@article{855,
abstract = {Motivation: The context of the start codon (typically, AUG) and the features of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream AUGs) might effect the initiation rate and, in the context of gene prediction, could reduce the accuracy of the identification of the authentic start. To reveal potential connections between the presence of upstream AUGs and other features of 5′ UTRs, such as their length and the start codon context, we undertook a systematic analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on the organism, contain upstream ATGs. A negative correlation was observed between the information content of the translation start signal and the length of the 5′ UTR. Similarly, a negative correlation exists between the 'strength' of the start context and the number of upstream ATGs. Typically, cDNAs containing long 5′ UTRs with multiple upstream ATGs have a 'weak' start context, and in contrast, cDNAs containing short 5′ UTRs without ATGs have 'strong' starts. These counter-intuitive results may be interpreted in terms of upstream AUGs having an important role in the regulation of translation efficiency by ensuring low basal translation level via double negative control and creating the potential for additional regulatory mechanisms. One of such mechanisms, supported by experimental studies of some mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative splicing.},
author = {Rogozin, Igor B and Kochetov, Alex V and Fyodor Kondrashov and Koonin, Eugene V and Milanesi, Luciano},
journal = {Bioinformatics},
number = {10},
pages = {890 -- 900},
publisher = {Oxford University Press},
title = {{Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a 'weak'context of the start codon}},
doi = {10.1093/bioinformatics/17.10.890},
volume = {17},
year = {2001},
}
@article{867,
abstract = {Genes with new functions often evolve by gene duplication. Alternative splicing is another means of evolutionary innovation in eukaryotes, which allows a single gene to encode functionally diverse proteins. We investigate a connection between these two evolutionary phenomena. For ∼10% of the described cases of substitution alternative splicing, such that either one or another amino acid sequence is included into the protein, evidence of origin by tandem exon duplication was found. This is a conservative estimate because alternative exons are typically short and, on many occasions, duplicates may have diverged beyond recognition. Dating exon duplications through a combination of the available experimental data on alternative splicing in orthologous genes from different species and computational analysis indicates that most of the duplications antedate at least the radiation of mammalian orders or even the radiation of vertebrate classes. At present, tandem exon duplication is the only mechanism of evolution of substitution alternative splicing that can be specifically demonstrated. Along with gene duplication, this could be a major route for generating functional diversity during evolution of multicellular eukaryotes.},
author = {Fyodor Kondrashov and Koonin, Eugene V},
journal = {Human Molecular Genetics},
number = {23},
pages = {2661 -- 2669},
publisher = {Oxford University Press},
title = {{Origin of alternative splicing by tandem exon duplication}},
doi = {10.1093/hmg/10.23.2661},
volume = {10},
year = {2001},
}
@article{874,
abstract = {Sex is thought to facilitate accumulation of initially rare beneficial mutations by allowing simultaneous allele replacements at many loci. However, this advantage of sex depends on a restrictive assumption that the fitness of a genotype is determined by fitness potential, a single intermediate variable to which all loci contribute additively, so that new alleles can accumulate in any order. Individual-based simulations of sexual and asexual populations reveal that under generic selection, sex often retards adaptive evolution. When new alleles are beneficial only if they accumulate in a prescribed order, a sexual population may evolve two or more times slower than an asexual population because only asexual reproduction allows some overlap of successive allele replacements. Many other fitness surfaces lead to an even greater disadvantage of sex. Thus, either sex exists in spite of its impact on the rate of adaptive allele replacements, or natural fitness surfaces have rather specific properties, at least at the scale of intrapopulation genetic variability.},
author = {Fyodor Kondrashov and Kondrashov, Alexey S},
journal = {PNAS},
number = {21},
pages = {12089 -- 12092},
publisher = {National Academy of Sciences},
title = {{Multidimensional epistasis and the disadvantage of sex}},
doi = {10.1073/pnas.211214298},
volume = {98},
year = {2001},
}
@inproceedings{4600,
abstract = {Model checking is a practical tool for automated debugging of embedded software. In model checking, a high-level description of a system is compared against a logical correctness requirement to discover inconsistencies. Since model checking is based on exhaustive state-space exploration and the size of the state space of a design grows exponentially with the size of the description, scalability remains a challenge. We have thus developed techniques for exploiting modular design structure during model checking, and the model checker jMocha (Java MOdel-CHecking Algorithm) is based on this theme. Instead of manipulating unstructured state-transition graphs, it supports the hierarchical modeling framework of reactive modules. jMocha is a growing interactive software environment for specification, simulation and verification, and is intended as a vehicle for the development of new verification algorithms and approaches. It is written in Java and uses native C-code BDD libraries from VIS. jMocha offers: (1) a GUI that looks familiar to Windows/Java users; (2) a simulator that displays traces in a message sequence chart fashion; (3) requirements verification both by symbolic and enumerative model checking; (4) implementation verification by checking trace containment; (5) a proof manager that aids compositional and assume-guarantee reasoning; and (6) SLANG (Scripting LANGuage) for the rapid and structured development of new verification algorithms. jMocha is available publicly at ; it is a successor and extension of the original Mocha tool that was entirely written in C.},
author = {Alur, Rajeev and de Alfaro, Luca and Grosu, Radu and Thomas Henzinger and Kang, Myong H and Kirsch, Christoph M and Majumdar, Ritankar S and Mang, Freddy Y and Wang, Bow Y},
pages = {835 -- 836},
publisher = {IEEE},
title = {{jMocha: A model-checking tool that exploits design structure}},
doi = {10.1109/ICSE.2001.919196},
year = {2001},
}
@inproceedings{4622,
abstract = {Conventional type systems specify interfaces in terms of values and domains. We present a light-weight formalism that captures the temporal aspects of software component interfaces. Specifically, we use an automata-based language to capture both input assumptions about the order in which the methods of a component are called, and output guarantees about the order in which the component calls external methods. The formalism supports automatic compatability checks between interface models, and thus constitutes a type system for component interaction. Unlike traditional uses of automata, our formalism is based on an optimistic approach to composition, and on an alternating approach to design refinement. According to the optimistic approach, two components are compatible if there is some environment that can make them work together. According to the alternating approach, one interface refines another if it has weaker input assumptions, and stronger output guarantees. We show that these notions have game-theoretic foundations that lead to efficient algorithms for checking compatibility and refinement.},
author = {de Alfaro, Luca and Thomas Henzinger},
pages = {109 -- 120},
publisher = {ACM},
title = {{Interface automata}},
doi = {10.1145/503209.503226},
year = {2001},
}
@inproceedings{4623,
abstract = {We classify component-based models of computation into component models and interface models. A component model specifies for each component howthe component behaves in an arbitrary environment; an interface model specifies for each component what the component expects from the environment. Component models support compositional abstraction, and therefore component-based verification. Interface models support compositional refinement, and therefore componentbased design. Many aspects of interface models, such as compatibility and refinement checking between interfaces, are properly viewed in a gametheoretic setting, where the input and output values of an interface are chosen by different players.},
author = {de Alfaro, Luca and Thomas Henzinger},
pages = {148 -- 165},
publisher = {ACM},
title = {{Interface theories for component-based design}},
doi = {10.1007/3-540-45449-7_11},
volume = {2211},
year = {2001},
}
@inproceedings{4632,
abstract = {We present a compositional trace-based model for probabilistic systems. The behavior of a system with probabilistic choice is a stochastic process, namely, a probability distribution on traces, or “bundle.” Consequently, the semantics of a system with both nondeterministic and probabilistic choice is a set of bundles. The bundles of a composite system can be obtained by combining the bundles of the components in a simple mathematical way. Refinement between systems is bundle containment. We achieve assume-guarantee compositionality for bundle semantics by introducing two scoping mechanisms. The first mechanism, which is standard in compositional modeling, distinguishes inputs from outputs and hidden state. The second mechanism, which arises in probabilistic systems, partitions the state into probabilistically independent regions.},
author = {de Alfaro, Luca and Thomas Henzinger and Jhala, Ranjit},
pages = {351 -- 365},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Compositional methods for probabilistic systems}},
doi = {10.1007/3-540-44685-0_24},
volume = {2154},
year = {2001},
}
@inproceedings{4633,
abstract = {A procedure for the analysis of state spaces is called symbolic if it manipulates not individual states, but sets of states that are represented by constraints. Such a procedure can be used for the analysis of infinite state spaces, provided termination is guaranteed. We present symbolic procedures, and corresponding termination criteria, for the solution of infinite-state games, which occur in the control and modular verification of infinite-state systems. To characterize the termination of symbolic procedures for solving infinite-state games, we classify these game structures into four increasingly restrictive categories:
1 Class 1 consists of infinite-state structures for which all safety and reachability games can be solved.
2 Class 2 consists of infinite-state structures for which all ω-regular games can be solved.
3 Class 3 consists of infinite-state structures for which all nested positive boolean combinations of ω-regular games can be solved.
4 Class 4 consists of infinite-state structures for which all nested boolean combinations of ω-regular games can be solved.
We give a structural characterization for each class, using equivalence relations on the state spaces of games which range from game versions of trace equivalence to a game version of bisimilarity. We provide infinite-state examples for all four classes of games from control problems for hybrid systems. We conclude by presenting symbolic algorithms for the synthesis of winning strategies (“controller synthesis”) for infinitestate games with arbitrary ω-regular objectives, and prove termination over all class-2 structures. This settles, in particular, the symbolic controller synthesis problem for rectangular hybrid systems.},
author = {de Alfaro, Luca and Thomas Henzinger and Majumdar, Ritankar S},
pages = {536 -- 550},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Symbolic algorithms for infinite-state games}},
doi = {10.1007/3-540-44685-0_36},
volume = {2154},
year = {2001},
}
@inproceedings{4634,
abstract = {A controller is an environment for a system that achieves a particular control objective by providing inputs to the system without constraining the choices of the system. For synchronous systems, where system and controller make simultaneous and interdependent choices, the notion that a controller must not constrain the choices of the system can be formalized by type systems for composability. In a previous paper, we solved the control problem for static and dynamic types: a static type is a dependency relation between inputs and outputs, and composition is well-typed if it does not introduce cyclic dependencies; a dynamic type is a set of static types, one for each state. Static and dynamic types, however, cannot capture many important digital circuits, such as gated clocks, bidirectional buses, and random-access memory. We therefore introduce more general type systems, so-called dependent and bidirectional types, for modeling these situations, and we solve the corresponding control problems.
In a system with a dependent type, the dependencies between inputs and outputs are determined gradually through a game of the system against the controller. In a system with a bidirectional type, also the distinction between inputs and outputs is resolved dynamically by such a game. The game proceeds in several rounds. In each round the system and the controller choose to update some variables dependent on variables that have already been updated. The solution of the control problem for dependent and bidirectional types is based on algorithms for solving these games.},
author = {de Alfaro, Luca and Thomas Henzinger and Mang, Freddy Y},
pages = {566 -- 581},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The control of synchronous systems, Part II}},
doi = {10.1007/3-540-44685-0_38},
volume = {2154},
year = {2001},
}
@inproceedings{4635,
abstract = {We show how model checking techniques can be applied to the analysis of connectivity and cost-of-traversal properties of Web sites.},
author = {de Alfaro, Luca and Thomas Henzinger and Mang, Freddy Y},
pages = {86 -- 87},
publisher = {ACM},
title = {{MCWEB: A model-checking tool for web-site debugging}},
year = {2001},
}
@inproceedings{4636,
abstract = {Abstract. Dynamic programs, or fixpoint iteration schemes, are useful for solving many problems on state spaces, including model checking on Kripke structures (“verification”), computing shortest paths on weighted graphs (“optimization”), computing the value of games played on game graphs (“control”). For Kripke structures, a rich fixpoint theory is available in the form of the µ-calculus. Yet few connections have been made between different interpretations of fixpoint algorithms. We study the question of when a particular fixpoint iteration scheme ϕ for verifying an ω-regular property Ψ on a Kripke structure can be used also for solving a two-player game on a game graph with winning objective Ψ. We provide a sufficient and necessary criterion for the answer to be affirmative in the form of an extremal-model theorem for games: under a game interpretation, the dynamic program ϕ solves the game with objective Ψ if and only if both (1) under an existential interpretation on Kripke structures, ϕ is equivalent to ∃Ψ, and (2) under a universal interpretation on Kripke structures, ϕ is equivalent to ∀Ψ. In other words, ϕ is correct on all two-player game graphs iff it is correct on all extremal game graphs, where one or the other player has no choice of moves. The theorem generalizes to quantitative interpretations, where it connects two-player games with costs to weighted graphs. While the standard translations from ω-regular properties to the µ-calculus violate (1) or (2), we give a translation that satisfies both conditions. Our construction, therefore, yields fixpoint iteration schemes that can be uniformly applied on Kripke structures, weighted graphs, game graphs, and game graphs with costs, in order to meet or optimize a given ω-regular objective.},
author = {de Alfaro, Luca and Thomas Henzinger and Majumdar, Ritankar S},
pages = {279 -- 290},
publisher = {IEEE},
title = {{From verification to control: dynamic programs for omega-regular objectives}},
doi = {10.1109/LICS.2001.932504},
year = {2001},
}
@article{1452,
abstract = {In this Note we present pairs of hyperkähler orbifolds which satisfy two different versions of mirror symmetry. On the one hand, we show that their Hodge numbers (or more precisely, stringy E-polynomials) are equal. On the other hand, we show that they satisfy the prescription of Strominger, Yau, and Zaslow (which in the present case goes back to Bershadsky, Johansen, Sadov and Vafa): that a Calabi-Yau and its mirror should fiber over the same real manifold, with special Lagrangian fibers which are tori dual to each other. Our examples arise as moduli spaces of local systems on a curve with structure group SL(n); the mirror is the corresponding space with structure group PGL(n). The special Lagrangian tori come from an algebraically completely integrable Hamiltonian system: the Hitchin system.},
author = {Tamas Hausel and Thaddeus, Michael},
journal = {Comptes Rendus de l'Academie des Sciences - Series I: Mathematics},
number = {4},
pages = {313 -- 318},
publisher = {Elsevier},
title = {{Examples of mirror partners arising from integrable systems}},
doi = {10.1016/S0764-4442(01)02057-2},
volume = {333},
year = {2001},
}
@article{1453,
abstract = {In this Letter we exhibit a one-parameter family of new Taub-NUT instantons parameterized by a half-line. The endpoint of the half-line will be the reducible Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form, while at an inner point we recover the Pope-Yuille instanton constructed as a projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra. Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT space with a point singularity, rescale the metric and project the obtained Levi-Civitá connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess the full U(2) symmetry, and thus provide more solutions to the recently proposed U(2) symmetric ansatz of Kim and Yoon.},
author = {Etesi, Gábor and Tamas Hausel},
journal = {Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics},
number = {1-2},
pages = {189 -- 199},
publisher = {Elsevier},
title = {{Geometric construction of new Yang-Mills instantons over Taub-NUT space}},
doi = {10.1016/S0370-2693(01)00821-8},
volume = {514},
year = {2001},
}
@article{1454,
abstract = {We address the problem of finding Abelian instantons of finite energy on the Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic 2-forms on the space. Gibbons found a non-topological L2 harmonic form in the Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate his construction in the case of the Euclidean Schwarzschild manifold and find a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number 2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold.},
author = {Etesi, Gábor and Tamas Hausel},
journal = {Journal of Geometry and Physics},
number = {1-2},
pages = {126 -- 136},
publisher = {Elsevier},
title = {{Geometric interpretation of Schwarzschild instantons}},
doi = {10.1016/S0393-0440(00)00040-1},
volume = {37},
year = {2001},
}
@article{888,
abstract = {BACKGROUND: Detection of changes in a protein's evolutionary rate may reveal cases of change in that protein's function. We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae), complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this rate constancy are probably due to changes in selective constraints associated with diversification between orthologs. Functional diversification between orthologs is thought to be a relatively rare event. However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins.},
author = {Jordan, Ingo K and Fyodor Kondrashov and Rogozin, Igor B and Tatusov, Roman L and Wolf, Yuri I and Koonin, Eugene V},
journal = {Genome Biology},
number = {12},
publisher = {BioMed Central},
title = {{Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins }},
doi = {10.1186/gb-2001-2-12-research0053},
volume = {2},
year = {2001},
}
@article{3927,
abstract = {TNF-alpha has been clearly identified as central mediator of T cell activation-induced acute hepatic injury in mice, e.g., Con A hepatitis. In this model, liver injury depends on both TNFRs, i.e., the 55-kDa TNFR1 as well as the 75-kDa TNFR2. We show in this report that the hepatic TNFRs are not transcriptionally regulated, but are regulated by receptor shedding. TNF directly mediates hepatocellular death by activation of TNFR1 but also induces the expression of inflammatory proteins, such as cytokines and adhesion molecules. Here we provide evidence that resistance of TNFR1(-/-) and TNFR2(-/-) mice against Con A hepatitis is not due to an impaired production of the central mediators TNF and IFN-gamma. Con A injection results in a massive induction of ICAM-1, VCAM-1, and E-selectin in the liver. Lack of either one of both TNFRs did not change adhesion molecule expression in the livers of Con A-treated mice, presumably reflecting the fact that other endothelial cell-activating cytokines up-regulated adhesion molecule expression. However, treatment of TNFR1(-/-) and TNFR2(-/-) mice with murine rTNF revealed a predominant role for TNFR1 for the induction of hepatic adhesion molecule expression. Pretreatment with blocking Abs against E- and P-selectin or of ICAM(-/-) mice with anti-VCAM-1 Abs failed to prevent Con A hepatitis, although accumulation of the critical cell population, i.e., CD4(+) T cells was significantly inhibited. Hence, up-regulation of adhesion molecules during acute hepatitis unlikely contributes to organ injury but rather represents a defense mechanism.},
author = {Wolf, Dominik and Hallmann, Rupert and Sass, Gabriele and Michael Sixt and Küsters, Sabine and Fregien, Bastian and Trautwein, Christian and Tiegs, Gisa},
journal = {Journal of Immunology},
number = {2},
pages = {1300 -- 1307},
publisher = {American Association of Immunologists},
title = {{TNF-α-induced expression of adhesion molecules in the liver is under the control of TNFR1--relevance for concanavalin A-induced hepatitis}},
volume = {166},
year = {2001},
}
@article{3928,
abstract = {Regulated adhesion of leukocytes to the extracellular matrix is essential for transmigration of blood vessels and subsequent migration into the stroma of inflamed tissues. Although beta(2)-integrins play an indisputable role in adhesion of polymorphonuclear granulocytes (PMN) to endothelium, we show here that beta(1)- and beta(3)-integrins but not beta(2)-integrin are essential for the adhesion to and migration on extracellular matrix molecules of the endothelial cell basement membrane and subjacent interstitial matrix. Mouse wild type and beta(2)-integrin null PMN and the progranulocytic cell line 32DC13 were employed in in vitro adhesion and migration assays using extracellular matrix molecules expressed at sites of extravasation in vivo, in particular the endothelial cell laminins 8 and 10. Wild type and beta(2)-integrin null PMN showed the same pattern of ECM binding, indicating that beta(2)-integrins do not mediate specific adhesion of PMN to the extracellular matrix molecules tested; binding was observed to the interstitial matrix molecules, fibronectin and vitronectin, via integrins alpha(5)beta(1) and alpha(v)beta(3), respectively; to laminin 10 via alpha(6)beta(1); but not to laminins 1, 2, and 8, collagen type I and IV, perlecan, or tenascin-C. PMN binding to laminins 1, 2, and 8 could not be induced despite surface expression of functionally active integrin alpha(6)beta(1), a major laminin receptor, demonstrating that expression of alpha(6)beta(1) alone is insufficient for ligand binding and suggesting the involvement of accessory factors. Nevertheless, laminins 1, 8, and 10 supported PMN migration, indicating that differential cellular signaling via laminins is independent of the extent of adhesion. The data demonstrate that adhesive and nonadhesive interactions with components of the endothelial cell basement membrane and subjacent interstitium play decisive roles in controlling PMN movement into sites of inflammation and illustrate that beta(2)-integrins are not essential for such interactions.},
author = {Michael Sixt and Hallmann, Rupert and Wendler, Olaf and Scharffetter-Kochanek, Karin and Sorokin, Lydia M},
journal = {Journal of Biological Chemistry},
number = {22},
pages = {18878 -- 18887},
publisher = {American Society for Biochemistry and Molecular Biology},
title = {{Cell adhesion and migration properties of β2-integrin negative polymorphonuclear granulocytes on defined extracellular matrix molecules. Relevance for leukocyte extravasation}},
doi = {10.1074/jbc.M010898200},
volume = {276},
year = {2001},
}
@article{3930,
abstract = {An active involvement of blood-brain barrier endothelial cell basement membranes in development of inflammatory lesions in the central nervous system (CNS) has not been considered to date. Here we investigated the molecular composition and possible function of the extracellular matrix encountered by extravasating T lymphocytes during experimental autoimmune encephalomyelitis (EAE). Endothelial basement membranes contained laminin 8 (alpha4beta1gamma1) and/or 10 (alpha5beta1gamma1) and their expression was influenced by proinflammatory cytokines or angiostatic agents. T cells emigrating into the CNS during EAE encountered two biochemically distinct basement membranes, the endothelial (containing laminins 8 and 10) and the parenchymal (containing laminins 1 and 2) basement membranes. However, inflammatory cuffs occurred exclusively around endothelial basement membranes containing laminin 8, whereas in the presence of laminin 10 no infiltration was detectable. In vitro assays using encephalitogenic T cell lines revealed adhesion to laminins 8 and 10, whereas binding to laminins 1 and 2 could not be induced. Downregulation of integrin alpha6 on cerebral endothelium at sites of T cell infiltration, plus a high turnover of laminin 8 at these sites, suggested two possible roles for laminin 8 in the endothelial basement membrane: one at the level of the endothelial cells resulting in reduced adhesion and, thereby, increased penetrability of the monolayer; and secondly at the level of the T cells providing direct signals to the transmigrating cells.},
author = {Michael Sixt and Engelhardt, Britta and Pausch, Friederike and Hallmann, Rupert and Wendler, Olaf and Sorokin, Lydia M},
journal = {Journal of Cell Biology},
number = {5},
pages = {933 -- 946},
publisher = {Rockefeller University Press},
title = {{Endothelial cell laminin isoforms, laminins 8 and 10, play decisive roles in T cell recruitment across the blood-brain barrier in experimental autoimmune encephalomyelitis}},
doi = {10.1083/jcb.153.5.933 },
volume = {153},
year = {2001},
}
@article{4001,
abstract = {The construction of shape spaces is studied from a mathematical and a computational viewpoint. A program is outlined reducing the problem to four tasks: the representation of geometry, the canonical deformation of geometry, the measuring of distance in shape space, and the selection of base shapes. The technical part of this paper focuses on the second task: the specification of a deformation mixing two or more shapes in continuously changing proportions. (C) 2001 Elsevier Science B.V All rights reserved.},
author = {Cheng, Ho-Lun and Herbert Edelsbrunner and Fu, Ping},
journal = {Computational Geometry: Theory and Applications},
number = {2-3},
pages = {191 -- 204},
publisher = {Elsevier},
title = {{Shape space from deformation}},
doi = {10.1016/S0925-7721(01)00021-9},
volume = {19},
year = {2001},
}
@article{4002,
abstract = {Shape deformation refers to the continuous change of one geometric object to another. We develop a software tool for planning, analyzing and visualizing deformations between two shapes in R-2. The deformation is generated automatically without any user intervention or specification of feature correspondences. A unique property of the tool is the explicit availability of a two-dimensional shape space, which can be used for designing the deformation either automatically by following constraints and objectives or manually by drawing deformation paths.},
author = {Cheng, Siu Wing and Herbert Edelsbrunner and Fu, Ping and Lam, Ka Po},
journal = {Computational Geometry: Theory and Applications},
number = {2-3},
pages = {205 -- 218},
publisher = {Elsevier},
title = {{Design and analysis of planar shape deformation}},
doi = {10.1016/S0925-7721(01)00020-7},
volume = {19},
year = {2001},
}