TY - JOUR
AB - For any N ≥ 2, let Z ⊂ ℙN be a geometrically integral algebraic variety of degree d. This article is concerned with the number Nz(B) of ℚ-rational points on Z which have height at most B. For any ε > 0, we establish the estimate NZ(B) = O d,ε,N(Bdim Z+ε), provided that d ≥ 6. As indicated, the implied constant depends at most on d, ε, and N.
AU - Timothy Browning
AU - Heath-Brown, Roger
AU - Salberger, Per
ID - 216
IS - 3
JF - Duke Mathematical Journal
TI - Counting rational points on algebraic varieties
VL - 132
ER -
TY - JOUR
AB - This paper is concerned with the average order of certain arithmetic functions, as they range over the values taken by binary forms.
AU - de la Bretèche, Régis
AU - Timothy Browning
ID - 218
IS - 3
JF - Acta Arithmetica
TI - Sums of arithmetic functions over values of binary forms
VL - 125
ER -
TY - CONF
AU - Lieb, Élliott H
AU - Robert Seiringer
AU - Solovej, Jan P
ID - 2333
TI - Ground-state energy of a dilute Fermi gas
VL - 412
ER -
TY - CONF
AU - Robert Seiringer
AU - Lieb, Élliott H
AU - Yngvason, Jakob
ED - Zambrini, Jean-Claude
ID - 2334
TI - One-dimensional behavior of dilute, trapped Bose gases in traps
ER -
TY - GEN
AB - We prove that the Gross-Pitaevskii equation correctly describes the ground state energy and corresponding one-particle density matrix of rotating, dilute, trapped Bose gases with repulsive two-body interactions. We also show that there is 100% Bose-Einstein condensation. While a proof that the GP equation correctly describes non-rotating or slowly rotating gases was known for some time, the rapidly rotating case was unclear because the Bose (i.e., symmetric) ground state is not the lowest eigenstate of the Hamiltonian in this case. We have been able to overcome this difficulty with the aid of coherent states. Our proof also conceptually simplifies the previous proof for the slowly rotating case. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state.
AU - Lieb, Élliott H
AU - Robert Seiringer
ID - 2363
IS - 2
T2 - Communications in Mathematical Physics
TI - Derivation of the Gross-Pitaevskii equation for rotating Bose gases
VL - 264
ER -
TY - JOUR
AB - We present an inequality that gives a lower bound on the expectation value of certain two-body interaction potentials in a general state on Fock space in terms of the corresponding expectation value for thermal equilibrium states of non-interacting systems and the difference in the free energy. This bound can be viewed as a rigorous version of first-order perturbation theory for many-body systems at positive temperature. As an application, we give a proof of the first two terms in a high density (and high temperature) expansion of the free energy of jellium with Coulomb interactions, both in the fermionic and bosonic case. For bosons, our method works above the transition temperature (for the non-interacting gas) for Bose-Einstein condensation.
AU - Robert Seiringer
ID - 2364
IS - 3
JF - Reviews in Mathematical Physics
TI - A correlation estimate for quantum many-body systems at positive temperature
VL - 18
ER -
TY - JOUR
AB - We consider a gas of fermions with non-zero spin at temperature T and chemical potential μ. We show that if the range of the interparticle interaction is small compared to the mean particle distance, the thermodynamic pressure differs to leading order from the corresponding expression for non-interacting particles by a term proportional to the scattering length of the interparticle interaction. This is true for any repulsive interaction, including hard cores. The result is uniform in the temperature as long as T is of the same order as the Fermi temperature, or smaller.
AU - Robert Seiringer
ID - 2365
IS - 3
JF - Communications in Mathematical Physics
TI - The thermodynamic pressure of a dilute fermi gas
VL - 261
ER -
TY - JOUR
AB - Inequalities are derived for power sums of the real part and the modulus of the eigenvalues of a Schrödinger operator with a complex-valued potential.
AU - Frank, Rupert L
AU - Laptev, Ari
AU - Lieb, Élliott H
AU - Robert Seiringer
ID - 2366
IS - 3
JF - Letters in Mathematical Physics
TI - Lieb-Thirring inequalities for Schrödinger operators with complex-valued potentials
VL - 77
ER -
TY - CHAP
AB - The recent experimental success in creating Bose-Einstein condensates of alkali atoms, honored by the Nobel prize awards in 2001 [1,5], led to renewed interest in the mathematical description of interacting Bose gases.
AU - Robert Seiringer
ED - Dereziński, Jan
ED - Siedentop, Heinz
ID - 2368
T2 - Large Coulomb Systems
TI - Dilute, trapped Bose gases and Bose-Einstein condensation
VL - 695
ER -
TY - CHAP
AB - One of the most remarkable recent developments in the study of ultracold Bose gases is the observation of a reversible transition from a Bose Einstein condensate to a state composed of localized atoms as the strength of a periodic, optical trapping potential is varied. In [1] a model of this phenomenon has been analyzed rigorously. The gas is a hard core lattice gas and the optical lattice is modeled by a periodic potential of strength λ. For small λ and temperature Bose- Einstein condensation (BEC) is proved to occur, while at large λ BEC disappears, even in the ground state, which is a Mott-insulator state with a characteristic gap. The inter-particle interaction is essential for this effect. This contribution gives a pedagogical survey of these results.
AU - Aizenman, Michael
AU - Lieb, Élliott H
AU - Robert Seiringer
AU - Solovej, Jan P
AU - Yngvason, Jakob
ED - Asch, Joachim
ED - Joye, Alain
ID - 2369
T2 - Mathematical Physics of Quantum Mechanics
TI - Bose-Einstein condensation as a quantum phase transition in an optical lattice
VL - 690
ER -
TY - CHAP
AU - Bang-Jensen, Jørgen
AU - Reed, Bruce
AU - Schacht, Bruce
AU - Šámal, Robert
AU - Toft, Bjarne
AU - Uli Wagner
ID - 2416
T2 - Topics in Discrete Mathematics
TI - On six problems posed by Jarik Nešetřil
VL - 26
ER -
TY - JOUR
AB - We show, with an elementary proof, that the number of halving simplices in a set of n points in 4 in general position is O(n4-2/45). This improves the previous bound of O(n4-1/134). Our main new ingredient is a bound on the maximum number of halving simplices intersecting a fixed 2-plane.
AU - Matoušek, Jiří
AU - Sharir, Micha
AU - Smorodinsky, Shakhar
AU - Uli Wagner
ID - 2429
IS - 2
JF - Discrete & Computational Geometry
TI - K-sets in four dimensions
VL - 35
ER -
TY - JOUR
AB - We consider an online version of the conflict-free coloring of a set of points on the line, where each newly inserted point must be assigned a color upon insertion, and at all times the coloring has to be conflict-free, in the sense that in every interval I there is a color that appears exactly once in I. We present deterministic and randomized algorithms for achieving this goal, and analyze their performance, that is, the maximum number of colors that they need to use, as a function of the number n of inserted points. We first show that a natural and simple (deterministic) approach may perform rather poorly, requiring Ω(√̃) colors in the worst case. We then derive two efficient variants of this simple algorithm. The first is deterministic and uses O(log 2 n) colors, and the second is randomized and uses O(log n) colors with high probability. We also show that the O(log 2 n) bound on the number of colors used by our deterministic algorithm is tight on the worst case. We also analyze the performance of the simplest proposed algorithm when the points are inserted in a random order and present an incomplete analysis that indicates that, with high probability, it uses only O(log n) colors. Finally, we show that in the extension of this problem to two dimensions, where the relevant ranges are disks, n colors may be required in the worst case.
AU - Chent, Ke
AU - Fiat, Amos
AU - Kaplan, Haim
AU - Levy, Meital B
AU - Matoušek, Jiří
AU - Mossel, Elchanan
AU - Pach, János
AU - Sharir, Micha
AU - Smorodinsky, Shakhar
AU - Uli Wagner
AU - Welzl, Emo
ID - 2430
IS - 5
JF - SIAM Journal on Computing
TI - Online conflict-free coloring for intervals
VL - 36
ER -
TY - CONF
AB - We prove an upper bound, tight up to a factor of 2, for the number of vertices of level at most t in an arrangement of n halfspaces in R , for arbitrary n and d (in particular, the dimension d is not considered constant). This partially settles a conjecture of Eckhoff, Linhart, and Welzl. Up to the factor of 2, the result generalizes McMullen's Upper Bound Theorem for convex polytopes (the case ℓ = O) and extends a theorem of Linhart for the case d ≤ 4. Moreover, the bound sharpens asymptotic estimates obtained by Clarkson and Shor. The proof is based on the h-matrix of the arrangement (a generalization, introduced by Mulmuley, of the h-vector of a convex polytope). We show that bounding appropriate sums of entries of this matrix reduces to a lemma about quadrupels of sets with certain intersection properties, and we prove this lemma, up to a factor of 2, using tools from multilinear algebra. This extends an approach of Alon and Kalai, who used linear algebra methods for an alternative proof of the classical Upper Bound Theorem. The bounds for the entries of the h-matrix also imply bounds for the number of i-dimensional faces, i > 0, at level at most ℓ. Furthermore, we discuss a connection with crossing numbers of graphs that was one of the main motivations for investigating exact bounds that are valid for arbitrary dimensions.
AU - Uli Wagner
ID - 2431
TI - On a geometric generalization of the Upper Bound Theorem
ER -
TY - CONF
AB - Often the properties of a single cell are considered as representative for a complete polymer electrolyte fuel cell stack or even a fuel cell system. In some cases this comes close, however, in many real cases differences on several scales become important. Cell interaction phenomena in fuel cell stacks that arise from inequalities between adjacent cells are investigated in detail experimentally. For that, a specialized 2-cell stack with advanced localized diagnostics was developed. The results show that inequalities propagate by electrical coupling, inhomogeneous cell polarization and inducing in-plane current in the common bipolar plate. The effects of the different loss-mechanisms are analyzed and quantified.
AU - Büchi, Felix N.
AU - Freunberger, Stefan Alexander
AU - Santis, Marco
ID - 7326
IS - 1
T2 - ECS Transactions
TI - What is learned beyond the scale of single cells?
VL - 3
ER -
TY - JOUR
AB - Propagation of performance changes to adjacent cells in polymer electrolyte fuel cell stacks is studied by means of voltage monitoring and local current density measurements in peripheral cells of the stack. A technical fuel cell stack has been modified by implementing two independent reactant and coolant supplies in order to deliberately change the performance of one cell (anomalous cell) and study the coupling phenomena to adjacent cells (coupling cells), while keeping the working conditions of the later cell-group unaltered.
Two anomalies are studied: (i) air starvation and (ii) thermal anomaly, in a single anomalous cell in the stack and their coupling to adjacent cells. The results have shown that anomalies inducing considerable changes in the local current density of the anomalous cell (such as air starvation) propagate to adjacent cells affecting their performance. The propagation of local current density changes takes place via the common bipolar plate due to its finite thickness and in-plane conductivity. Consequently, anomalies which do not strongly influence the local current density distribution (such as a thermal anomaly under the studied working conditions) do not propagate to adjacent cells.
AU - Santis, Marco
AU - Freunberger, Stefan Alexander
AU - Papra, Matthias
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7327
IS - 2
JF - Journal of Power Sources
SN - 0378-7753
TI - Experimental investigation of coupling phenomena in polymer electrolyte fuel cell stacks
VL - 161
ER -
TY - JOUR
AB - An experimental technique for measuring the current density distribution with a resolution smaller than the channel/rib scale of the flow field in polymer electrolyte fuel cells (PEFCs) is presented. The electron conductors in a plane perpendicular to the channel direction are considered as two-dimensional resistors. Hence, the current density is obtained from the solution of Laplace's equation with the potentials at current collector and reaction layer as boundary conditions. Using ohmic drop for calculating the local current, detailed knowledge of all resistances involved is of prime importance. In particular, the contact resistance between the gas diffusion layer (GDL) and flow field rib, as well as GDL bulk conductivity, are strongly dependent on clamping pressure. They represent a substantial amount of the total ohmic drop and therefore require careful consideration. The detailed experimental setup as well as the concise procedure for quantitative data evaluation is described. Finally, the method is applied successfully to a cell operated on pure oxygen and air up to high current densities. The results show that electrical and ionic resistances seem to govern the current distribution at low current regimes, whereas mass transport limitations locally hamper the current production at high loads.
AU - Freunberger, Stefan Alexander
AU - Reum, Mathias
AU - Evertz, Jörg
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7328
IS - 11
JF - Journal of The Electrochemical Society
SN - 0013-4651
TI - Measuring the current distribution in PEFCs with sub-millimeter resolution
VL - 153
ER -
TY - JOUR
AB - A novel measurement principle for measuring the current distribution in polymer electrolyte fuel cells (PEFCs) is introduced. It allows, in contrast to all other known techniques, for the first time for a resolution smaller than the channel/rib scale of the flow field in PEFCs. The current density is obtained by considering the electron conductors in the cell as a two-dimensional resistor with the voltage drop caused by the current. The method was applied to a cell operated on oxygen up to high current densities. The results show that the ohmic resistances govern the current distribution in the low current regime, whereas mass transport limitations hamper the current production under the land at high loads.
AU - Freunberger, Stefan Alexander
AU - Reum, Mathias
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7329
IS - 9
JF - Electrochemistry Communications
SN - 1388-2481
TI - Expanding current distribution measurement in PEFCs to sub-millimeter resolution
VL - 8
ER -
TY - JOUR
AB - Polymer electrolyte fuel cells (PE fuel cells) working with air at low stoichiometries (<2.0) and standard electrochemical components show a high degree of inhomogeneity in the current density distribution over the active area. An inhomogeneous current density distribution leads to a non-uniform utilization of the active area, which could negatively affect the time of life of the cells. Furthermore, it is also believed to lower cell performance. In this work, the homogenization of the current density, realized by means of tailored cathodes with along-the-air-channel redistributed catalyst loadings, is investigated. The air stoichiometry range for which a homogenization of the current density is achieved depends upon the gradient with which the catalyst is redistributed along the air channel. A gentle increasing catalyst loading profile homogenizes the current density at relatively higher air stoichiometries, while a steeper profile is suited better for lower air stoichiometries. The results show that a homogenization of the current density by means of redistributed catalyst loading has negative effects on cell performance. Model calculations corroborate the experimental findings on homogenization of the current density and deliver an explanation for the decrease in cell performance.
AU - Santis, M.
AU - Freunberger, Stefan Alexander
AU - Reiner, A.
AU - Büchi, F.N.
ID - 7330
IS - 25
JF - Electrochimica Acta
SN - 0013-4686
TI - Homogenization of the current density in polymer electrolyte fuel cells by in-plane cathode catalyst gradients
VL - 51
ER -
TY - JOUR
AB - A previously developed mathematical model for water management and current density distribution in a polymer electrolyte fuel cell (PEFCs) is employed to investigate the effects of cooling strategies on cell performance. The model describes a two-dimensional slice through the cell along the channels and through the entire cell sandwich including the coolant channels and the bipolar plate. Arbitrary flow arrangements of fuel, oxidant, and coolant stream directions can be described. Due to the serious impact of temperature on all processes in the PEFC, both the relative direction of the coolant stream to the gas streams and its mass flow turns out to significantly affect the cell performance. Besides influencing the electrochemical reaction and all kinds of mass transfer temperature, variations predominantly alter the local membrane hydration distribution and subseqently its conductivity.
AU - Freunberger, Stefan Alexander
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7331
IS - 5
JF - Journal of The Electrochemical Society
SN - 0013-4651
TI - In-plane effects in large-scale PEFCs: II. The influence of cooling strategy on cell performance
VL - 153
ER -
TY - JOUR
AB - A quasi-two-dimensional, along-the-channel mass and heat-transfer model for a proton exchange membrane fuel cell (PEFC) is described and validated against experimental current distribution data. The model is formulated in a dimensional manner, i.e., local transport phenomena are treated one-dimensional in through-plane direction and coupled in-plane by convective transport in the gas and coolant channels. Thus, a two-dimensional slice running through the repetitive unit of a cell from the anode channel via membrane-electrode assembly (MEA) and cathode channel to the coolant channel and from inlet to outlet is modeled. The aim of the work is to elucidate the influence of operating conditions such as feed gas humidities and stoichiometric ratios on the along-the-channel current density distribution and to identify the distinct underlying voltage loss mechanisms. Furthermore, a complicated technical flow field is modeled by a combination of co- and counterflow subdomains and compared with experimental current densities.
AU - Freunberger, Stefan Alexander
AU - Santis, Marco
AU - Schneider, Ingo A.
AU - Wokaun, Alexander
AU - Büchi, Felix N.
ID - 7332
IS - 2
JF - Journal of The Electrochemical Society
SN - 0013-4651
TI - In-plane effects in large-scale PEMFCs
VL - 153
ER -
TY - JOUR
AB - It is commonly believed that both the average length and the frequency of microsatellites correlate with genome size. We have estimated the frequency and the average length for 69 perfect dinucleotide microsatellites in an insect with an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae). Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat arrays are 1.4 to 2 times longer than in other insect species. The average repeat number in C. biguttulus lies in the range of higher vertebrates. Natural populations are highly variable. At least 30 alleles per locus were found and the expected heterozygosity is above 0.95 at all three loci studied. In contrast, the observed heterozygosity is much lower (≤0.51), which could be caused by long null alleles.
AU - Ustinova, Jana
AU - Achmann, Roland
AU - Cremer, Sylvia
AU - Mayer, Frieder
ID - 3908
IS - 2
JF - Journal of Molecular Evolution
TI - Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus
VL - 62
ER -
TY - JOUR
AB - Invasive species often dramatically change native species communities by directly and indirectly out-competing native species. We studied the direct interference abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA & ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers towards three native Lasius ant species that occur at the edge of a L. neglectus supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus (OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack rate of L. neglectus and behavioural dominance throughout the aggressive encounters. Attacks of L. neglectus were performed fastest and most frequent against L. grandis, and also the highest antennation frequencies were observed in encounters between these two species. This could be due to the largest difference in body size, or due to a greater overlap in ecological niche between L. neglectus and L. grandis compared to the other two native species. There was only weak support for L. neglectus workers from the periphery of the supercolony to be more aggressive relative to workers from the centre, even though the former encounter native ant species on a daily basis at the edge of the supercolony.
AU - Cremer, Sylvia
AU - Ugelvig, Line V
AU - Lommen, Suzanne
AU - Petersen, Klaus
AU - Pedersen, Jes
ID - 3912
JF - Myrmecological News
TI - Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain
VL - 9
ER -
TY - JOUR
AB - Many invasive ant species, such as the Argentine ant or the red imported fire ant, have huge colonies with thousands of mass-foraging workers, which quickly monopolise resources and therefore represent a considerable threat to the native ant fauna. Cardiocondyla obscurior and several other species of this myrmicine genus have similarly been transferred throughout the tropics by human activities. However, because their colonies are tiny and workers forage solitarily, Cardiocondyla are often not recognized as successful invaders. Here, we document that the life history of Cardiocondyla closely resembles that of the more conspicuous tramp species, with polygyny, intranidal mating, budding, worker sterility, low genetic variability, and possibly also unicoloniality. Given that introduced Cardiocondyla may locally reach a very high population density, the effects of these stealthy invaders on the native arthropod fauna should receive more attention.
AU - Heinze, Jürgen
AU - Cremer, Sylvia
AU - Eckl, Norbert
AU - Schrempf, Alexandra
ID - 3913
IS - 1
JF - Insectes Sociaux
TI - Stealthy invaders: the biology of Cardiocondyla tramp ants
VL - 53
ER -
TY - JOUR
AB - We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable.
AU - Moder, Karl
AU - Schlick Steiner, Birgit
AU - Steiner, Florian
AU - Cremer, Sylvia
AU - Christian, Erhard
AU - Seifert, Bernhard
ID - 3914
IS - 1
JF - Journal of Zoological Systematics and Evolutionary Research
TI - Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study
VL - 45
ER -
TY - JOUR
AB - OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and tissue content of EGFR has been directly associated with poor prognosis in patients with ovarian cancer. The uPA system plays a role in pericellular proteolysis, cell migration, invasion, and is over-expressed in ovarian cancer. This study explored the effects of EGF on uPAR expression in the ovarian cancer cell line OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration assay, time-lapse video microscopy, real-time PCR, assays for cellular binding of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well as EGF-stimulated cells, is present only in the intact, not the cleaved, form. Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas non-occupied receptor sites were not increased. In addition, EGF treatment resulted in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased internalization of uPAR, since the complex is internalized together with uPAR. Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression of uPAR. In addition, we found an immediate increase of uPAR after exposing the cells to EGF and this was accompanied by a transient increase of cell migration. The increase of cell surface uPAR in response to EGF is accompanied by increased release of the soluble form of uPAR (suPAR) to the medium as well as by increased cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis inhibitor colchicine even though cell migration was inhibited, suggesting that the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased cell surface uPAR in response to EGF stimulation results from mobilization of uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and decreased internalization and degradation of uPAR. Both the anti-uPAR antibody R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa inhibited cell migration in response to uPA as well as to EGF, suggesting that EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.
AU - Henic, Emir
AU - Michael Sixt
AU - Hansson, Stefan
AU - Høyer-Hansen, Gunilla
AU - Casslén, Bertil
ID - 3932
IS - 1
JF - Gynecologic Oncology
TI - EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor
VL - 101
ER -
TY - JOUR
AB - T cells develop in the thymus in a highly specialized cellular and extracellular microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly found in the medulla of the human thymic lobules. Using high-resolution light microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like structure, together with other typical basement membrane components including collagen type IV, nidogen and perlecan. Other interstitial matrix components, such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated with these structures. Three-dimensional (3D) confocal microscopy suggested a tubular structure, whereas immunoelectron and transmission electron microscopy showed that the core of these tubes contained fibrillar collagens enwrapped by the LN-5-containing membrane. These medullary conduits are surrounded by thymic epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and tenascin-C. Dendritic cells were also detected in close vicinity to the conduits. Both of these stromal cell types express major histocompatibility complex (MHC) class II molecules capable of antigen presentation. The conduits are connected to blood vessels but, with an average diameter of 2 mum, they are too small to transport cells. However, evidence is provided that smaller molecules such as a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in the conduits. These results clearly demonstrate that a conduit system, which is also known from secondary lymphatic organs such as lymph nodes and spleen, is present in the medulla of the human thymus, and that it might serve to transport small blood-borne molecules or chemokines to defined locations within the medulla.
AU - Drumea-Mirancea, Mihaela
AU - Wessels, Johannes T
AU - Müller, Claudia A
AU - Essl, Mike
AU - Eble, Johannes A
AU - Tolosa, Eva
AU - Koch, Manuel
AU - Reinhardt, Dieter P
AU - Michael Sixt
AU - Sorokin, Lydia
AU - Stierhof, York-Dieter
AU - Schwarz, Heinz
AU - Klein, Gerd
ID - 3934
IS - Pt 7
JF - Journal of Cell Science
TI - Characterization of a conduit system containing laminin-5 in the human thymus: a potential transport system for small molecules
VL - 119
ER -
TY - JOUR
AB - Integrins regulate cell behavior through the assembly of multiprotein complexes at the site of cell adhesion. Parvins are components of such a multiprotein complex. They consist of three members (alpha-, beta-, and gamma-parvin), form a functional complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin has been reported to be expressed in hematopoietic organs. In the present study, we report the expression pattern of the parvins in hematopoietic cells and the phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent antibody response and lymphocyte and dendritic cell migration. These data indicate that despite the high expression of gamma-parvin in hematopoietic cells it must play a more subtle role for blood cell homeostasis.
AU - Chu, Haiyan
AU - Thievessen, Ingo
AU - Michael Sixt
AU - Lämmermann, Tim
AU - Waisman, Ari
AU - Braun, Attila
AU - Noegel, Angelika A
AU - Fässler, Reinhard
ID - 3935
IS - 5
JF - Molecular and Cellular Biology
TI - γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent antibody response
VL - 26
ER -
TY - JOUR
AB - At least eight of the twelve known members of the beta1 integrin family are expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1 has received most attention as a main factor mediating firm adhesion to the endothelium during blood cell extravasation. Therapeutic trials are ongoing into the use of antibodies and small molecule inhibitors to target this interaction and hence obtain anti-inflammatory effects. However, extravasation is only one possible process that is mediated by beta1 integrins and there is evidence that they also mediate leukocyte retention and positioning in the tissue, lymphocyte activation and possibly migration within the interstitium. Genetic mouse models where integrins are selectively deleted on blood cells have been used to investigate these functions and further studies will be invaluable to critically evaluate therapeutic trials.
AU - Michael Sixt
AU - Bauer, Martina
AU - Lämmermann, Tim
AU - Fässler, Reinhard
ID - 3936
IS - 5
JF - Current Opinion in Cell Biology
TI - β1 integrins: zip codes and signaling relay for blood cells
VL - 18
ER -
TY - JOUR
AB - Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures.
AU - Ban, Yih-En Andrew
AU - Rudolph, Johannes
AU - Zhou, Pei
AU - Herbert Edelsbrunner
ID - 3978
IS - 4
JF - Proteins: Structure, Function and Bioinformatics
TI - Evaluating the quality of NMR structures by local density of protons
VL - 62
ER -
TY - JOUR
AB - Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion.
AU - Ban, Yih-En Andrew
AU - Herbert Edelsbrunner
AU - Rudolph, Johannes
ID - 3979
IS - 3
JF - Journal of the ACM
TI - Interface surfaces for protein-protein complexes
VL - 53
ER -
TY - JOUR
AB - Given a smoothly embedded 2-manifold in R-3, we define the elevation of a point as the height difference to a canonically defined second point on the same manifold. Our definition is invariant under rigid motions and can be used to define features such as lines of discontinuous or continuous but non-smooth elevation. We give an algorithm for finding points of locally maximum elevation, which we suggest mark cavities and protrusions and are useful in matching shapes as for example in protein docking.
AU - Agarwal, Pankaj K
AU - Herbert Edelsbrunner
AU - Harer, John
AU - Wang, Yusu
ID - 3980
IS - 4
JF - Discrete & Computational Geometry
TI - Extreme elevation on a 2-manifold
VL - 36
ER -
TY - JOUR
AU - Harold Vladar
AU - González,J. A
ID - 4235
JF - Journal of Theoretical Biology
TI - Dynamic response of cancer under the influence of immunological activity and therapy
ER -
TY - JOUR
AB - In finite populations, genetic drift generates interference between selected loci, causing advantageous alleles to be found more often on different chromosomes than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson effect” generates indirect selection to increase recombination rates. We present a new method to quantify the strength of this selection. Our model represents a new beneficial allele (A) entering a population as a single copy, while another beneficial allele (B) is sweeping at another locus. A third locus affects the recombination rate between selected loci. Using a branching process model, we calculate the probability distribution of the number of copies of A on the different genetic backgrounds, after it is established but while it is still rare. Then, we use a deterministic model to express the change in frequency of the recombination modifier, due to hitchhiking, as A goes to fixation. We show that this method can give good estimates of selection for recombination. Moreover, it shows that recombination is selected through two different effects: it increases the fixation probability of new alleles, and it accelerates selective sweeps. The relative importance of these two effects depends on the relative times of occurrence of the beneficial alleles.
AU - Roze, Denis
AU - Nicholas Barton
ID - 4248
IS - 3
JF - Genetics
TI - The Hill-Robertson effect and the evolution of recombination
VL - 173
ER -
TY - GEN
AB - A recent analysis has shown that divergence between human and chimpanzee varies greatly across the genome. Although this is consistent with ‘hybridisation’ between the diverging human and chimp lineages, such observations can be explained more simply by the null model of allopatric speciation.
AU - Nicholas Barton
ID - 4250
IS - 16
T2 - Current Biology
TI - Evolutionary Biology: How did the human species form?
VL - 16
ER -
TY - JOUR
AB - Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library 2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt, wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken. Ferner werden neue Anforderungen an Bibliothekare diskutiert.
AU - Patrick Danowski
AU - Heller,Lambert
ID - 4345
IS - 11
JF - Bibliotheksdienst
TI - Bibliothek 2.0 - Die Bibliothek der Zukunft?
VL - 40
ER -
TY - JOUR
AB - BACKGROUND: Character mapping on phylogenies has played an important, if not critical role, in our understanding of molecular, morphological, and behavioral evolution. Until very recently we have relied on parsimony to infer character changes. Parsimony has a number of serious limitations that are drawbacks to our understanding. Recent statistical methods have been developed that free us from these limitations enabling us to overcome the problems of parsimony by accommodating uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS: SIMMAP has been developed to implement stochastic character mapping that is useful to both molecular evolutionists, systematists, and bioinformaticians. Researchers can address questions about positive selection, patterns of amino acid substitution, character association, and patterns of morphological evolution. CONCLUSION: Stochastic character mapping, as implemented in the SIMMAP software, enables users to address questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these quantities is accommodated by using MCMC samples from their respective posterior distributions.
AU - Jonathan Bollback
ID - 4351
JF - BMC Bioinformatics
TI - SIMMAP: stochastic character mapping of discrete traits on phylogenies
VL - 7
ER -
TY - JOUR
AB - Anopheles darlingi is the primary malaria vector in Latin America, and is especially important in Amazonian Brazil. Historically, control efforts have been focused on indoor house spraying using a variety of insecticides, but since the mid-1990s there has been a shift to patient treatment and focal insecticide fogging. Anopheles darlingi was believed to have been significantly reduced in a gold-mining community, Peixoto de Azevedo (in Mato Grosso State), in the early 1990s by insecticide use during a severe malaria epidemic. In contrast, although An. darlingi was eradicated from some districts of the city of Belem (the capital of Para State) in 1968 to reduce malaria, populations around the water protection area in the eastern district were treated only briefly. To investigate the population structure of An. darlingi including evidence for a population bottleneck in Peixoto, we analyzed eight microsatellite loci of 256 individuals from seven locations in Brazil: three in Amapa State, three in Para State, and one in Mato Grosso State. Allelic diversity and mean expected heterozygosity were high for all populations (mean number alleles/locus and H(E) were 13.5 and 0.834, respectively) and did not differ significantly between locations. Significant heterozygote deficits were associated with linkage disequilibrium, most likely due to either the Wahlund effect or selection. We found no evidence for a population bottleneck in Peixoto, possibly because the reduction was not extreme enough to be detected. Overall estimates of long-term N(e) varied from 92.4 individuals under the linkage disequilibrium model to infinity under the heterozygote excess model. Fixation indices and analysis of molecular variance demonstrated significant differentiation between locations north and south of the Amazon River, suggesting a degree of genetic isolation between them, attributed to isolation by distance.
AU - Conn, Jan E
AU - Vineis, Joseph H
AU - Jonathan Bollback
AU - Onyabe, David Y
AU - Wilkerson, Richard C
AU - Povoa, Marinete M
ID - 4352
IS - 5
JF - The American Journal of Tropical Medicine and Hygiene
TI - Population structure of the malaria vector Anopheles darlingi in a malaria-endemic region of eastern Amazonian Brazil
VL - 74
ER -
TY - CONF
AU - Thomas Wies
AU - Kuncak, Viktor
AU - Lam,Patrick
AU - Podelski,Andreas
AU - Rinard,Martin
ID - 4359
TI - Field Constraint Analysis
ER -
TY - CONF
AU - Maler, Oded
AU - Dejan Nickovic
AU - Pnueli,Amir
ID - 4373
TI - Real Time Temporal Logic: Past, Present, Future
ER -
TY - CONF
AU - Maler, Oded
AU - Dejan Nickovic
AU - Pnueli,Amir
ID - 4374
TI - From MITL to Timed Automata
ER -
TY - CONF
AU - Alur, Rajeev
AU - Pavol Cerny
AU - Zdancewic,Steve
ID - 4401
TI - Preserving Secrecy Under Refinement
ER -
TY - CONF
AB - We propose and evaluate a new algorithm for checking the universality of nondeterministic finite automata. In contrast to the standard algorithm, which uses the subset construction to explicitly determinize the automaton, we keep the determinization step implicit. Our algorithm computes the least fixed point of a monotone function on the lattice of antichains of state sets. We evaluate the performance of our algorithm experimentally using the random automaton model recently proposed by Tabakov and Vardi. We show that on the difficult instances of this probabilistic model, the antichain algorithm outperforms the standard one by several orders of magnitude. We also show how variations of the antichain method can be used for solving the language-inclusion problem for nondeterministic finite automata, and the emptiness problem for alternating finite automata.
AU - De Wulf, Martin
AU - Doyen, Laurent
AU - Thomas Henzinger
AU - Raskin, Jean-François
ID - 4406
TI - Antichains: A new algorithm for checking universality of finite automata
VL - 4144
ER -
TY - CONF
AB - We summarize some current trends in embedded systems design and point out some of their characteristics, such as the chasm between analytical and computational models, and the gap between safety-critical and best-effort engineering practices. We call for a coherent scientific foundation for embedded systems design, and we discuss a few key demands on such a foundation: the need for encompassing several manifestations of heterogeneity, and the need for constructivity in design. We believe that the development of a satisfactory Embedded Systems Design Science provides a timely challenge and opportunity for reinvigorating computer science.
AU - Thomas Henzinger
AU - Sifakis, Joseph
ID - 4431
TI - The embedded systems design challenge
VL - 4085
ER -
TY - CONF
AB - We add freeze quantifiers to the game logic ATL in order to specify real-time objectives for games played on timed structures. We define the semantics of the resulting logic TATL by restricting the players to physically meaningful strategies, which do not prevent time from diverging. We show that TATL can be model checked over timed automaton games. We also specify timed optimization problems for physically meaningful strategies, and we show that for timed automaton games, the optimal answers can be approximated to within any degree of precision.
AU - Thomas Henzinger
AU - Prabhu, Vinayak S
ID - 4432
TI - Timed alternating-time temporal logic
VL - 4202
ER -
TY - CONF
AB - We present an assume-guarantee interface algebra for real-time components. In our formalism a component implements a set of task sequences that share a resource. A component interface consists of an arrival rate function and a latency for each task sequence, and a capacity function for the shared resource. The interface specifies that the component guarantees certain task latencies depending on assumptions about task arrival rates and allocated resource capacities. Our algebra defines compatibility and refinement relations on interfaces. Interface compatibility can be checked on partial designs, even when some component interfaces are yet unknown. In this case interface composition computes as new assumptions the weakest constraints on the unknown components that are necessary to satisfy the specified guarantees. Interface refinement is defined in a way that ensures that compatible interfaces can be refined and implemented independently. Our algebra thus formalizes an interface-based design methodology that supports both the incremental addition of new components and the independent stepwise refinement of existing components. We demonstrate the flexibility and efficiency of the framework through simulation experiments.
AU - Thomas Henzinger
AU - Matic, Slobodan
ID - 4436
TI - An interface algebra for real-time components
ER -
TY - CONF
AB - The synthesis of reactive systems requires the solution of two-player games on graphs with ω-regular objectives. When the objective is specified by a linear temporal logic formula or nondeterministic Büchi automaton, then previous algorithms for solving the game require the construction of an equivalent deterministic automaton. However, determinization for automata on infinite words is extremely complicated, and current implementations fail to produce deterministic automata even for relatively small inputs. We show how to construct, from a given nondeterministic Büchi automaton, an equivalent nondeterministic parity automaton that is good for solving games with objective . The main insight is that a nondeterministic automaton is good for solving games if it fairly simulates the equivalent deterministic automaton. In this way, we omit the determinization step in game solving and reactive synthesis. The fact that our automata are nondeterministic makes them surprisingly simple, amenable to symbolic implementation, and allows an incremental search for winning strategies.
AU - Thomas Henzinger
AU - Piterman, Nir
ID - 4437
TI - Solving games without determinization
VL - 4207
ER -
TY - JOUR
AB - One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternation-free fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment.
AU - Thomas Henzinger
AU - Kupferman, Orna
AU - Majumdar, Ritankar S
ID - 4451
IS - 2
JF - Theoretical Computer Science
TI - On the universal and existential fragments of the mu-calculus
VL - 354
ER -
TY - CONF
AB - We consider the problem if a given program satisfies a specified safety property. Interesting programs have infinite state spaces, with inputs ranging over infinite domains, and for these programs the property checking problem is undecidable. Two broad approaches to property checking are testing and verification. Testing tries to find inputs and executions which demonstrate violations of the property. Verification tries to construct a formal proof which shows that all executions of the program satisfy the property. Testing works best when errors are easy to find, but it is often difficult to achieve sufficient coverage for correct programs. On the other hand, verification methods are most successful when proofs are easy to find, but they are often inefficient at discovering errors. We propose a new algorithm, Synergy, which combines testing and verification. Synergy unifies several ideas from the literature, including counterexample-guided model checking, directed testing, and partition refinement.This paper presents a description of the Synergy algorithm, its theoretical properties, a comparison with related algorithms, and a prototype implementation called Yogi.
AU - Gulavani, Bhargav S
AU - Thomas Henzinger
AU - Kannan, Yamini
AU - Nori, Aditya V
AU - Rajamani, Sriram K
ID - 4523
TI - Synergy: A new algorithm for property checking
ER -
TY - CONF
AB - We designed and implemented a new programming language called Hierarchical Timing Language (HTL) for hard realtime systems. Critical timing constraints are specified within the language,and ensured by the compiler. Programs in HTL are extensible in two dimensions without changing their timing behavior: new program modules can be added, and individual program tasks can be refined. The mechanism supporting time invariance under parallel composition is that different program modules communicate at specified instances of time. Time invariance under refinement is achieved by conservative scheduling of the top level. HTL is a coordination language, in that individual tasks can be implemented in "foreign" languages. As a case study, we present a distributed HTL implementation of an automotive steer-by-wire controller.
AU - Ghosal, Arkadeb
AU - Thomas Henzinger
AU - Iercan, Daniel
AU - Kirsch, Christoph M
AU - Sangiovanni-Vincentelli, Alberto
ID - 4526
TI - A hierarchical coordination language for interacting real-time tasks
ER -