@inproceedings{2340,
abstract = {
Recent experimental breakthroughs in the treatment of dilute Bose gases have renewed interest in their quantum mechanical description, respectively in approximations to it. The ground state properties of dilute Bose gases confined in external potentials and interacting via repulsive short range forces are usually described by means of the Gross-Pitaevskii energy functional. In joint work with Elliott H. Lieb and Jakob Yngvason its status as an approximation for the quantum mechanical many-body ground state problem has recently been rigorously clarified. We present a summary of this work, for both the two-and three-dimensional case.
},
author = {Robert Seiringer},
editor = {Demuth, Michael and Schultze, Bert-Wolfgang},
pages = {307 -- 314},
publisher = {Birkhäuser},
title = {{Bosons in a trap: Asymptotic exactness of the Gross-Pitaevskii ground state energy formula}},
doi = {10.1007/978-3-0348-8231-6},
volume = {126},
year = {2001},
}
@article{2341,
abstract = {We study the ground state properties of an atom with nuclear charge Z and N bosonic "electrons" in the presence of a homogeneous magnetic field B. We investigate the mean field limit N→∞ with N / Z fixed, and identify three different asymptotic regions, according to B≪Z2,B∼Z2,andB≫Z2 . In Region 1 standard Hartree theory is applicable. Region 3 is described by a one-dimensional functional, which is identical to the so-called Hyper-Strong functional introduced by Lieb, Solovej and Yngvason for atoms with fermionic electrons in the region B≫Z3 ; i.e., for very strong magnetic fields the ground state properties of atoms are independent of statistics. For Region 2 we introduce a general magnetic Hartree functional, which is studied in detail. It is shown that in the special case of an atom it can be restricted to the subspace of zero angular momentum parallel to the magnetic field, which simplifies the theory considerably. The functional reproduces the energy and the one-particle reduced density matrix for the full N-particle ground state to leading order in N, and it implies the description of the other regions as limiting cases.},
author = {Baumgartner, Bernhard and Robert Seiringer},
journal = {Annales Henri Poincare},
number = {1},
pages = {41 -- 76},
publisher = {Birkhäuser},
title = {{Atoms with bosonic "electrons" in strong magnetic fields}},
doi = {10.1007/PL00001032},
volume = {2},
year = {2001},
}
@article{2345,
abstract = {We give upper bounds for the number of spin-1/2 particles that can be bound to a nucleus of charge Z in the presence of a magnetic field B, including the spin-field coupling. We use Lieb's strategy, which is known to yield Nc < 2Z + 1 for magnetic fields that go to zero at infinity, ignoring the spin-field interaction. For particles with fermionic statistics in a homogeneous magnetic field our upper bound has an additional term of the order of Z × min {(B/Z3)2/5, 1 + | 1n(B/Z3)|2}.},
author = {Robert Seiringer},
journal = {Journal of Physics A: Mathematical and General},
number = {9},
pages = {1943 -- 1948},
publisher = {IOP Publishing Ltd.},
title = {{On the maximal ionization of atoms in strong magnetic fields}},
doi = {10.1088/0305-4470/34/9/311},
volume = {34},
year = {2001},
}
@article{2346,
abstract = {By means of a generalization of the Fefferman - de la Llave decomposition we derive a general lower bound on the interaction energy of one-dimensional quantum systems. We apply this result to a specific class of lowest Landau band wave functions.},
author = {Hainzl, Christian and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {2},
pages = {133 -- 142},
publisher = {Springer},
title = {{Bounds on one-dimensional exchange energies with application to lowest Landau band quantum mechanics}},
doi = {10.1023/A:1010951905548},
volume = {55},
year = {2001},
}
@article{2347,
abstract = {We consider the ground state properties of an inhomogeneous two-dimensional Bose gas with a repulsive, short range pair interaction and an external confining potential. In the limit when the particle number N is large but ρ̄a2 is small, where ρ̄ is the average particle density and a the scattering length, the ground state energy and density are rigorously shown to be given to leading order by a Gross-Pitaevskii (GP) energy functional with a coupling constant g ∼ 1/| 1n(ρ̄a2)|. In contrast to the 3D case the coupling constant depends on N through the mean density. The GP energy per particle depends only on Ng. In 2D this parameter is typically so large that the gradient term in the GP energy functional is negligible and the simpler description by a Thomas-Fermi type functional is adequate.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {17 -- 31},
publisher = {Springer},
title = {{A rigorous derivation of the Gross-Pitaevskii energy functional for a two-dimensional Bose gas}},
doi = {10.1007/s002200100533},
volume = {224},
year = {2001},
}
@article{2348,
abstract = {This paper concerns the asymptotic ground state properties of heavy atoms in strong, homogeneous magnetic fields. In the limit when the nuclear charge Z tends to ∞ with the magnetic field B satisfying B ≫ Z4/3 all the electrons are confined to the lowest Landau band. We consider here an energy functional, whose variable is a sequence of one-dimensional density matrices corresponding to different angular momentum functions in the lowest Landau band. We study this functional in detail and derive various interesting properties, which are compared with the density matrix (DM) theory introduced by Lieb, Solovej and Yngvason. In contrast to the DM theory the variable perpendicular to the field is replaced by the discrete angular momentum quantum numbers. Hence we call the new functional a discrete density matrix (DDM) functional. We relate this DDM theory to the lowest Landau band quantum mechanics and show that it reproduces correctly the ground state energy apart from errors due to the indirect part of the Coulomb interaction energy.},
author = {Hainzl, Christian and Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {229 -- 248},
publisher = {Springer},
title = {{A discrete density matrix theory for atoms in strong magnetic fields}},
doi = {10.1007/s002200100373},
volume = {217},
year = {2001},
}
@article{2419,
abstract = {For an absolutely continuous probability measure μ. on ℝd and a nonnegative integer k, let S̃k(μ, 0) denote the probability that the convex hull of k + d + 1 random points which are i.i.d. according to μ contains the origin 0. For d and k given, we determine a tight upper bound on S̃k(μ, 0), and we characterize the measures in ℝd which attain this bound. As we will see, this result can be considered a continuous analogue of the Upper Bound Theorem for the maximal number of faces of convex polytopes with a given number of vertices. For our proof we introduce so-called h-functions, continuous counterparts of h-vectors of simplicial convex polytopes.},
author = {Uli Wagner and Welzl, Emo},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {205 -- 219},
publisher = {Springer},
title = {{A continuous analogue of the Upper Bound Theorem}},
doi = {10.1007/s00454-001-0028-9},
volume = {26},
year = {2001},
}
@article{2604,
abstract = {Cutaneous antidromic vasodilatation and plasma extravasation, two phenomena that occur in neurogenic inflammation, are partially blocked by substance P (SP) receptor antagonists and are known to be mediated in part by mast cell-released substances, such as histamine, serotonin, and nitric oxide. In an attempt to provide a morphological substrate for the above phenomena, we applied light and electron microscopic immunocytochemistry to investigate the pattern of SP innervation of blood vessels and its relationship to mast cells in the skin of the rat lower lip. Furthermore, we examined the distribution of SP (neurokinin-1) receptors and their relationship to SP-immunoreactive (IR) fibers. Our results confirmed that SP-IR fibers are found in cutaneous nerves and that terminal branches are observed around blood vessels and penetrating the epidermis. SP-IR fibers also innervated hair follicles and sebaceous glands. At the ultrastructural level, SP-IR varicosities were observed adjacent to arterioles, capillaries, venules, and mast cells. The varicosities possessed both dense core vesicles and agranular synaptic vesicles. We quantified the distance between SP-IR varicosities and blood vessel endothelial cells. SP-IR terminals were located within 0.23-5.99 μm from the endothelial cell layer in 82.7% of arterioles, in 90.2% of capillaries, and in 86.9% of venules. Although there was a trend for SP-IR fibers to be located closer to the endothelium of venules, this difference was not significant. Neurokinin-1 receptor (NK-1r) immunoreactivity was most abundant in the upper dermis and was associated with the wall of blood vessels. NK-1r were located in equal amounts on the walls of arterioles, capillaries, and venules that were innervated by SP-IR fibers. The present results favor the concept of a participation of SP in cutaneous neurogenic vasodilatation and plasma extravasation both by an action on blood vessels after binding to the NK-1r and by causing the release of substances from mast cells after diffusion through the connective tissue.},
author = {Ruocco, Isabella I and Cuello, Augusto C and Ryuichi Shigemoto and Ribeiro-da-Silva, Alfredo},
journal = {Journal of Comparative Neurology},
number = {4},
pages = {466 -- 480},
publisher = {Wiley-Blackwell},
title = {{Light and electron microscopic study of the distribution of substance P-immunoreactive fibers and neurokinin-1 receptors in the skin of the rat lower lip}},
doi = {10.1002/cne.1114},
volume = {432},
year = {2001},
}
@article{2605,
abstract = {The granular layer of the cerebellar cortex consists of densely packed neuronal cells, classified into granule cells and large interneurons. In this study, we provide a comparative survey of large granular layer interneurons in the adult rat cerebellum based on both morphological and neurochemical criteria. To this end, double immunofluorescence histochemistry was performed by combining antibodies against the cytoplasmic antigen Rat-303, calretinin, the metabotropic glutamate receptor mGluR2 and somatostatin. Based on Rat-303/calretinin double immunohistochemistry, three distinct populations of large granular layer interneurons could be discerned: cells immunopositive for Rat-303, calretinin or both. Rat-303 or calretinin single-labeled cells represented Golgi cells and unipolar brush cells, respectively. Rat-303/calretinin double-labeled cells located just underneath the Purkinje cell layer represented Lugaro cells. Morphometrical analysis distinguished two populations of Rat-303-positive Golgi cells according to their location: vermis versus hemisphere. Immunostaining for the metabotropic glutamate receptor mGluR2 combined with Rat-303 or calretinin revealed that the majority of Golgi cells (about 90%) appeared to be mGluR2 positive. Lugaro cells were mGluR2 negative. In addition, a limited population of large polymorphous interneurons in the depth of the granular layer with morphological features resembling Golgi cells also displayed Rat-303/calretinin immunoreactivity and were mGluR2 negative. Double immunohistochemistry for Rat-303 and somatostatin revealed three populations of labeled cells in the depth of the granular layer. Besides double-labeled Golgi cells, Rat-303 or somatostatin single-labeled cells were present. Based on mGluR2/somatostatin and calretinin/somatostatin double immunostainings, Rat-303 single-labeled cells were found to correspond to Rat-303/calretinin-positive, mGluR2-negative Golgi-like cells, while the identity of somatostatin single-labeled cells remained unclear. The data presented in this article elaborate previous reports on the morphological and neurochemical differentiation of large interneurons in the rat cerebellar granular layer. In addition, they indicate that the current classification of these cells into Golgi cells, Lugaro cells and unipolar brush cells does not describe the observed neurochemical heterogeneity.},
author = {Geurts, Frederik J and Timmermans, Jean P and Ryuichi Shigemoto and De Schutter, Erik},
journal = {Neuroscience},
number = {2},
pages = {499 -- 512},
publisher = {Elsevier},
title = {{Morphological and neurochemical differentiation of large granular layer interneurons in the adult rat cerebellum}},
doi = {10.1016/S0306-4522(01)00058-6},
volume = {104},
year = {2001},
}
@article{2606,
abstract = {Glutamate receptors have been linked to the regulation of several developmental events in the CNS. By using cortical slices of early postnatal mice, we show that in layer I cells, glutamate produces intracellular calcium ([Ca2+]i) elevations mediated by ionotropic and metabotropic glutamate receptors (mGluRs). The contribution of mGluRs to these responses was demonstrated by application of tACPD, an agonist to groups I and II mGluRs, which evoked [Ca2+]i increases that could be reversibly blocked by MCPG, an antagonist to groups I and II mGluRs. In the absence of extracellular Ca2+, repetitive applications of tACPD or quisqualate, an agonist to group I mGluRs, elicited decreasing [Ca2+]i responses that were restored by refilling a thapsigargin-sensitive Ca2+ store. The use of specific group I mGluR agonists CHPG and DHPG indicated that the functional mGluR in layer I was of the mGluR1 subtype. Subtype specific antibodies confirmed the presence of mGlur1α, but not mGluR5, in Cajal-Retzius (Reelin-immunoreactive) neurons.},
author = {Martínez, Galán J and López-Bendito, Guillermina and Luján, Rafael and Ryuichi Shigemoto and Fairén, Alfonso and Valdeolmillos, Miguel},
journal = {European Journal of Neuroscience},
number = {6},
pages = {1147 -- 1154},
publisher = {Wiley-Blackwell},
title = {{Cajal-Retzius cells in early postnatal mouse cortex selectively express functional metabotropic glutamate receptors}},
doi = {10.1046/j.0953-816X.2001.01494.x},
volume = {13},
year = {2001},
}
@article{2607,
abstract = {Alternative splicing in the mGluR5 gene generates two different receptor isoforms, of which expression is developmentally regulated. However, little is known about the functional significance of mGluR5 splice variants. We have examined the functional coupling, subcellular targeting, and effect on neuronal differentiation of epitope-tagged mGluR5 isoforms by expression in neuroblastoma NG108-15 cells. We found that both mGluR5 splice variants give rise to comparable [Ca2+]i transients and have similar pharmacological profile. Tagged receptors were shown by immunofluorescence to be inserted in the plasma membrane. In undifferentiated cells the subcellular localization of the two mGluR5 isoforms was partially segregated, whereas in differentiated cells the labeling largely redistributed to the newly formed neurites. Interestingly, we demonstrate that mGluR5 splice variants dramatically influence the formation and maturation of neurites; mGluR5a hinders the acquisition of mature neuronal traits and mGluR5b fosters the elaboration and extension of neurites. These effects are partly inhibited by MPEP.},
author = {Mion, Silvia and Corti, Corrado and Neki, Akio and Ryuichi Shigemoto and Corsi, Mauro A and Fumagalli, Guido F and Ferraguti, Francesco},
journal = {Molecular and Cellular Neuroscience},
number = {6},
pages = {957 -- 972},
publisher = {Academic Press},
title = {{Bidirectional regulation of neurite elaboration by alternatively spliced metabotropic glutamate receptor 5 (mGluR5) isoforms}},
doi = {10.1006/mcne.2001.0993},
volume = {17},
year = {2001},
}
@article{2608,
abstract = {The regulation of neurotransmitter receptors during synapse formation has been studied extensively at the neuromuscular junction, but little is known about the development of excitatory neurotransmitter receptors during synaptogenesis in central synapses. In this study we show qualitatively and quantitatively that a receptor undergoes changes in localisation on the surface of rat Purkinje cells during development in association with its excitatory synapses. The presence of mGluR1α at parallel and climbing fibre synapses on developing Purkinje cells was studied using high-resolution immunoelectron microscopy. Immunoreactivity for mGluR1α was detected from embryonic day 18 in Purkinje cells, and showed dramatic changes in its localisation with age. At early postnatal ages (P0 and P3), mGluR1α was found both in somata and stem dendrites but was not usually associated with synaptic contacts. At P7, mGluR1α became concentrated in somatic spines associated with climbing fibres and in the growing dendritic arborisation even before innervation by parallel fibres. During the second and third postnatal week, when spines and parallel fibre synapses were generated, mGluR1α became progressively concentrated in the molecular layer, particularly in the synaptic specialisations. As a result, during the fourth postnatal week, the pattern and level of mGluR1α expression became similar to the adult and mGluR1α appeared in high density in perisynaptic sites. Our results indicate that mGluR1α is present in the developing Purkinje cells prior to their innervation by climbing and parallel fibres and demonstrate that this receptor undergoes a dynamic and specific regulation during postnatal development in association with the establishment of synaptic inputs to Purkinje cell.},
author = {López-Bendito, Guillermina and Ryuichi Shigemoto and Luján, Rafael and Juíz, José M},
journal = {Neuroscience},
number = {2},
pages = {413 -- 429},
publisher = {Elsevier},
title = {{Developmental changes in the localisation of the mGluR1α subtype of metabotropic glutamate receptors in Purkinje cells}},
doi = {10.1016/S0306-4522(01)00188-9},
volume = {105},
year = {2001},
}
@article{2609,
abstract = {The metabotropic glutamate receptors (mGluRs) have distinct distribution patterns in the CNS but subtypes within group I or group III mGluRs share similar ultrastructural localization relative to neurotransmitter release sites: group I mGluRs are concentrated in an annulus surrounding the edge of the postsynaptic density, whereas group III mGluRs are concentrated in the presynaptic active zone. One of the group II subtypes, mGluR2, is expressed in both pre- and postsynaptic elements, having no close association with synapses. In order to determine if such a distribution is common to another group II subtype, mGluR3, an antibody was raised against a carboxy-terminus of mGluR3 and used for light and electron microscopic immunohistochemistry in the mouse CNS. The antibody reacted strongly with mGluR3, but it also reacted, though only weakly, with mGluR2. Therefore, to examine mGluR3-selective distribution, we used mGluR2-deficient mice as well as wild-type mice. Strong immunoreactivity for mGluR3 was found in the cerebral cortex, striatum, dentate gyrus of the hippocampus, olfactory tubercle, lateral septal nucleus, lateral and basolateral amygdaloid nuclei, and nucleus of the lateral olfactory tract. Pre-embedding immunoperoxidase and immunogold methods revealed mGluR3 labeling in both presynaptic and postsynaptic elements, and also in glial profiles. Double labeling revealed that the vast majority of mGluR3 in presynaptic elements is not closely associated with glutamate and GABA release sites in the striatum and thalamus, respectively. However, in the spines of the dentate granule cells, the highest receptor density was found in perisynaptic sites (20% of immunogold particles within 60 nm from the edge of postsynaptic membrane specialization) followed by a decreasing receptor density away from the synapses (to ∼5% of particles per 60 nm). Furthermore, 19% of immunogold particles were located in asymmetrical postsynaptic specialization, indicating an association of mGluR3 to glutamatergic synapses. The present results indicate that the localization of mGluR3 is rather similar to that of group I mGluRs in the postsynaptic elements, suggesting a unique functional role of mGluR3 in glutamatergic neurotransmission in the CNS.},
author = {Tamaru, Y and Nomura, Sakashi and Mizuno, Noboru and Ryuichi Shigemoto},
journal = {Neuroscience},
number = {3},
pages = {481 -- 503},
publisher = {Elsevier},
title = {{Distribution of metabotropic glutamate receptor mGluR3 in the mouse CNS: Differential location relative to pre- and postsynaptic sites}},
doi = {10.1016/S0306-4522(01)00305-0},
volume = {106},
year = {2001},
}
@article{2610,
abstract = {To study the role of mGlu7 receptors (mGluR7), we used homologous recombination to generate mice lacking this metabotropic receptor subtype (mGluR7 -/-). After the serendipitous discovery of a sensory stimulus-evoked epileptic phenotype, we tested two convulsant drugs, pentylenetetrazole (PTZ) and bicuculline. In animals aged 12 weeks and older, subthreshold doses of these drugs induced seizures in mGluR7 -/-, but not in mGluR7 +/-, mice. PTZ-induced seizures were inhibited by three standard anticonvulsant drugs, but not by the group III selective mGluR agonist (R,S)-4-phosphonophenylglycine (PPG). Consistent with the lack of signs of epileptic activity in the absence of specific stimuli, mGluR7 -/- mice showed no major changes in synaptic properties in two slice preparations. However, slightly increased excitability was evident in hippocampal slices. In addition, there was slower recovery from frequency facilitation in cortical slices, suggesting a role for mGluR7 as a frequency-dependent regulator in presynaptic terminals. Our findings suggest that mGluR7 receptors have a unique role in regulating neuronal excitability and that these receptors may be a novel target for the development of anticonvulsant drugs.},
author = {Sansig, Gilles and Bushell, Trevor J and Clarke, Vernon R and Rozov, Andrei and Burnashev, Nail A and Portet, Chantal and Gasparini, Fabrizio and Schmutz, Markus and Klebs, Klaus and Ryuichi Shigemoto and Flor, Peter J and Kühn, Rainer and Knoepfel, Thomas and Schroeder, Markus and Hampson, David R and Collett, Valerie J and Zhang, Congxiao and Duvoisin, Robert M and Collingridge, Graham L and Van Der Putten, Herman V},
journal = {Journal of Neuroscience},
number = {22},
pages = {8734 -- 8745},
publisher = {Society for Neuroscience},
title = {{Increased seizure susceptibility in mice lacking metabotropic glutamate receptor 7}},
volume = {21},
year = {2001},
}
@article{2611,
abstract = {Research using animal models of neuropathic pain has revealed sympathetic sprouting onto dorsal root ganglion cells. More recently, sensory fibre sprouting onto dorsal root ganglion cells has also been observed. Previous work in our laboratory demonstrated persistent sympathetic fibre sprouting in the skin of the rat lower lip following sensory denervation of this region. Therefore, we applied immunocytochemistry to determine the effects of sympathectomies on the terminal fields of sensory fibres. The superior cervical ganglia were removed bilaterally and the effects on the innervation of the skin of the rat lower lip were observed 1, 2, 3, 4, 6 and 8 weeks post-surgery. Substance P and dopamine-β-hydroxylase immunoreactivities were used to identify a subset of sensory and sympathetic fibres, respectively. We also assessed neurokinin-1 receptor immunoreactivity. Quantitative data was obtained with the aid of an image analysis system. In controls, the epidermis and upper dermis were innervated by substance P-immunoreactive fibres only and upper dermal blood vessels possessed the highest density of neurokinin-1 receptor immunoreactivity. Blood vessels in the lower dermis were innervated by both substance P- and dopamine-β-hydroxylase-immunoreactive fibres. Following sympathectomies, substance P-immunoreactive fibres in the epidermis and upper dermis were more intensely labelled only 1 and 2 weeks post-surgery when compared to sham controls. The length of substance P-immunoreactive fibres in this region was also increased only on the second week. Neurokinin-1 receptor immunoreactivity in the upper dermis was slightly decreased 1 and 2 weeks post-surgery. In the lower dermis, substance P-immunoreactive fibres associated with blood vessels were more intensely labelled only 1 and 2 weeks post-surgery, and at all post-surgical time points studied, blood vessels in this region were devoid of dopamine-β-hydroxylase-immunoreactive fibres. The length of substance P-immunoreactive fibres was increased from the first to the third week post-surgery in the lower dermis. These results indicate that sympathectomies lead to transient changes in substance P-immunoreactive fibre innervation and neurokinin-1 receptor expression in rat lower lip skin. The effects are most prominent in the lower dermis probably due to a greater local concentration of nerve growth factor in this region. The plasticity of the interactions between sensory and sympathetic fibres may prove important in the regulation of skin microcirculation and in the generation of painful sensations under normal conditions or following peripheral nerve injuries.},
author = {Ruocco, Isabella I and Cuello, Augusto C and Ryuichi Shigemoto and Ribeiro-da-Silva, Alfredo},
journal = {Neuroscience},
number = {1},
pages = {157 -- 166},
publisher = {Elsevier},
title = {{Sympathectomies lead to transient substance P-immunoreactive sensory fibre plasticity in the rat skin}},
doi = {10.1016/S0306-4522(01)00158-0},
volume = {108},
year = {2001},
}
@article{2612,
abstract = {We examined immunoreactivities for γ-aminobutyric acidB-receptor (GABABR) subtypes, GABABR1 and GABABR2, in the mesencephalic trigeminal nucleus neurons (MTN neurons) of the rat. Immunoreactivity for GABABR1 was prominent in cell bodies of MTN, whereas that for GABABR2 was very weak, if existed. For electron microscopy, the immunogold-silver method for GABABR1 was combined with the immunoperoxidase method for glutamic acid decarboxylase (GAD: the synthetic enzyme of GABA). Immunogold-silver particles indicating GABABR1 immunoreactivity were distributed widely in the cytoplasm of the cell bodies postsynaptic to GAD-immunoreactive axon terminals, but were rarely associated with synaptic membrane specialization or extrasynaptic sites of plasma membrane. It has been indicated that GABABR1 may not be transported to plasma membrane when no GABABR2 exists. Thus, it was presumed that GABABR1 in the cell body of the rat MTN neurons might not be involved in the synaptic transmission.},
author = {Li, Jin-Lian and Ryuichi Shigemoto and Kulik, Ákos and Chen, Peng and Nomura, Sakashi and Kaneko, Takeshi and Mizuno, Noboru},
journal = {Neuroscience Letters},
number = {1-2},
pages = {93 -- 97},
publisher = {Elsevier},
title = {{Immunocytochemical localization of GABAB receptors in mesencephalic trigeminal nucleus neurons in the rat}},
doi = {10.1016/S0304-3940(01)02321-7},
volume = {315},
year = {2001},
}
@article{2709,
author = {László Erdös},
journal = {ICMP: International Congress on Mathematical Physics},
pages = {273 -- 281},
publisher = {World Scientific Publishing},
title = {{Long time dynamics of an electron in a weakly coupled phonon field}},
year = {2001},
}
@article{2734,
abstract = {In this paper we describe an intrinsically geometric way of producing magnetic fields on S3 and R3 for which the corresponding Dirac operators have a non-trivial kernel. In many cases we are able to compute the dimension of the kernel. In particular we can give examples where the kernel has any given dimension. This generalizes the examples of Loss and Yau [1].},
author = {László Erdös and Solovej, Jan P},
journal = {Reviews in Mathematical Physics},
number = {10},
pages = {1247 -- 1280},
publisher = {World Scientific Publishing},
title = {{The kernel of Dirac operators on S3 and R3}},
doi = {10.1142/S0129055X01000983},
volume = {13},
year = {2001},
}
@article{2735,
abstract = {We establish the exact low-energy asymptotics of the integrated density of states (Lifschitz tail) in a homogeneous magnetic field and Poissonian impurities with a repulsive single-site potential of Gaussian decay. It has been known that the Gaussian potential tail discriminates between the so-called "classical" and "quantum" regimes, and precise asymptotics are known in these cases. For the borderline case, the coexistence of the classical and quantum regimes was conjectured. Here we settle this last remaining open case to complete the full picture of the magnetic Lifschitz tails.},
author = {László Erdös},
journal = {Probability Theory and Related Fields},
number = {2},
pages = {219 -- 236},
publisher = {Springer},
title = {{Lifschitz tail in a magnetic field: Coexistence of classical and quantum behavior in the borderline case}},
doi = {10.1007/PL00008803},
volume = {121},
year = {2001},
}
@article{2736,
abstract = {We consider the time evolution of N bosonic particles interacting via a mean field Coulomb potential. Suppose the initial state is a product wavefunction. We show that at any finite time the correlation functions factorize in the limit N → ∞. Furthermore, the limiting one particle density matrix satisfies the nonlinear Hartree equation. The key ingredients are the uniqueness of the BBGKY hierarchy for the correlation functions and a new apriori estimate for the many-body Schrödinger equations.},
author = {László Erdös and Yau, Horng-Tzer},
journal = {Advances in Theoretical and Mathematical Physics},
number = {6},
pages = {1169 -- 1205},
publisher = {International Press},
title = {{Derivation of the nonlinear Schrödinger equation from a many body Coulomb system}},
volume = {5},
year = {2001},
}
@article{841,
author = {Wolf, Yuri I and Fyodor Kondrashov and Koonin, Eugene V},
journal = {Trends in Genetics},
number = {9},
pages = {499 -- 501},
publisher = {Elsevier},
title = {{Footprints of primordial introns on the eukaryotic genome: still no clear traces }},
doi = {10.1016/S0168-9525(01)02376-9},
volume = {17},
year = {2001},
}
@article{851,
abstract = {The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis.},
author = {Rogozin, Igor B and Fyodor Kondrashov and Glazko, Galina V},
journal = {Human Mutation},
number = {2},
pages = {83 -- 102},
publisher = {Wiley-Blackwell},
title = {{Use of mutation spectra analysis software}},
doi = {10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E},
volume = {17},
year = {2001},
}
@article{8521,
abstract = {We continue the previous article's discussion of bounds, for prevalent diffeomorphisms of smooth compact manifolds, on the growth of the number of periodic points and the decay of their hyperbolicity as a function of their period $n$. In that article we reduced the main results to a problem, for certain families of diffeomorphisms, of bounding the measure of parameter values for which the diffeomorphism has (for a given period $n$) an almost periodic point that is almost nonhyperbolic. We also formulated our results for $1$-dimensional endomorphisms on a compact interval. In this article we describe some of the main techniques involved and outline the rest of the proof. To simplify notation, we concentrate primarily on the $1$-dimensional case.},
author = {Kaloshin, Vadim and Hunt, Brian R.},
issn = {1079-6762},
journal = {Electronic Research Announcements of the American Mathematical Society},
keywords = {General Mathematics},
number = {5},
pages = {28--36},
publisher = {American Mathematical Society},
title = {{A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II}},
doi = {10.1090/s1079-6762-01-00091-9},
volume = {7},
year = {2001},
}
@article{8522,
abstract = {For diffeomorphisms of smooth compact manifolds, we consider the problem of how fast the number of periodic points with period $n$grows as a function of $n$. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for $C^2$ or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call ``prevalence'', the growth is not much faster than exponential. Specifically, we show that for each $\delta > 0$, there is a prevalent set of ( $C^{1+\rho}$ or smoother) diffeomorphisms for which the number of period $n$ points is bounded above by $\operatorname{exp}(C n^{1+\delta})$ for some $C$ independent of $n$. We also obtain a related bound on the decay of the hyperbolicity of the periodic points as a function of $n$. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity shows this to be a subtle and complex phenomenon, reminiscent of KAM theory.},
author = {Kaloshin, Vadim and Hunt, Brian R.},
issn = {1079-6762},
journal = {Electronic Research Announcements of the American Mathematical Society},
keywords = {General Mathematics},
number = {4},
pages = {17--27},
publisher = {American Mathematical Society},
title = {{A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I}},
doi = {10.1090/s1079-6762-01-00090-7},
volume = {7},
year = {2001},
}
@article{8524,
abstract = {A number α∈R is diophantine if it is not well approximable by rationals, i.e. for some C,ε>0 and any relatively prime p,q∈Z we have |αq−p|>Cq−1−ε. It is well-known and is easy to prove that almost every α in R is diophantine. In this paper we address a noncommutative version of the diophantine properties. Consider a pair A,B∈SO(3) and for each n∈Z+ take all possible words in A, A -1, B, and B - 1 of length n, i.e. for a multiindex I=(i1,i1,…,im,jm) define |I|=∑mk=1(|ik|+|jk|)=n and \( W_n(A,B ) = \{W_{\cal I}(A,B) = A^{i_1} B^{j_1} \dots A^{i_m} B^{j_m}\}_{|{\cal I|}=n \).¶Gamburd—Jakobson—Sarnak [GJS] raised the problem: prove that for Haar almost every pair A,B∈SO(3) the closest distance of words of length n to the identity, i.e. sA,B(n)=min|I|=n∥WI(A,B)−E∥, is bounded from below by an exponential function in n. This is the analog of the diophantine property for elements of SO(3). In this paper we prove that s A,B (n) is bounded from below by an exponential function in n 2. We also exhibit obstructions to a “simple” proof of the exponential estimate in n.},
author = {Kaloshin, Vadim and Rodnianski, I.},
issn = {1016-443X},
journal = {Geometric And Functional Analysis},
number = {5},
pages = {953--970},
publisher = {Springer Nature},
title = {{Diophantine properties of elements of SO(3)}},
doi = {10.1007/s00039-001-8222-8},
volume = {11},
year = {2001},
}
@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},
}
@inproceedings{4005,
abstract = {This paper describes an algorithm for maintaining an approximating triangulation of a deforming surface in R-3. The triangulation adapts dynamically to changing shape, curvature, and topology of the surface.},
author = {Cheng, Ho-Lun and Dey, Tamal K and Herbert Edelsbrunner and Sullivan, John},
pages = {47 -- 56},
publisher = {SIAM},
title = {{Dynamic skin triangulation}},
year = {2001},
}
@article{4006,
abstract = {The 180 models collected in this paper are produced by sampling and wrapping point sets on tubes. The surfaces are represented as triangulated 2-manifolds and available as st1-files from the author's web site at www.cs.duke.edu/similar toedels. Each tube is obtained by thickening a circle or a smooth torus knot, and for some we use the degrees of freedom in the thickening process to encode meaningful information, such as curvature or torsion.},
author = {Herbert Edelsbrunner},
journal = {Journal of Universal Computer Science},
number = {5},
pages = {379 -- 399},
publisher = {Springer},
title = {{180 wrapped tubes}},
doi = {10.3217/jucs-007-05-0379},
volume = {7},
year = {2001},
}
@article{4007,
abstract = {This paper describes an algorithm for maintaining an approximating triangulation of a deforming surface in R 3 . The surface is the envelope of an infinite family of spheres defined and controlled by a finite collection of weighted points. The triangulation adapts dynamically to changing shape, curvature, and topology of the surface. },
author = {Cheng, Ho-Lun and Dey, Tamal K and Herbert Edelsbrunner and Sullivan, John},
journal = {Discrete & Computational Geometry},
number = {4},
pages = {525 -- 568},
publisher = {Springer},
title = {{Dynamic skin triangulation}},
doi = {10.1007/s00454-001-0007-1},
volume = {25},
year = {2001},
}
@article{4200,
abstract = {Zebrafish embryos homozygous for the masterblind (mb1) mutation exhibit a striking phenotype in which the eyes and telencephalon are reduced or absent and diencephalic fates expand to the front of the brain. Here we show that mb1(-/-) embryos carry an amino-acid change at a conserved site in the Wnt pathway scaffolding protein, Axin1. The amino-acid substitution present in the mbl allele abolishes the binding of Axin to Gsk3 and affects Tcf-dependent transcription. Therefore, Gsk3 activity may be decreased in mbl(-/-) embryos and in support of this possibility, overexpression of either wild-type Axin1 or Gsk3 beta can restore eye and telencephalic fates to mb1(-/-) embryos. Our data reveal a crucial role for Axin1-dependent inhibition of the Wnt pathway in the early regional subdivision of the anterior neural plate into telencephalic, diencephalic, and eye-forming territories.},
author = {Heisenberg, Carl-Philipp J and Houart, Corinne and Take Uchi, Masaya and Rauch, Gerd and Young, Neville and Coutinho, Pedro and Masai, Ichiro and Caneparo, Luca and Concha, Miguel and Geisler, Robert and Dale, Trevor and Wilson, Stephen and Stemple, Derek},
journal = {Genes and Development},
number = {11},
pages = {1427 -- 1434},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{A mutation in the Gsk3-binding domain of zebrafish Masterblind/Axin1 leads to a fate transformation of telencephalon and eyes to diencephalon}},
doi = {10.1101/gad.194301},
volume = {15},
year = {2001},
}
@article{4229,
abstract = {Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species, such as Qβ and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in gene regulation. Using nucleotide sequences from the coat and replicase genes we present the first statistical estimate of phylogeny for the family Leviviridae using maximum-likelihood and Bayesian estimation. Our analyses reveal that the coliphage species are a monophyletic group consisting of two clades representing the genera Levivirus and Allolevivirus. The Pseudomonas species PP7 diverged from its common ancestor with the coliphage prior to the ancient split between these genera and their subsequent diversification. Differences in genome size, gene composition, and gene expression are shown with a high probability to have changed along the lineage leading to the Allolevivirus through gene expansion. The change in genome size of the Allolevivirus ancestor may have catalyzed subsequent changes that led to their current genome organization and gene expression.},
author = {Jonathan Bollback and Huelsenbeck, John P},
journal = {Journal of Molecular Evolution},
number = {2},
pages = {117 -- 128},
publisher = {Springer},
title = {{Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae)}},
doi = {10.1007/s002390010140},
volume = {52},
year = {2001},
}