The Viral Macrodomain Counters Host Antiviral ADP-Ribosylation

This work is licensed under a Creative Commons Attribution 4.0 International License.Macrodomains, enzymes that remove ADP-ribose from proteins, are encoded by several families of RNA viruses and have recently been shown to counter innate immune responses to virus infection. ADP-ribose is covalently attached to target proteins by poly-ADP-ribose polymerases (PARPs), using nicotinamide adenine dinucleotide (NAD+) as a substrate. This modification can have a wide variety of effects on proteins including alteration of enzyme activity, protein–protein interactions, and protein stability. Several PARPs are induced by interferon (IFN) and are known to have antiviral properties, implicating ADP-ribosylation in the host defense response and suggesting that viral macrodomains may counter this response. Recent studies have demonstrated that viral macrodomains do counter the innate immune response by interfering with PARP-mediated antiviral defenses, stress granule formation, and pro-inflammatory cytokine production. Here, we will describe the known functions of the viral macrodomains and review recent literature demonstrating their roles in countering PARP-mediated antiviral responses

Numerical Methods for Electronic Structure Calculations of Materials

This is the published version. Copyright 2010 Society for Industrial and Applied MathematicsThe goal of this article is to give an overview of numerical problems encountered when determining the electronic structure of materials and the rich variety of techniques used to solve these problems. The paper is intended for a diverse scientific computing audience. For this reason, we assume the reader does not have an extensive background in the related physics. Our overview focuses on the nature of the numerical problems to be solved, their origin, and the methods used to solve the resulting linear algebra or nonlinear optimization problems. It is common knowledge that the behavior of matter at the nanoscale is, in principle, entirely determined by the Schrödinger equation. In practice, this equation in its original form is not tractable. Successful but approximate versions of this equation, which allow one to study nontrivial systems, took about five or six decades to develop. In particular, the last two decades saw a flurry of activity in developing effective software. One of the main practical variants of the Schrödinger equation is based on what is referred to as density functional theory (DFT). The combination of DFT with pseudopotentials allows one to obtain in an efficient way the ground state configuration for many materials. This article will emphasize pseudopotential-density functional theory, but other techniques will be discussed as well

The Comparative Study of Biaxial Bending Analysis of Steel Sections Using AISC and Eurocode Approaches

ABSTRACT This study investigates the capacity of the steel section using both AISC and Eurocode approaches by Robot Structure Analysis software. Three types of steel sections were subject to biaxial bending by applying loads to both main axes and examined by both approaches. The concept of Fisher was also adopted as an approach. The findings suggested that the Eurocode approach is more conservative in the design of steel sections subject to biaxial bending as it takes into account the level at which the load is applied, the type of the section whether rolled or welded and its height-to-width ratio (lateral buckling effect), the effects which are not considered in AISC approach. The AISC approach considers the shear center of the section as the level at which the loads are applied. The conservatism of the results was more pronounced when the section is close to H-section. Fisher`s concept of structural design of biaxial bending of structural steel is more conservative than both AISC and Eurocode approaches of analysis

Beneficiation of some Egyptian Glass Sands

The attrition-scrubbing of some Egyptian glass sands was necessary for the disintegration of the ferruginous clayey coating on quartz grains. The effects of time of attrition-ing, impeller speed and solid/liquid ration were investi-gated. Classification of the scrubbed sands resulted in the removal of a slimy fraction and yielded a product having 0.065% Fe. Acid attritioning of sand with commer-cial HCL at room temperature did not affect the iron, coat-ing quartz particles

Parallel Self-Consistent-Field Calculations via Chebyshev-Filtered Subspace Acceleration

Solving the Kohn-Sham eigenvalue problem constitutes the most computationally expensive part in self-consistent density functional theory (DFT) calculations. In a previous paper, we have proposed a nonlinear Chebyshev-filtered subspace iteration method, which avoids computing explicit eigenvectors except at the first SCF iteration. The method may be viewed as an approach to solve the original nonlinear Kohn-Sham equation by a nonlinear subspace iteration technique, without emphasizing the intermediate linearized Kohn-Sham eigenvalue problem. It reaches self-consistency within a similar number of SCF iterations as eigensolver-based approaches. However, replacing the standard diagonalization at each SCF iteration by a Chebyshev subspace filtering step results in a significant speedup over methods based on standard diagonalization. Here, we discuss an approach for implementing this method in multi-processor, parallel environment. Numerical results are presented to show that the method enables to perform a class of highly challenging DFT calculations that were not feasible before

The Coincidence Problem in Holographic f(R) Gravity

It is well-known that $f(R)$ gravity models formulated in Einstein conformal frame are equivalent to Einstein gravity together with a minimally coupled scalar field. In this case, the scalar field couples with the matter sector and the coupling term is given by the conformal factor. We apply the holographic principle to such interacting models. In a spatially flat universe, we show that the Einstein frame representation of $f(R)$ models leads to a constant ratio of energy densities of dark matter to dark energy.Comment: 10 pages, no figure

Transport Properties in Ferromagnetic Josephson Junction between Triplet Superconductors

Charge and spin Josephson currents in a ballistic superconductor-ferromagnet-superconductor junction with spin-triplet pairing symmetry are studied using the quasiclassical Eilenberger equation. The gap vector of superconductors has an arbitrary relative angle with respect to magnetization of the ferromagnetic layer. We clarify the effects of the thickness of ferromagnetic layer and magnitude of the magnetization on the Josephson charge and spin currents. We find that 0-\pi transition can occur except for the case that the exchange field and d-vector are in nearly perpendicular configuration. We also show how spin current flows due to misorientation between the exchange field and d-vector.Comment: 6 pages, 8 figure

Anterior Ocular Biometrics as Measured by Ultrasound Biomicroscopy

Background: High frequency ultrasonography (ultrasound biomicroscopy; UBM) is an ophthalmic diagnostic tool that can be used to measure the depth of the anterior segment (ASD), the anterior chamber angle (ACA), as well as thicknesses of the iris and the ciliary body (CB). Methods: The anterior segment dimensions and thicknesses were measured by Sonomed 35-MHz. Results: Measurements for 95 eyes from 52 adults were analyzed. The mean and median ASD and ACA were 2.91, 2.92 ± 0.41 mm and 34.1, 34.3 ± 12.1 degrees, respectively. The angle superiorly was wider than inferiorly (p = 0.04). At the root of the iris, the mid of the iris, and the juxtapupillary edge of the iris, the iris thicknesses (median, mean) were 0.40, 0.41 ± 0.1, 0.50, 0.51 ± 0.1, and 0.70, 0.71 ± 0.1 mm, respectively. The thicknesses of CB and CB together with the ciliary processes (median, mean), were 0.70, 0.71 ± 0.15 mm and 1.36, 1.41 ± 0.15 mm, respectively. The upper quadrant of both the iris and the CB was significantly thicker than the lower quadrant (p = 0.04). Conclusions: Our biometric measurements for the anterior segment can be used as normative data for anterior segment depth and angle and iris and ciliary body thickness in normal eyes

Poultry and Beef Meat as Potential Seedbeds for Antimicrobial Resistant Enterotoxigenic Bacillus Species: A Materializing Epidemiological and Potential Severe Health Hazard

Although Bacillus cereus is of particular concern in food safety and public health, the role of other Bacillus species was overlooked. Therefore, we investigated the presence of eight enterotoxigenic genes, a hemolytic gene and phenotypic antibiotic resistance profiles of Bacillusspecies in retail meat samples. From 255 samples, 124 Bacillus isolates were recovered, 27 belonged to B. cereusand 97 were non-B. cereus species. Interestingly, the non-B. cereus isolates carried the virulence genes and exhibited phenotypic virulence characteristics as the B. cereus. However, correlation matrix analysis revealed the B. cereus group positively correlates with the presence of the genes hblA, hblC, and plc, and the detection of hemolysis (p \u3c 0.05), while the other Bacillus sp. groups are negatively correlated. Tests for antimicrobial resistance against ten antibiotics revealed extensive drug and multi-drug resistant isolates. Statistical analyses didn’t support a correlation of antibiotic resistance to tested virulence factors suggesting independence of these phenotypic markers and virulence genes. Of special interest was the isolation of Paenibacillus alvei and Geobacillus stearothermophilus from the imported meat samples being the first recorded. The isolation of non-B. cereus species carrying enterotoxigenic genes in meat within Egypt, suggests their impact on food safety and public health and should therefore not be minimised, posing an area that requires further research