@inproceedings{4497, abstract = {HyTech is a tool for the automated analysis of embedded systems. This document, designed for the first-time user of HyTech, guides the reader through the underlying system model, and through the input language for describing and analyzing systems. The guide gives several examples of usage, and some hints for gaining maximal computational efficiency from the tool. The version of HyTech described in this guide was released in August 1995, and is available through anonymous ftp from ftp.cs.cornell.edu in the directory pub/tah/HyTech, and through the World-Wide Web via HyTech's home page http:/www.cs.cornell.edu/Info/People/tah/hytech.html.}, author = {Henzinger, Thomas A and Ho, Pei and Wong Toi, Howard}, booktitle = {1st International Workshop on Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783540606307}, location = {Aarhus, Denmark}, pages = {41 -- 71}, publisher = {Springer}, title = {{A user guide to HyTech}}, doi = {10.1007/3-540-60630-0_3}, volume = {1019}, year = {1995}, } @inproceedings{4498, abstract = {We present algorithms for computing similarity relations of labeled graphs. Similarity relations have applications for the refinement and verification of reactive systems. For finite graphs, we present an O(mn) algorithm for computing the similarity relation of a graph with n vertices and m edges (assuming m⩾n). For effectively presented infinite graphs, we present a symbolic similarity-checking procedure that terminates if a finite similarity relation exists. We show that 2D rectangular automata, which model discrete reactive systems with continuous environments, define effectively presented infinite graphs with finite similarity relations. It follows that the refinement problem and the ∀CTL* model-checking problem are decidable for 2D rectangular automata}, author = {Henzinger, Monika H and Henzinger, Thomas A and Kopke, Peter}, booktitle = {Proceedings of IEEE 36th Annual Foundations of Computer Science}, isbn = {0818671831}, issn = {0272-5428}, location = {Milwaukee, WI, United States of America}, pages = {453 -- 462}, publisher = {IEEE}, title = {{Computing simulations on finite and infinite graphs}}, doi = {10.1109/SFCS.1995.492576}, year = {1995}, } @inproceedings{4499, abstract = {We describe a new implementation of HYTECH, a symbolic model checker for hybrid systems. Given a parametric description of an embedded system as a collection of communicating automata, HYTECH automatically computes the conditions on the parameters under which the system satisfies its safety and timing requirements. While the original HYTECH prototype was based on the symbolic algebra tool Mathematica, the new implementation is written in C++ and builds on geometric algorithms instead of formula manipulation. The new HYTECH offers a cleaner and more expressive input language, greater portability, superior performance (typically two to three orders of magnitude), and new features such as diagnostic error-trace generation. We illustrate the effectiveness of the new implementation by applying HYTECH to the automatic parametric analysis of the generic railroad crossing benchmark problem and to an active structure control algorithm}, author = {Henzinger, Thomas A and Ho, Pei and Wong Toi, Howard}, booktitle = {Proceedings 16th IEEE Real-Time Systems Symposium}, isbn = {0818673370}, location = {Pisa, Italy}, pages = {56 -- 65}, publisher = {IEEE}, title = {{HyTech: The next generation}}, doi = {10.1109/REAL.1995.495196 }, year = {1995}, } @inproceedings{4500, abstract = {We investigate the expressive power of timing restrictions on labeled transition systems. In particular, we show how constraints on clock variables together with a uniform liveness condition—the divergence of time—can express Büchi, Muller, Streett, Rabin, and weak and strong fairness conditions on a given labeled transition system. We then consider the effect, on both timed and time-abstract expressiveness, of varying the following parameters: time domain (discrete or dense), number of clocks, number of states, and size of constants used in timing restrictions.}, author = {Henzinger, Thomas A and Kopke, Peter and Wong Toi, Howard}, booktitle = {22nd International Colloquium on Automata, Languages and Programming }, isbn = {9783540600848}, location = {Szeged, Hungary}, pages = {417 -- 428}, publisher = {Springer}, title = {{The expressive power of clocks}}, doi = {10.1007/3-540-60084-1_93}, volume = {944}, year = {1995}, } @inproceedings{4502, abstract = {Hybrid automata model systems with both digital and analog components, such as embedded control programs. Many verification tasks for such programs can be expressed as reachability problems for hybrid automata. By improving on previous decidability and undecidability results, we identify the precise boundary between decidability and undecidability of the reachability problem for hybrid automata. On the positive side, we give an (optimal) PSPACE reachability algorithm for the case of initialized rectangular automata, where all analog variables follow trajectories within piecewise-linear envelopes and are reinitialized whenever the envelope changes. Our algorithm is based on the construction of a timed automaton that contains all reachability information about a given initialized rectangular automaton. The translation has practical significance for verification, because it guarantees the termination of symbolic procedures for the reachability analysis of initialized rectangular automata. The translation also preserves the omega-languages of initialized rectangular automata with bounded nondeterminism. On the negative side, we show that several slight generalizations of initialized rectangular automata lead to an undecidable reachability problem. In particular, we prove that the reachability problem is undecidable for timed automata augmented with a single stopwatch.}, author = {Henzinger, Thomas A and Kopke, Peter and Puri, Anuj and Varaiya, P.}, booktitle = {Proceedings of the 27th annual ACM symposium on Theory of computing}, isbn = {9780897917186}, location = {Las Vegas, NV, United States of America}, pages = {373 -- 382}, publisher = {ACM}, title = {{What's decidable about hybrid automata?}}, doi = {10.1145/225058.225162}, year = {1995}, } @inproceedings{4518, abstract = {The analysis, verification, and control of hybrid automata with finite bisimulations can be reduced to finite-state problems. We advocate a time-abstract, phase-based methodology for checking if a given hybrid automaton has a finite bisimulation. First, we factor the automaton into two components, a boolean automaton with a discrete dynamics on the finite state space B m and a euclidean automaton with a continuous dynamics on the infinite state space n . Second, we investigate the phase portrait of the euclidean component. In this fashion, we obtain new decidability results for hybrid systems as well as new, uniform proofs of known decidability results.}, author = {Henzinger, Thomas A}, booktitle = {22nd International Colloquium on Automata, Languages and Programming }, isbn = {9783540600848}, location = {Szeged, Hungary}, pages = {324 -- 335}, publisher = {Springer}, title = {{Hybrid automata with finite bisimulations}}, doi = {10.1007/3-540-60084-1_85}, volume = {944}, year = {1995}, } @inproceedings{4587, abstract = {We argue that the standard constraints on liveness conditions in nonblocking trace models—machine closure for closed systems, and receptiveness for open systems—are unnecessarily weak and complex, and that liveness should, instead, be specified by augmenting transition systems with acceptance conditions that satisfy a locality constraint. First, locality implies machine closure and receptiveness, and thus permits the composition and modular verification of live transition systems. Second, while machine closure and receptiveness are based on infinite games, locality is based on repeated finite games, and thus easier to check. Third, no expressive power is lost by the restriction to local liveness conditions. We illustrate the appeal of local liveness using the model of Fair Reactive Systems, a nonblocking trace model of communicating processes.}, author = {Alur, Rajeev and Henzinger, Thomas A}, booktitle = {7th International Conference on Computer Aided Verification}, isbn = {978-3-540-60045-9}, location = {Liege, Belgium}, pages = {166 -- 179}, publisher = {Springer}, title = {{Local liveness for compositional modeling of fair reactive systems}}, doi = {10.1007/3-540-60045-0_49}, volume = {939}, year = {1995}, } @article{4613, abstract = {We present a general framework for the formal specification and algorithmic analysis of hybrid systems. A hybrid system consists of a discrete program with an analog environment. We model hybrid systems as finite automata equipped with variables that evolve continuously with time according to dynamical laws. For verification purposes, we restrict ourselves to linear hybrid systems, where all variables follow piecewise-linear trajectories. We provide decidability and undecidability results for classes of linear hybrid systems, and we show that standard program-analysis techniques can be adapted to linear hybrid systems. In particular, we consider symbolic model-checking and minimization procedures that are based on the reachability analysis of an infinite state space. The procedures iteratively compute state sets that are definable as unions of convex polyhedra in multidimensional real space. We also present approximation techniques for dealing with systems for which the iterative procedures do not converge.}, author = {Alur, Rajeev and Courcoubetis, Costas and Halbwachs, Nicolas and Henzinger, Thomas A and Ho, Pei and Nicollin, Xavier and Olivero, Alfredo and Sifakis, Joseph and Yovine, Sergio}, issn = {0304-3975}, journal = {Theoretical Computer Science}, number = {1}, pages = {3 -- 34}, publisher = {Elsevier}, title = {{The algorithmic analysis of hybrid systems}}, doi = {10.1016/0304-3975(94)00202-T}, volume = {138}, year = {1995}, } @article{6162, abstract = {The tra-1 gene is the terminal global selector of somatic sex in Caenorhabditis elegans: High tra-1 activity elicits female somatic development while low tra-1 activity elicits male development. Previous genetic studies defined a cascade of negatively interacting genes that regulates tra-1 activity in response to the primary sex-determining signal. Here, we investigate the last step in this regulatory cascade, by studying rare gain-of-function (gf) mutations of tra-1 that direct female somatic development irrespective of the upstream sex-determining signal. These mutations appear to abolish negative regulation of tra-1 in male tissues. We identify the lesions associated with 29 of these mutations and find that all affect a short stretch of amino acid residues present in both protein products of the tra-1 gene. Twenty-six alleles are associated with single nonconservative amino acid substitutions. Two alleles affect tra-1 RNA splicing and generate messages that omit part or all of the exon encoding this short stretch. These results suggest that sexual regulation of tra-1 is achieved post-translationally, by an inhibitory protein-protein interaction. The amino acid stretch altered by the tra-1(gf) mutations may define a site of interaction for negative regulators of tra-1. The stretch includes a potential phosphorylation site for glycogen synthase kinase 3 and may be conserved in the human gene GLI3, a homolog of tra-1 identified previously.}, author = {de Bono, Mario and Zarkower, D. and Hodgkin, J.}, issn = {08909369}, journal = {Genes and Development}, number = {2}, pages = {155--167}, publisher = {CSH Press}, title = {{Dominant feminizing mutations implicate protein-protein interactions as the main mode of regulation of the nematode sex-determining gene tra-1}}, doi = {10.1101/gad.9.2.155}, volume = {9}, year = {1995}, } @inbook{3454, abstract = {The study of gene expression and regulation in the central nervous system (CNS) is a daunting task because of the diversity of neuronal phenotypes and the complexity of many protein classes. Molecular cloning revealed the presence of a large number of different protein families in the CNS, each comprising several members. Ligand-gated ion channels may serve as an example to illustrate this point (for review, see Unwin, 1993). Heterologous expression combined with electrophysiological analysis suggests that ligand-gated channels are multimeric proteins with functional properties depending on the subunit composition. Very little is known, however, about how the functional properties of the recombinant and native receptors relate to each other. Thus, it is of eminent importance to elucidate the subunit expression profile in different types of neurons in the CNS and to correlate this with the functional properties of the native receptors.}, author = {Monyer, Hannah and Jonas, Peter M}, booktitle = {Single-channel recording}, editor = {Sakmann, Bert and Neher, Erwin}, isbn = {978-0-306-44870-6}, pages = {357 -- 373}, publisher = {Plenum}, title = {{Polymerase chain reaction analysis of ion channel expression in single neurons of brain slices}}, doi = {10.1007/978-1-4419-1229-9_16}, year = {1995}, } @inbook{3455, abstract = {At a synapse, the transmitter is stored in synaptic vesicles and is released into the synaptic cleft almost instantaneously upon fusion of these vesicles with the presynaptic membrane. Subsequently, the transmitter diffuses to ligand-gated ion channels in the postsynaptic density, binds to them, and thereby causes channel activation. Unfortunately, we have estimates neither of the exact amount of transmitter in the synaptic vesicle nor of the concentration in the synaptic cleft reaching the postsynaptic receptors, and in some cases even the identity of the transmitter is unknown. These questions may be addressed by modeling of release and diffusion. Such a theoretical approach, however, is based on several assumptions, some of which lack experimental evidence.}, author = {Jonas, Peter M}, booktitle = {Single-channel recording}, editor = {Sakmann, Bert and Neher, Erwin}, isbn = {978-0-306-44870-6}, pages = {231 -- 243}, publisher = {Plenum}, title = {{Fast application of agonists to isolated membrane patches}}, doi = {10.1007/978-1-4419-1229-9_10}, year = {1995}, } @article{3461, author = {Jonas, Peter M and Burnashev, Nail}, issn = {0896-6273}, journal = {Neuron}, number = {5}, pages = {987 -- 990}, publisher = {Elsevier}, title = {{Molecular mechanisms controlling calcium entry through AMPA-type glutamate receptor channels}}, doi = {10.1016/0896-6273(95)90087-X}, volume = {15}, year = {1995}, } @article{3478, abstract = {1. Properties of dendritic glutamate receptor (GluR) channels were investigated using fast application of glutamate to outside-out membrane patches isolated from the apical dendrites of CA3 and CA1 pyramidal neurons in rat hippocampal slices. CA3 patches were formed (15-76 μm from the soma) in the region of messy fibre (MF) synapses, and CA1 patches (25-174 μm from the soma) in the region of Schaffer collateral (SC) innervation. 2. Dual-component responses consisting of a rapidly rising and decaying component followed by a second, substantially slower, component were elicited by 1 ms pulses of 1 mM glutamate in the presence of 10 μM glycine and absence of external Mg2+. The fast component was selectively blocked by 2-5 μM 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) and the slow component by 30 μM D-2-amino-5-phosphonopentanoic acid (D-AP5), suggesting that the fast and slow components were mediated by the GluR channels of the L-α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) and NMDA type, respectively. The peak amplitude ratio of the NMDA to AMPA receptor-mediated components varied between 0.03 and 0.62 in patches from both CA3 and CA1 dendrites. Patches lacking either component were rarely observed. 3. The peak current-voltage (I-V) relationship of the fast component was almost linear, whereas the I-V relationship of the slow component showed a region of negative slope in the presence of 1 mM external Mg2+. The reversal potential for both components was close to 0 mV. 4. Kainate-preferring GluR channels did not contribute appreciably to the response to glutamate. The responses to 100 ms pulses of 1 mM glutamate were mimicked by application of 1 mM AMPA, whereas 1 mM kainate produced much smaller, weakly desensitizing currents. This suggests that the fast component is primarily mediated by the action of glutamate on AMPA-preferring receptors. 5. The mean elementary conductance of AMPA receptor channels was about 10 pS, as estimated by non-stationary fluctuation analysis. The permeability of these channels to Ca2+ was low (~5% of the permeability to Cs+). 6. The elementary conductance of NMDA receptor channels was larger, with a main conductance state of about 45 pS. These channels were 3.6 times more permeable to Ca2+ than to Cs+. 7. AMPA receptor-mediated currents activated rapidly in response to 1 ms pulses of 1 mM glutamate and deactivated with a predominant, fast time constant and a smaller, slower component (τ1≃2 ms, τ2≃8 ms, contributing ~80 and ~20% to the total decay amplitude, respectively). Desensitization of the current during a 100 ms pulse was best fitted by two time constants (τ1≃10 ms, ~60%; τ2≃34 ms, ~40%). 8. NMDA receptor-mediated currents in response to 1 ms pulses of 1 mM glutamate activated and deactivated much more slowly than AMPA receptor-mediated currents. The time course could be described by a single exponential rising phase (τ≃7 ms) followed by a double exponential decay (τ1≃200 ms, ~80%; τ2≃1-3 s, ~20%). 9. Mg2+ blocked the NMDA component in a voltage-dependent manner, with a half-maximal inhibitory concentration (IC50) of 21 μM at -80 mV. At physiological Mg2+ concentrations, block of the NMDA component could be rapidly relieved with voltage jumps from negative to positive potentials. Block of the current upon return to negative potentials occurred almost instantaneously. 10. Zn2+ also selectively-blocked the NMDA receptor-mediated current with an IC50 of 22 μM, but this block differed from that of Mg2+ in that it showed little voltage dependence. Rapid application of Zn2+ together with glutamate produced partial block of the current. More block was observed if Zn2+ and glutamate were co-applied when NMDA receptor channels were already open. 11. The functional properties of dendritic GluRs were similar to those found at the soma. Knowledge of these properties facilitated simulations investigating the contribution of coactivated AMPA and NMDA receptors to synaptic depolarization and Ca2+ entry into dendritic spines. Because of its slow deactivation, the NMDA receptor-mediated current contributes substantially to depolarization and Ca2+ entry and is susceptible to modulation over a period of seconds, either by backpropagating action potentials or by the release of Zn2+ from presynaptic boutons.}, author = {Spruston, Nelson and Jonas, Peter M and Sakmann, Bert}, issn = {0022-3751}, journal = {Journal of Physiology}, number = {Pt 2}, pages = {325 -- 352}, publisher = {Wiley-Blackwell}, title = {{Dendritic glutamate receptor channels in rat hippocampal CA3 and CA1 pyramidal neurons}}, doi = {10.1113/jphysiol.1995.sp020521}, volume = {482}, year = {1995}, } @article{3479, abstract = {1. Glutamate receptor (GluR) channels were studied in basket cells in the dentate gyrus of rat hippocampal slices. Basket cells were identified by their location, dendritic morphology and high frequency of action potentials generated during sustained current injection. 2. Dual-component currents were activated by fast application of glutamate to outside-out membrane patches isolated from basket cell somata (10 μM glycine, no external Mg2+). The fast component was selectively blocked by 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX), the slow component by D-2-amino-5-phosphonopentanoic acid (D-AP5). This suggests that the two components were mediated by α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptor (AMPAR)/kainate receptor and N-methyl-D-aspartate receptor (NMDAR) channels, respectively. The mean ratio of the peak current of the NMDAR component to that of the AMPAR/kainate receptor component was 0.22 (1 ms pulses of 10 mM glutamate). 3. The AMPAR/kainate receptor component, which was studied in isolation in the presence of D-AP5, was identified as AMPAR mediated on the basis of the preferential activation by AMPA as compared with kainate, the weak desensitization of kainate-activated currents, the cross-desensitization between AMPA and kainate, and the reduction of desensitization by cyclothiazide. 4. Deactivation of basket cell AMPARs following 1 ms pulses of glutamate occurred with a time constant (τ) of 1.2 ± 0.1 ms (mean ± S.E.M.). During 100 ms glutamate pulses, AMPARs desensitized with a τ of 3.7 ± 0.2 ms. 5. The peak current-voltage (I-V) relation of AMPAR-mediated currents in Na+-rich extracellular solution showed a reversal potential of -4.0 ± 2.6 mV and was characterized by a doubly rectifying shape. The conductance of single AMPAR channels was estimated as 22.6 ± 1.6 pS using non-stationary fluctuation analysis. AMPARs expressed in hippocampal basket cells mere highly Ca2+ permeable (P(Ca)/P(K) = 1.79). 6. NMDARs in hippocampal basket cells were studied in isolation in the presence of CNQX. Deactivation of NMDARs activated by glutamate pulses occurred bi-exponentially with mean τ values of 266 ± 23 ms (76%) and 2620 ± 383 ms (24%). 7. The peak I-V relation of the NMDAR-mediated component in Na+-rich extracellular solution showed a reversal potential of 1.5 ± 0.6 mV and a region of negative slope at negative membrane potentials in the presence of external Mg2+, due to voltage-dependent block by these ions. The conductance of single NMDAR channels in the main open state was 50.2 ± 1.8 pS. NMDARs in hippocampal basket cells were highly permeable to Ca2+ (P(Ca)/P(K) = 6.68). 8. AMPARs in hippocampal basket cells are characterized by about threefold faster kinetics and twentyfold higher Ca2+ permeability than AMPARs in hippocampal granule or pyramidal cells. Simulations show that the Ca2+ influx through basket cell AMPARs is comparable to that through NMDARs at negative membrane potentials with physiological concentrations of Ca2+ and Mg2+. This suggests a dual pathway of synaptically mediated Ca2+ entry into interneurones.}, author = {Koh, Duk and Geiger, Jörg and Jonas, Peter M and Sakmann, Bert}, issn = {0022-3751}, journal = {Journal of Physiology}, number = {Pt 2}, pages = {383 -- 402}, publisher = {Wiley-Blackwell}, title = {{Ca(2+)-permeable AMPA and NMDA receptor channels in basket cells of rat hippocampal dentate gyrus}}, doi = {10.1113/jphysiol.1995.sp020737}, volume = {485}, year = {1995}, } @article{3480, abstract = {Recording of glutamate-activated currents in membrane patches was combine with RT-PCR-mediated AMPA receptor (AMPAR) subunit mRNA analysis in single identified cells of rat brain slices. Analysis of AMPARs in principal neurons end interneurons of hippocampus and neocortex and in auditory relay neurons and Bergmann glial cells indicates that the GluR-B subunit in its flip version determines formation of receptors with relatively slow gating, whereas the GluR-D subunit promotes assembly of more rapidly gated receptors. The relation between Ca 2+ permeability of AMPAR channels and the relative GluR-B mRNA abundance is consistent with the dominance of this subunit in determining the Ca 2+ permeability of native receptors. The results suggest that differential expression of GluR-B and GluR-D subunit genes, as well as splicing end editing of their mRNAs, account for the differences in gating and Ca 2+ permeability of native AMPAR channels.}, author = {Geiger, Jörg and Melcher, Thorsten and Koh, Duk and Sakmann, Bert and Seeburg, Peter and Jonas, Peter M and Monyer, Hannah}, issn = {0896-6273}, journal = {Neuron}, number = {1}, pages = {193 -- 204}, publisher = {Elsevier}, title = {{Relative abundance of subunit mRNAs determines gating and Ca(2+) permeability of AMPA receptors in principal neurons and interneurons in rat CNS}}, doi = {10.1016/0896-6273(95)90076-4}, volume = {15}, year = {1995}, } @article{3481, abstract = {1. The influence of intracellular factors on current rectification of different subtypes of native α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptors (AMPARs) was studied in rat brain slices by combining fast application of glutamate with patch pipette perfusion. 2. The peak current-voltage (I-V) relation of the AMPARs expressed in Bergmann glial cells of cerebellum and dentate gyrus (DG) basket cells of hippocampus was weakly rectifying in outside-out patches and nystatin-perforated vesicles, but showed a doubly rectifying shape with a region of reduced slope between 0 and +40 mV in nucleated patches. The I-V relation of AMPARs expressed in hippocampal CA3 pyramidal neurones was linear in all recording configurations. 3. Intracellular application of 2.5 μM spermine, a naturally occurring polyamine, blocked outward currents in outside-oat patches from Bergmann glial cells and DG basket cells in a voltage-dependent manner, generating I-V relations with a doubly rectifying shape which were similar to those recorded in nucleated patches. AMPARs in CA3 pyramidal cell patches were unaffected by 25 μM spermine. 4. The half-maximal blocking concentration of spermine at +40 mV was 0.3 μM in Bergmann glial cell patches and 1.5 μM in DG basket cell patches, whereas it was much higher (≥ 100 μM) for CA3 pyramidal. cell patches. Spermidine also affected current rectification, but with lower affinity. The block of outward current by polyamines following voltage jumps developed within < 0.5 ms. 5. We conclude that current rectification, rather than being an intrinsic property of the Ca2+ permeable AMPAR channel, is generated by polyamine block.}, author = {Koh, Duk and Burnashev, Nail and Jonas, Peter M}, issn = {0022-3751}, journal = {Journal of Physiology}, number = {Pt 2}, pages = {305 -- 312}, publisher = {Wiley-Blackwell}, title = {{Block of native Ca(2+)-permeable AMPA receptors in rat brain by intracellular polyamines generates double rectification}}, doi = {10.1113/jphysiol.1995.sp020813}, volume = {486}, year = {1995}, } @inproceedings{3551, abstract = {Common geometric models for proteins and other molecules are the space filling diagram, the solvent accessible surface, and the molecular surface. We describe software that computes metric properties of these models, including volume and surface area. It also measures voids or empty space enclosed by the protein, and it keeps track of surface area contributions of individual atoms. The software is based on 3-dimensional alpha complexes and on inclusion-exclusion formulas with terms derived from the simplices in this complex.}, author = {Edelsbrunner, Herbert and Facello, Michael and Fu, Ping and Liang, Jie}, booktitle = {Proceedings of the 28th Annual Hawaii International Conference on System Sciences}, isbn = {0-8186-6930-6}, location = {Wailea, HI, United States of America}, pages = {256 -- 264}, publisher = {IEEE}, title = {{Measuring proteins and voids in proteins}}, doi = {10.1109/HICSS.1995.375331}, year = {1995}, } @inproceedings{3552, abstract = {The concept of an α-shape of a finite set of points in R^d, with weights, is defined and illustrated. An α-shape is a polytope which is not necessarily convex nor connected and can be derived from the (weighted) Delaunay triangulation of the point set, with a parameter controlling the desired level of detail. The set of all α values leads to a descrete family of shapes capturing the intuitive notion of ``crude'' versus ``fine'' shapes of a point set. Software that computes such shapes in R^2 and R^3 is available via anonymous ftp from: ftp://ftp.ncsa.uiuc.edu/Visualization/Alpha-shape/ }, author = {Akkiraju, Nataraj and Edelsbrunner, Herbert and Facello, Michael and Fu, Ping and Mücke, Ernst and Varela, Carlos}, pages = {63 -- 66}, publisher = {Elsevier}, title = {{Alpha shapes: definition and software}}, year = {1995}, } @misc{3597, author = {Kirkpatrick, Mark and Barton, Nicholas H}, booktitle = {Nature}, issn = {0028-0836}, pages = {388 -- 389}, publisher = {Nature Publishing Group}, title = {{Déjà vu all over again}}, doi = {10.1038/377388a0}, volume = {377}, year = {1995}, } @article{3636, abstract = {Observations on the means, variances, and covariances of quantitative traits across hybrid zones can give information similar to that from Mendelian markers. In addition, they can identify particular traits through which the cline is maintained. We describe a survey of six traits across the hybrid zone between Bombina bombina and Bombina variegata (Amphibia: Discoglossidae) near Pescenica in Croatia. We obtained laboratory measuments of the belly pattern, skin thickness, mating call, skeletal form, egg size, and the developmental time of tadpoles. Although offspring from hybrid populations showed no evidence of reduced viability, a third of the F1 families failed completely, irrespective of the direction of the cross. All traits differed significantly between the taxa. Clines in belly pattern, skin thickness, mating call, and skeletal form were closely concordant with clines in four diagnostic enzyme loci. However, the cline in developmental time was displaced towards bombina, and the cline in egg size was displaced towards variegata. This discordance could be because the traits are not inherited additively or because they are subject to different selection pressures. We favor the latter explanation in the case of developmental time. We show that moderate selection acting directly on a trait suffices to shift its position; rather stronger selection is needed to change its width appreciably. Within hybrid populations, there are significant associations among quantitative traits, and between traits and enzymes. Phenotypic variances also increase in hybrid populations. These observations can be explained by linkage disequilibria among the underlying loci. However, the average magnitude of the covariance between traits is about half that expected from the linkage disequilibria between enzyme loci. The discrepancy is not readily explained by nonadditive gene action. This puzzle is now unresolved and calls for further investigation.}, author = {Nürnberger, Beate and Barton, Nicholas H and Maccallum, Catriona and Gilchrist, Jason and Appleby, Michael}, issn = {0014-3820}, journal = {Evolution}, number = {6}, pages = {1224 -- 1238}, publisher = {Wiley-Blackwell}, title = {{Natural selection on quantitative traits in the Bombina hybrid zone}}, doi = {10.1111/j.1558-5646.1995.tb04449.x}, volume = {49}, year = {1995}, }