Adjacency Matrices of Configuration Graphs

In 1960, Hoffman and Singleton \cite{HS60} solved a celebrated equation for square matrices of order $n$, which can be written as $$(\kappa - 1) I_n + J_n - A A^{\rm T} = A$$ where $I_n$, $J_n$, and $A$ are the identity matrix, the all one matrix, and a $(0,1)$--matrix with all row and column sums equal to $\kappa$, respectively. If $A$ is an incidence matrix of some configuration $\cal C$ of type $n_\kappa$, then the left-hand side $\Theta(A):= (\kappa - 1)I_n + J_n - A A^{\rm T}$ is an adjacency matrix of the non--collinearity graph $\Gamma$ of $\cal C$. In certain situations, $\Theta(A)$ is also an incidence matrix of some $n_\kappa$ configuration, namely the neighbourhood geometry of $\Gamma$ introduced by Lef\`evre-Percsy, Percsy, and Leemans \cite{LPPL}. The matrix operator $\Theta$ can be reiterated and we pose the problem of solving the generalised Hoffman--Singleton equation $\Theta^m(A)=A$. In particular, we classify all $(0,1)$--matrices $M$ with all row and column sums equal to $\kappa$, for $\kappa = 3,4$, which are solutions of this equation. As a by--product, we obtain characterisations for incidence matrices of the configuration $10_3F$ in Kantor's list \cite{Kantor} and the $17_4$ configuration #1971 in Betten and Betten's list \cite{BB99}

Beyond XSPEC: Towards Highly Configurable Analysis

We present a quantitative comparison between software features of the defacto standard X-ray spectral analysis tool, XSPEC, and ISIS, the Interactive Spectral Interpretation System. Our emphasis is on customized analysis, with ISIS offered as a strong example of configurable software. While noting that XSPEC has been of immense value to astronomers, and that its scientific core is moderately extensible--most commonly via the inclusion of user contributed "local models"--we identify a series of limitations with its use beyond conventional spectral modeling. We argue that from the viewpoint of the astronomical user, the XSPEC internal structure presents a Black Box Problem, with many of its important features hidden from the top-level interface, thus discouraging user customization. Drawing from examples in custom modeling, numerical analysis, parallel computation, visualization, data management, and automated code generation, we show how a numerically scriptable, modular, and extensible analysis platform such as ISIS facilitates many forms of advanced astrophysical inquiry.Comment: Accepted by PASP, for July 2008 (15 pages

Sis1 potentiates the stress response to protein aggregation and elevated temperature

Cells adapt to conditions that compromise protein conformational stability by activating various stress response pathways, but the mechanisms used in sensing misfolded proteins remain unclear. Moreover, aggregates of disease proteins often fail to induce a productive stress response. Here, using a yeast model of polyQ protein aggregation, we identified Sis1, an essential Hsp40 co-chaperone of Hsp70, as a critical sensor of proteotoxic stress. At elevated levels, Sis1 prevented the formation of dense polyQ inclusions and directed soluble polyQ oligomers towards the formation of permeable condensates. Hsp70 accumulated in a liquid-like state within this polyQ meshwork, resulting in a potent activation of the HSF1 dependent stress response. Sis1, and the homologous DnaJB6 in mammalian cells, also regulated the magnitude of the cellular heat stress response, suggesting a general role in sensing protein misfolding. Sis1/DnaJB6 functions as a limiting regulator to enable a dynamic stress response and avoid hypersensitivity to environmental changes. Identifying factors that enable cells to induce a potent stress response to amyloid-like aggregation can provide further insight into the mechanism of stress regulation. Here, the authors express polyglutamine-expanded Huntingtin as a model disease protein in yeast cells and perform a genetic screen for chaperone factors that allow yeast cells to activate a potent stress response. They identify Sis1, an essential Hsp40 co-chaperone of Hsp70, as a critical sensor of proteotoxic stress and further show that both Sis1 and its mammalian homolog DnaJB6 regulate the magnitude of the cellular heat stress response, indicating that this mechanism is conserved.FRAP experiments were performed at the Max Planck Institute of Biochemistry Imaging Core Facility

Quantum Monte Carlo Study of Strongly Correlated Electrons: Cellular Dynamical Mean-Field Theory

We study the Hubbard model using the Cellular Dynamical Mean-Field Theory (CDMFT) with quantum Monte Carlo (QMC) simulations. We present the algorithmic details of CDMFT with the Hirsch-Fye QMC method for the solution of the self-consistently embedded quantum cluster problem. We use the one- and two-dimensional half-filled Hubbard model to gauge the performance of CDMFT+QMC particularly for small clusters by comparing with the exact results and also with other quantum cluster methods. We calculate single-particle Green's functions and self-energies on small clusters to study their size dependence in one- and two-dimensions.Comment: 14 pages, 18 figure

Grid generation for time dependent problems: Criteria and methods

The problem of generating local mesh refinements when solving time dependent partial differential equations was examined. The problem of creating an appropriate grid, given a mesh function h defined over the spatial domain is discussed. A data structure which permits efficient use of the resulting grid is described. A good choice for h is an estimate of the local truncation error, and several ways to estimate it are discussed. The efficiency and implementation problems of these error estimates were compared

Therapie bei Progression und Rezidiv des Ovarialkarzinoms

Secondary surgery after failure of primary treatment is a promising and reasonable option only for patients with a relapse-free interval of at least 6-12 months who should have ideally achieved a tumor-free status after primary therapy. As after primary surgery, size of residual tumor is the most significant predictor of survival after secondary surgery. Even in the case of multiple tumor sites, complete removal of the tumor can be achieved in nearly 30% of the patients. Treatment results are much better in specialized oncology centers with optimal interdisciplinary cooperation compared with smaller institutions. Chemotherapy can be used both for consolidation after successful secondary surgery and for palliation in patients with inoperable recurrent disease. Since paclitaxel has been integrated into first-line chemotherapy, there is no defined standard for second-line chemotherapy. Several cytotoxic agents have shown moderate activity in this setting, including treosulfan, epirubicin, and newer agents such as topotecan, gemcitabine, vinorelbine, and PEG(polyethylene glycol)-liposomal doxorubicin. Thus, the German Arbeitsgemeinschaft Gynakologische Onkologie (AGO) has initiated several randomized studies in patients with recurrent ovarian cancer in order to define new standards for second-line chemotherapy

Formation of toxic oligomers of polyQ-expanded Huntingtin by prion-mediated cross-seeding

Manifestation of aggregate pathology in Huntington's disease is thought to be facilitated by a preferential vulnerability of affected brain cells to age-dependent proteostatic decline. To understand how specific cellular backgrounds may facilitate pathologic aggregation, we utilized the yeast model in which polyQ-expanded Huntingtin forms aggregates only when the endogenous prion-forming protein Rnq1 is in its amyloid-like prion [PIN+] conformation. We employed optogenetic clustering of polyQ protein as an orthog-onal method to induce polyQ aggregation in prion-free [pin-] cells. Optogenetic aggregation circumvented the prion requirement for the formation of detergent-resistant polyQ inclusions but bypassed the formation of toxic polyQ oligomers, which accumulated specifically in [PIN+] cells. Reconstitution of aggregation in vitro suggested that these polyQ oligomers formed through direct templating on Rnq1 prions. These findings shed light on the mechanism of prion-mediated formation of oligomers, which may play a role in triggering polyQ pathology in the patient brain

An agent-based approach to immune modelling

This study focuses on trying to understand why the range of experience with respect to HIV infection is so diverse, especially as regards to the latency period. The challenge is to determine what assumptions can be made about the nature of the experience of antigenic invasion and diversity that can be modelled, tested and argued plausibly. To investigate this, an agent-based approach is used to extract high-level behaviour which cannot be described analytically from the set of interaction rules at the cellular level. A prototype model encompasses local variation in baseline properties contributing to the individual disease experience and is included in a network which mimics the chain of lymphatic nodes. Dealing with massively multi-agent systems requires major computational efforts. However, parallelisation methods are a natural consequence and advantage of the multi-agent approach. These are implemented using the MPI library

Breakup of the aligned H2_2 molecule by xuv laser pulses: A time-dependent treatment in prolate spheroidal coordinates

We have carried out calculations of the triple-differential cross section for one-photon double ionization of molecular hydrogen for a central photon energy of $75$~eV, using a fully {\it ab initio}, nonperturbative approach to solve the time-dependent \Schro equation in prolate spheroidal coordinates. The spatial coordinates $\xi$ and $\eta$ are discretized in a finite-element discrete-variable representation. The wave packet of the laser-driven two-electron system is propagated in time through an effective short iterative Lanczos method to simulate the double ionization of the hydrogen molecule. For both symmetric and asymmetric energy sharing, the present results agree to a satisfactory level with most earlier predictions for the absolute magnitude and the shape of the angular distributions. A notable exception, however, concerns the predictions of the recent time-independent calculations based on the exterior complex scaling method in prolate spheroidal coordinates [Phys.~Rev.~A~{\bf 82}, 023423 (2010)]. Extensive tests of the numerical implementation were performed, including the effect of truncating the Neumann expansion for the dielectronic interaction on the description of the initial bound state and the predicted cross sections. We observe that the dominant escape mode of the two photoelectrons dramatically depends upon the energy sharing. In the parallel geometry, when the ejected electrons are collected along the direction of the laser polarization axis, back-to-back escape is the dominant channel for strongly asymmetric energy sharing, while it is completely forbidden if the two electrons share the excess energy equally.Comment: 17 pages, 9 figure