Transparent Fault-tolerance in Parallel Orca Programs

With the advent of large-scale parallel computing systems, making parallel programs fault-tolerant becomes an important problem, because the probability of a failure increases with the number of processors. In this paper, we describe a very simple scheme for rendering a class of parallel Orca programs fault-tolerant. Also, we discuss our experience with implementing this scheme on Amoeba. Our approach works for parallel applications that are not interactive. The approach is based on making a globally consistent checkpoint from time to time and rolling back to the last checkpoint when a processor fails. Making a consistent global checkpoint is easy in Orca, because its implementation is based on reliable broadcast. The advantages of our approach are its simplicity, ease of implementation, low overhead, and transparency to the Orca programmer. 1

Computing singularities of perturbation series

Many properties of current \emph{ab initio} approaches to the quantum many-body problem, both perturbational or otherwise, are related to the singularity structure of Rayleigh--Schr\"odinger perturbation theory. A numerical procedure is presented that in principle computes the complete set of singularities, including the dominant singularity which limits the radius of convergence. The method approximates the singularities as eigenvalues of a certain generalized eigenvalue equation which is solved using iterative techniques. It relies on computation of the action of the perturbed Hamiltonian on a vector, and does not rely on the terms in the perturbation series. Some illustrative model problems are studied, including a Helium-like model with $\delta$-function interactions for which M{\o}ller--Plesset perturbation theory is considered and the radius of convergence found.Comment: 11 figures, submitte

A novel mechanism of RNase L inhibition: Theiler\u27s virus L* protein prevents 2-5A from binding to RNase L

<div><p>The OAS/RNase L pathway is one of the best-characterized effector pathways of the IFN antiviral response. It inhibits the replication of many viruses and ultimately promotes apoptosis of infected cells, contributing to the control of virus spread. However, viruses have evolved a range of escape strategies that act against different steps in the pathway. Here we unraveled a novel escape strategy involving Theiler’s murine encephalomyelitis virus (TMEV) L* protein. Previously we found that L* was the first viral protein binding directly RNase L. Our current data show that L* binds the ankyrin repeats R1 and R2 of RNase L and inhibits 2’-5’ oligoadenylates (2-5A) binding to RNase L. Thereby, L* prevents dimerization and oligomerization of RNase L in response to 2-5A. Using chimeric mouse hepatitis virus (MHV) expressing TMEV L*, we showed that L* efficiently inhibits RNase L <i>in vivo</i>. Interestingly, those data show that L* can functionally substitute for the MHV-encoded phosphodiesterase ns2, which acts upstream of L* in the OAS/RNase L pathway, by degrading 2-5A.</p></div

Theoretical Considerations on the Effect of Ion Formation Conditions on the Transmission Through a Laser Microprobe Mass Analyzer

A theoretical study on the ion transmission through the laser microprobe mass analyzer LAMMA 500 was made using ray-tracing computer programs. The calculations reveal that the ion transmission is strongly affected by the initial conditions of ion formation. Chromatic and spherical aberrations give rise to considerable discrimination in the univoltage lens. A correlation is attempted between measured and theoretical transmission curves. For the latter a physically plausible plasma model was initially assumed to generate the input parameters, i.e., locus of ion formation and angular and energy distributions of the ions (atomic and cluster ions). The model needs correction for aberration and space-charge effects : comparison of experimental and calculated ion transmission curves suggests, indeed, a more important contribution of particles with high energy and emitted under large angles, than initially assumed

Inhibition of HIV virus by neutralizing Vhh attached to dual functional liposomes encapsulating dapivirine

Although highly active antiretroviral therapy (HAART) has greatly improved the life expectancy of HIV/AIDS patients, the treatment is not curative. It is a global challenge which fosters an urgent need to develop an effective drug or neutralizing antibody delivery approach for the prevention and treatment of this disease. Due to the low density of envelope spikes with restricted mobility present on the surface of HIV virus, which limit the antibody potency and allow virus mutation and escape from the immune system, it is important for a neutralizing antibody to form bivalent or multivalent bonds with the virus. Liposome constructs could fulfil this need due to the flexible mobility of the membrane with its attached antibodies and the capacity for drug encapsulation. In this study, we evaluated the neutralization activity of a range of liposome formulations in different sizes coated with anti-gp120 llama antibody fragments (Vhhs) conjugated via either non-covalent metal chelation or a covalent linkage. The non-covalent construct demonstrated identical binding affinity to HIV-1 envelope glycoprotein gp120 and neutralizing ability for HIV virus as free Vhh. Although covalently linked Vhh showed significant binding affinity to gp120, it unexpectedly had a lower neutralization potency. This may be due to the comparability in size of the viral and liposome particles restricting the number which can be bound to the liposome surface so involving only a fraction of the antibodies, whereas non-covalently attached antibodies dissociate from the surface after acting with gp120 and free the remainder to bind further viruses. Covalently conjugated Vhh might also trigger the cellular uptake of a liposome-virion complex. To explore the possible ability of the antibody-coated liposomes to have a further function, we encapsulated the hydrophobic antiviral drug dapivirine into both of the non-covalently and covalently conjugated liposome formulations, both of which revealed high efficacy in reducing viral replication in vitro. Thus, dual function liposomes may lead to a novel strategy for the prophylaxis of HIV/AIDS by combining the neutralizing activity of Vhh with antiviral effects of high drug concentrations

Variação da condutividade hidráulica do solo não saturado determinada em condições de campo utilizando análises simplificadas de experimentos de drenagem interna

Experimentally determined values of unsaturated soil hydraulic conductivity are presented for an Alfisol of the county of Piracicaba, S.P., Brazil. Simultaneous measurements of soil water content and pressure head are made along a 125 m transect within an irrigated field during the internal drainage process. Calculations of the soil hydraulic conductivity were made using the instantaneous profile method (Watson, 1966) and the unit gradient method (LIBARDI et al., 1980). The spatial variability of the soil hydraulic conductivity manifested along the transect indicates the need to develop a field method to measure K(theta) within prescribed fiducial limits, taking into account quantitative evaluation of spatial and temporal variances associated with the mathematical model, instrument calibration and soil properties.São apresentados dados experimentais de condutividade hidráulica do solo, para uní Alfisol (terra roxa estruturada) do Município de Piracicaba,SP - Brasil. Medidas simultâneas de umidade do solo e de potencial total da água no solo foram realizadas ao longo de uma transeção de 125 m, dentro de um campo irrigado, durante o processo de drenagem interna. Os cálculos de condutividade hidráulica foram feitos utilizando o método do perfil instantâneo (WATSON, 1966) e o método do gradiente unitário (LIBARDI et al., 1980). A variabilidade espacial da condutividade hidráulica do solo observada ao longo da transeção aponta a necessidade do desenvolvimento de método de campo para a medida de K (teta) dentro de limites preestabelecidos de precisão, levando em conta a medida quantitativa das variâncias temporal e espacial associadas ao modelo matemático, a calibração dos instrumentos e as propriedades do solo

The Escherichia coli RnlA–RnlB toxin–antitoxin complex: production, characterization and crystallization

The Escherichia coli rnlAB operon encodes a toxin–antitoxin module that is involved in protection against infection by bacteriophage T4. The full-length RnlA–RnlB toxin–antitoxin complex as well as the toxin RnlA were purified to homogeneity and crystallized. When the affinity tag is placed on RnlA, RnlB is largely lost during purification and the resulting crystals exclusively comprise RnlA. A homogeneous preparation of RnlA–RnlB containing stoichiometric amounts of both proteins could only be obtained using a His tag placed C-terminal to RnlB. Native mass spectrometry and SAXS indicate a 1:1 stoichiometry for this RnlA–RnlB complex. Crystals of the RnlA–RnlB complex belonged to space group C2, with unit-cell parameters a = 243.32, b = 133.58, c = 55.64 Å, β = 95.11°, and diffracted to 2.6 Å resolution. The presence of both proteins in the crystals was confirmed and the asymmetric unit is likely to contain a heterotetramer with RnlA2:RnlB2 stoichiometry