@article{8492,
abstract = {We demonstrate for different protein samples that 2D 1H−15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to measure fast hydrogen−deuterium exchange rate constants along the backbone of a small globular protein fragment by real-time 2D NMR.},
author = {Schanda, Paul and Brutscher, Bernhard},
issn = {0002-7863},
journal = {Journal of the American Chemical Society},
keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
number = {22},
pages = {8014--8015},
publisher = {American Chemical Society},
title = {{Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds}},
doi = {10.1021/ja051306e},
volume = {127},
year = {2005},
}
@article{209,
author = {Timothy Browning and Heath-Brown, Roger},
journal = {Inventiones Mathematicae},
number = {3},
pages = {553 -- 573},
publisher = {Unknown},
title = {{Equal sums of three powers}},
doi = {10.1007/s00222-004-0360-9},
volume = {157},
year = {2004},
}
@article{2308,
abstract = {It is widely believed that the inflammatory events mediated by microglial activation contribute to several neurodegenerative processes. Alzheimer's disease, for example, is characterized by an accumulation of β-amyloid protein (Aβ) in neuritic plaques that are infiltrated by reactive microglia and astrocytes. Although Aβ and its fragment 25-35 exert a direct toxic effect on neurons, they also activate microglia. Microglial activation is accompanied by morphological changes, cell proliferation, and release of various cytokines and growth factors. A number of scientific reports suggest that the increased proliferation of microglial cells is dependent on ionic membrane currents and in particular on chloride conductances. An unusual chloride ion channel known to be associated with macrophage activation is the chloride intracellular channel-1 (CLIC1). Here we show that Aβ stimulation of neonatal rat microglia specifically leads to the increase in CLIC1 protein and to the functional expression of CLIC1 chloride conductance, both barely detectable on the plasma membrane of quiescent cells. CLIC1 protein expression in microglia increases after 24 hr of incubation with Aβ, simultaneously with the production of reactive nitrogen intermediates and of tumor necrosis factor-α (TNF-α). We demonstrate that reducing CLIC1 chloride conductance by a specific blocker [IAA-94 (R(+)-[(6,7-dichloro-2-cyclopentyl-2,3-dihydro-2-methyl-1-oxo-1H-inden-5yl)-oxy] acetic acid)] prevents neuronal apoptosis in neurons cocultured with Aβ-treated microglia. Furthermore, we show that small interfering RNAs used to knock down CLIC1 expression prevent TNF-α release induced by Aβ stimulation. These results provide a direct link between Aβ-induced microglial activation and CLIC1 functional expression.},
author = {Gaia Novarino and Fabrizi, Cinzia and Tonini, Raffaella and Denti, Michela A and Malchiodi, Albedi F and Lauro, Giuliana M and Sacchetti, Benedetto and Paradisi, Silvia and Ferroni, Arnaldo and Curmi, Paul M G and Breit, Samuel N and Mazzanti, Michele},
journal = {Journal of Neuroscience},
number = {23},
pages = {5322 -- 5330},
publisher = {Society for Neuroscience},
title = {{Involvement of the intracellular ion channel CLIC1 in microglia-mediated β-amyloid-induced neurotoxicity}},
doi = {10.1523/JNEUROSCI.1170-04.2004},
volume = {24},
year = {2004},
}
@article{2355,
abstract = {The BMV conjecture for traces, which states that Tr exp(A - λB) is the Laplace transform of a positive measure, is shown to be equivalent to two other statements: (i) The polynomial λ → Tr(A + λB) p has only non-negative coefficients for all A, B ≥ 0, p ∈ ℕ and (ii) λ → Tr(A + λB)-p is the Laplace transform of a positive measure for A, B ≥ 0, p > 0.},
author = {Lieb, Élliott H and Robert Seiringer},
journal = {Journal of Statistical Physics},
number = {1-2},
pages = {185 -- 190},
publisher = {Springer},
title = {{ Equivalent forms of the Bessis-Moussa-Villani conjecture}},
doi = {10.1023/B:JOSS.0000019811.15510.27},
volume = {115},
year = {2004},
}
@article{2356,
abstract = {Recent experimental and theoretical work has shown that there are conditions in which a trapped, low-density Bose gas behaves like the one-dimensional delta-function Bose gas solved years ago by Lieb and Liniger. This is an intrinsically quantum-mechanical phenomenon because it is not necessary to have a trap width that is the size of an atom - as might have been supposed - but it suffices merely to have a trap width such that the energy gap for motion in the transverse direction is large compared to the energy associated with the motion along the trap. Up to now the theoretical arguments have been based on variational - perturbative ideas or numerical investigations. In contrast, this paper gives a rigorous proof of the one-dimensional behavior as far as the ground state energy and particle density are concerned. There are four parameters involved: the particle number, N, transverse and longitudinal dimensions of the trap, r and L, and the scattering length a of the interaction potential. Our main result is that if r/L → 0 and N → ∞ the ground state energy and density can be obtained by minimizing a one-dimensional density functional involving the Lieb-Liniger energy density with coupling constant ∼ a/r 2. This density functional simplifies in various limiting cases and we identify five asymptotic parameter regions altogether. Three of these, corresponding to the weak coupling regime, can also be obtained as limits of a three-dimensional Gross-Pitaevskii theory. We also show that Bose-Einstein condensation in the ground state persists in a part of this regime. In the strong coupling regime the longitudinal motion of the particles is strongly correlated. The Gross-Pitaevskii description is not valid in this regime and new mathematical methods come into play.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {347 -- 393},
publisher = {Springer},
title = {{One-dimensional behavior of dilute, trapped Bose gases}},
doi = {10.1007/s00220-003-0993-3},
volume = {244},
year = {2004},
}
@article{2360,
abstract = {An optical lattice model developed that is similar to the Bose-Hubbard model to describe the transition between Bose-Einstein condensation (BEC) and a Mott insulator state was analyzed. It was found that the system was a hard core lattice gas at half of the maximum density and the optical lattice was modeled by a periodic potential of strength λ. It was also observed that the interparticle interaction was essential for this transition that occurred even in the ground state. The results show that all the essential features could be proved rigorously such as the existence of BEC for small λ and its suppression for a large λ.},
author = {Aizenman, Michael and Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {2},
pages = {023612 -- 1--0236121--2},
publisher = {American Physical Society},
title = {{Bose-Einstein quantum phase transition in an optical lattice model}},
doi = {10.1103/PhysRevA.70.023612},
volume = {70},
year = {2004},
}
@inbook{2417,
author = {Lovász, László and Vesztergombi, Katalin and Uli Wagner and Welzl, Emo},
booktitle = {Towards a Theory of Geometric Graphs},
editor = {Pach, János},
pages = {139 -- 148},
publisher = {American Mathematical Society},
title = {{Convex quadrilaterals and k-sets }},
doi = {10.1090/conm/342},
volume = {342},
year = {2004},
}
@article{2425,
abstract = {A finite set N ⊂ Rd is a weak ε-net for an n-point set X ⊂ Rd (with respect to convex sets) if N intersects every convex set K with |K ∩ X| ≥ εn. We give an alternative, and arguably simpler, proof of the fact, first shown by Chazelle et al., that every point set X in Rd admits a weak ε-net of cardinality O(ε-dpolylog(1/ε)). Moreover, for a number of special point sets (e.g., for points on the moment curve), our method gives substantially better bounds. The construction yields an algorithm to construct such weak ε-nets in time O(n ln(1/ε)).},
author = {Matoušek, Jiří and Uli Wagner},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {195 -- 206},
publisher = {Springer},
title = {{New constructions of weak ε-nets}},
doi = {10.1007/s00454-004-1116-4},
volume = {32},
year = {2004},
}
@article{2426,
abstract = {We introduce the adaptive neighborhood graph as a data structure for modeling a smooth manifold M embedded in some Euclidean space ℝ d. We assume that M is known to us only through a finite sample P ⊂ M, as is often the case in applications. The adaptive neighborhood graph is a geometric graph on P. Its complexity is at most min{2O(k)n, n2}, where n = P and k = dim M, as opposed to the n[d/2] complexity of the Delaunay triangulation, which is often used to model manifolds. We prove that we can correctly infer the connected components and the dimension of M from the adaptive neighborhood graph provided a certain standard sampling condition is fulfilled. The running time of the dimension detection algorithm is d20(k7 log k) for each connected component of M. If the dimension is considered constant, this is a constant-time operation, and the adaptive neighborhood graph is of linear size. Moreover, the exponential dependence of the constants is only on the intrinsic dimension k, not on the ambient dimension d. This is of particular interest if the co-dimension is high, i.e., if k is much smaller than d, as is the case in many applications. The adaptive neighborhood graph also allows us to approximate the geodesic distances between the points in P.},
author = {Giesen, Joachim and Uli Wagner},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {245 -- 267},
publisher = {Springer},
title = {{Shape dimension and intrinsic metric from samples of manifolds}},
doi = {10.1007/s00454-004-1120-8},
volume = {32},
year = {2004},
}
@misc{2461,
author = {Sauer, Michael and Friml, Jirí},
booktitle = {Development},
number = {23},
pages = {5774 -- 5775},
publisher = {Company of Biologists},
title = {{The Matryoshka dolls of plant polarity}},
doi = {10.1242/dev.01463},
volume = {131},
year = {2004},
}
@article{7333,
abstract = {The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system.},
author = {Santis, M. and Schmid, D. and Ruge, M. and Freunberger, Stefan Alexander and Büchi, F.N.},
issn = {1615-6846},
journal = {Fuel Cells},
number = {3},
pages = {214--218},
publisher = {Wiley},
title = {{Modular stack-internal air humidification concept-verification in a 1 kW stack}},
doi = {10.1002/fuce.200400028},
volume = {4},
year = {2004},
}
@article{7334,
abstract = {Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. },
author = {Mantzaras, John and Freunberger, Stefan Alexander and Büchi, Felix N. and Roos, Markus and Brandstätter, Wilhelm and Prestat, Michel and Gauckler, Ludwig J. and Andreaus, Bernhard and Hajbolouri, Faegheh and Senn, Stephan M. and Poulikakos, Dimos and Chaniotis, Andreas K. and Larrain, Diego and Autissier, Nordahl and Maréchal, François},
issn = {0009-4293},
journal = {CHIMIA International Journal for Chemistry},
number = {12},
pages = {857--868},
publisher = {Swiss Chemical Society},
title = {{Fuel cell modeling and simulations}},
doi = {10.2533/000942904777677029},
volume = {58},
year = {2004},
}
@article{7706,
abstract = {The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance.},
author = {Brunet, Anne and Sweeney, Lora Beatrice Jaeger and Sturgill, J Fitzhugh and Chua, Katrin and Greer, Paul and Lin, Yingxi and Tran, Hien and Ross, Sarah and Mostoslavsky, Raul and Cohen, Haim and Hu, Linda and Chen, Hwei-Ling and Jedrychowski, Mark and Gygi, Steven and Sinclair, David and Alt, Frederick and Greenberg, Michael},
issn = {0036-8075},
journal = {Science},
number = {5666},
pages = {2011--2015},
publisher = {American Association for the Advancement of Science},
title = {{Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase}},
doi = {10.1126/science.1094637},
volume = {303},
year = {2004},
}
@article{3918,
abstract = {Wingless (ergatoid) males of the tramp ant Cardiocondyla minutior attack and kill their young ergatoid rivals and thus attempt to monopolize mating with female sexuals reared in the colony. Because of the different strength of local mate competition in colonies with one or several reproductive queens, we expected the production of new ergatoid males to vary with queen number. Sex ratios were mostly female-biased, but in contrast to the sympatric species C. obscurior (Cremer and Heinze, 2002) neither the percentage of ergatoid males nor of female sexuals among the first 20 sexuals produced varied considerably with queen number. As in C. obscurior, experimental colony fragmentation led to the production of winged males, whereas in unfragmented control colonies only ergatoid males eclosed.},
author = {Heinze, Jürgen and Böttcher, A. and Cremer, Sylvia},
journal = {Insectes Sociaux},
number = {3},
pages = {275 -- 278},
publisher = {Springer},
title = {{Production of winged and wingless males in the ant, Cardiocondyla minutior}},
doi = {10.1007/s00040-004-0740-6},
volume = {51},
year = {2004},
}
@article{3929,
abstract = {The Nef protein of human and simian immunodeficiency virus (HIV/SIV) is believed to interfere with T cell activation signals by forming a signaling complex at the plasma membrane. Composition and function of the complex are not fully understood. Here we report that Nef recruits the Polycomb Group (PcG) protein Eed, so far known as a nuclear factor and repressor of transcription, to the membrane of cells. The Nef-induced translocation of Eed led to a potent stimulation of Tat-dependent HIV transcription, implying that Eed removal from the nucleus is required for optimal Tat function. Similar to Nef action, activation of integrin receptors recruited Eed to the plasma membrane, also leading to enhanced Tat/Nef-mediated transcription. Our results suggest a link between membrane-associated activation processes and transcriptional derepression and demonstrate how HIV exploits this mechanism.},
author = {Witte, Vanessa and Laffert, Bernd and Rosorius, Olaf and Lischka, Peter and Blume, Katja and Galler, Gunther and Stilper, Andrea and Willbold, Dieter and D'Aloja, Paola and Michael Sixt and Kolanus, Johanna and Ott, Melanie and Kolanus, Waldemar and Schuler, Gerold and Baur, Andreas S},
journal = {Molecular Cell},
number = {2},
pages = {179 -- 190},
publisher = {Cell Press},
title = {{HIV-1 Nef mimics an integrin receptor signal that recruits the polycomb group protein Eed to the plasma membrane}},
doi = {10.1016/S1097-2765(04)00004-8},
volume = {13},
year = {2004},
}
@article{3931,
abstract = {Hyaluronan is an unsulfated glycosaminoglycan (GAG) that is ubiquitously expressed in the extracellular matrix (ECM) of all vertebrates, where hyaluronan rich matrices constitute a particular permissive environment for the development of complex biological structures and also for tumor progression. Because of its conserved structure and ubiquitous expression, antibodies for its histochemical detection cannot be produced. We have engineered a fusion protein, neurocan-GFP, and expressed it as a secreted molecule in mammalian cells. Neurocan-GFP fusion protein specifically binds to hyaluronan and directly visualizes hyaluronan on tissue sections, revealing a very detailed picture of hyaluronan distribution. The fluorescent fusion protein can be used in combination with antibodies and nuclear markers for double or triple staining. In addition, it is suitable to visualize hyaluronan on living cells by time-lapse video microscopy. The successful production and application of the neurocan-GFP fusion protein opens up new perspectives for using GFP fusion proteins as detection tools in histological and cytological studies complementing conventional antibody and biotin/avidin techniques.},
author = {Zhang, Hui and Baader, Stephan L and Michael Sixt and Kappler, Joachim and Rauch, Uwe},
journal = {Journal of Histochemistry and Cytochemistry},
number = {7},
pages = {915 -- 922},
publisher = {Histochemical Society},
title = {{Neurocan-GFP fusion protein: a new approach to detect hyaluronan on tissue sections and living cells}},
doi = {10.1369/jhc.3A6221.2004},
volume = {52},
year = {2004},
}
@article{3984,
abstract = {We combine topological and geometric methods to construct a multiresolution representation for a function over a two-dimensional domain. In a preprocessing stage, we create the Morse-Smale complex of the function and progressively simplify its topology by cancelling pairs of critical points. Based on a simple notion of dependency among these cancellations, we construct a hierarchical data structure supporting traversal and reconstruction operations similarly to traditional geometry-based representations. We use this data structure to extract topologically valid approximations that satisfy error bounds provided at runtime.},
author = {Bremer, Peer-Timo and Herbert Edelsbrunner and Hamann, Bernd and Pascucci, Valerio},
journal = {IEEE Transactions on Visualization and Computer Graphics},
number = {4},
pages = {385 -- 396},
publisher = {IEEE},
title = {{A topological hierarchy for functions on triangulated surfaces}},
doi = {10.1109/TVCG.2004.3},
volume = {10},
year = {2004},
}
@article{3985,
abstract = {Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.},
author = {Cole-McLaughlin, Kree and Herbert Edelsbrunner and Harer, John and Natarajan, Vijay and Pascucci, Valerio},
journal = {Discrete & Computational Geometry},
number = {2},
pages = {231 -- 244},
publisher = {Springer},
title = {{Loops in Reeb graphs of 2-manifolds}},
doi = {10.1007/s00454-004-1122-6},
volume = {32},
year = {2004},
}
@article{3986,
abstract = {The motion of a biomolecule greatly depends on the engulfing solution, which is mostly water. Instead of representing individual water molecules, it is desirable to develop implicit solvent models that nevertheless accurately represent the contribution of the solvent interaction to the motion. In such models, hydrophobicity is expressed as a weighted sum of atomic surface areas. The derivatives of these weighted areas contribute to the force that drives the motion. In this paper we give formulas for the weighted and unweighted area derivatives of a molecule modeled as a space-filling diagram made up of balls in motion. Other than the radii and the centers of the balls, the formulas are given in terms of the sizes of circular arcs of the boundary and edges of the power diagram. We also give inclusion-exclusion formulas for these sizes.},
author = {Bryant, Robert and Herbert Edelsbrunner and Koehl, Patrice and Levitt, Michael},
journal = {Discrete & Computational Geometry},
number = {3},
pages = {293 -- 308},
publisher = {Springer},
title = {{The area derivative of a space-filling diagram}},
doi = {10.1007/s00454-004-1099-1},
volume = {32},
year = {2004},
}
@article{3987,
abstract = {We consider scientific data sets that describe density functions over three-dimensional geometric domains. Such data sets are often large and coarsened representations are needed for visualization and analysis. Assuming a tetrahedral mesh representation, we construct such representations with a simplification algorithm that combines three goals: the approximation of the function, the preservation of the mesh topology, and the improvement of the mesh quality. The third goal is achieved with a novel extension of the well-known quadric error metric. We perform a number of computational experiments to understand the effect of mesh quality improvement on the density map approximation. In addition, we study the effect of geometric simplification on the topological features of the function by monitoring its critical points.},
author = {Natarajan, Vijay and Herbert Edelsbrunner},
journal = {IEEE Transactions on Visualization and Computer Graphics},
number = {5},
pages = {587 -- 597},
publisher = {IEEE},
title = {{Simplification of three-dimensional density maps}},
doi = {10.1109/TVCG.2004.32},
volume = {10},
year = {2004},
}