author = {Leonid Sazanov and Burrows, Paul A and Nixon, Peter J},
journal = {Biochemical Society Transactions},
number = {3},
pages = {739 -- 743},
publisher = {Portland Press},
title = {{Detection and characterization of a complex I-like NADH-specific dehydrogenase from pea thylakoids}},
volume = {24},
year = {1996},
}
@article{1952,
abstract = {Two strains of Rhodospirillum rubrum were constructed in which, by a gene dosage effect, the transhydrogenase activity of isolated chromatophores was increased 7-10-fold and 15-20-fold, respectively. The H+/H- ratio (the ratio of protons translocated per hydride ion equivalent transferred from NADPH to an NAD+ analogue, acetyl pyridine adenine dinucleotide), determined by a spectroscopic technique, was approximately 1.0 for chromatophores from the over-expressing strains, but was only approximately 0.6 for wild-type chromatophores. Highly-coupled proteoliposomes were prepared containing purified transhydrogenase from beef-heart mitochondria. Using the same technique, the H+/H- ratio was close to 1.0 for these proteoliposomes. It is suggested that the mechanistic H+/H- ratio is indeed unity, but that a low ratio is obtained in wild-type chromatophores because of inhomogeneity in the vesicle population.},
author = {Bizouarn, Tania and Leonid Sazanov and Aubourg, Sébastien and Jackson, Julie B},
journal = {Biochimica et Biophysica Acta - Bioenergetics},
number = {1},
pages = {4 -- 12},
publisher = {Elsevier},
title = {{Estimation of the H+/H- ratio of the reaction catalysed by the nicotinamide nucleotide transhydrogenase in chromatophores from over-expressing strains of Rhodospirillum rubrum and in liposomes inlaid with the purified bovine enzyme}},
doi = {10.1016/0005-2728(95)00125-5},
volume = {1273},
year = {1996},
}
@article{2492,
abstract = {The metabotropic glutamate receptor subtypes mGluR2 and mGluR5, which are thought to be coupled respectively to the inhibitory cyclic adenosine monophosphate (cAMP) cascade and the phosphatidylinositol hydrolysis/Ca2+ cascade, are known to be expressed on Golgi cells in the granular layer of the rat cerebellar cortex. In the present immunohistochemical study with a monoclonal antibody against mGluR2 and a polyclonal antibody for mGluR5, we examined whether or not mGluR2- and mGluR5-like immunoreactivities were both present in single Golgi cells in the rat cerebellar cortex. In double immunofluorescence histochemistry, no Golgi cells showed mGluR2- and mGluR5-like immunoreactivities simultaneously. Of the total number of Golgi cells immunoreactive for mGluR2 or mGluR5, about 90% were mGluR2-like immunoreactive, and about 10% were mGluR5-like immunoreactive. Golgi cells with mGluR2-like immunoreactivity were distributed evenly in the granular layer of all the cerebellar regions, while those with mGluR5-like immunoreactivity were distributed more frequently in the I, II, VII-X lobules of the vermis and the copula pyramidis of the hemisphere than in other cerebellar regions. The results indicate that Golgi cells containing mGluR2 are segregated from those possessing mGluR5. These two populations of Golgi cells, each equipped with a different metabolic glutamate receptor coupled to a different intracellular signal transduction system, may play different roles in the glutamatergic neuronal circuits in the cerebellar cortex.},
author = {Neki, Akio and Ohishi, Hitoshi and Kaneko, Takeshi and Ryuichi Shigemoto and Nakanishi, Shigetada and Mizuno, Noboru},
journal = {Neuroscience},
number = {3},
pages = {815 -- 826},
publisher = {Elsevier},
title = {{Metabotropic glutamate receptors mGluR2 and mGluR5 are expressed in two non-overlapping populations of Golgi cells in the rat cerebellum}},
doi = {10.1016/0306-4522(96)00316-8},
volume = {75},
year = {1996},
}
@article{2562,
abstract = {A monoclonal antibody against a metabotropic glutamate receptor, mGluR2, was produced by using a glutathione S-transferase (GST) fusion protein containing an N-terminal sequence of rat mGluR2. Intense mGluR2-like immunoreactivity (mGluR2-LI) was seen mainly in neuropil of the cerebral cortical regions, hippocampus, olfactory bulb, some diencephalic nuclei, dorsal cochlear nucleus and cerebellar cortex. In the cerebellar cortex, mGluR2-LI was seen only in Golgi cells. In Ammon's hem, mGluR2-LI was marked in the stratum lucidum of CA3 and the stratum lacunosum-moleculare of CA1-CA3, but not detected in the stratum pyramidale. The results indicate that mGluR2 is located not only presynaptically but also postsynaptically.},
author = {Neki, Akio and Ohishi, Hitoshi and Kaneko, Takeshi and Ryuichi Shigemoto and Nakanishi, Shigetada and Mizuno, Noboru},
journal = {Neuroscience Letters},
number = {3},
pages = {197 -- 200},
publisher = {Elsevier},
title = {{Pre- and postsynaptic localization of a metabotropic glutamate receptor, mGluR2, in the rat brain: An immunohistochemical study with a monoclonal antibody}},
doi = {10.1016/0304-3940(95)12248-6},
volume = {202},
year = {1996},
}