Simulation of gamma-ray spectra for a variety of user-specified detector designs

The gamma-ray spectrum simulation program BSIMUL was designed to allow the operator to follow the path of a gamma-ray through a detector, shield and collimator whose dimensions are entered by the operator. It can also be used to simulate spectra that would be generated by a detector. Several improvements have been made to the program within the last few months. The detector, shield and collimator dimensions can now be entered through an interactive menu whose options are discussed below. In addition, spectra containing more than one gamma-ray energy can now be generated with the menu - for isotopes listed in the program. Adding isotopes to the main routine is also quite easy. Subroutines have been added to enable the operator to specify the material and dimensions of a collimator. This report details the progress made in simulating gamma-ray spectra for a variety of user-specified detector designs. In addition, a short discussion of work done in the related areas of pulse shape analysis and the spectral analysis is included. The pulse shape analysis and spectral analysis work is being performed pursuant to the requirements of contract F-94-C-0006, for the Advanced Research Projects Agency and the U.S. Air Force

Progress report for the Monte-Carlo gamma-ray spectrum simulation program BSIMUL

The progress made during 1995 on the Monte-Carlo gamma-ray spectrum simulation program BSIMUL is discussed. Several features have been added, including the ability to model shields that are tapered cylinders. Several simulations were made on the Near Earth Asteroid Rendezvous detector

Simulation of the Interactions Between Gamma-Rays and Detectors Using BSIMUL

Progress made during 1995 on the Monte-Carlo gamma-ray spectrum simulation program BSIMUL is discussed. Several features have been added, including the ability to model shield that are tapered cylinders. Several simulations were made on the Near Earth Asteroid Rendezvous detector

A Kernel for Open Source Drug Discovery in Tropical Diseases

Open source drug discovery, a promising alternative avenue to conventional patent-based drug development, has so far remained elusive with few exceptions. A major stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. This paper introduces the results from a newly assembled computational pipeline for identifying protein targets for drug discovery in ten organisms that cause tropical diseases. We have also experimentally tested two promising targets for their binding to commercially available drugs, validating one and invalidating the other. The resulting kernel provides a base of drug targets and lead candidates around which an open source community can nucleate. We invite readers to donate their judgment and in silico and in vitro experiments to develop these targets to the point where drug optimization can begin

A Network-Based Multi-Target Computational Estimation Scheme for Anticoagulant Activities of Compounds

BACKGROUND: Traditional virtual screening method pays more attention on predicted binding affinity between drug molecule and target related to a certain disease instead of phenotypic data of drug molecule against disease system, as is often less effective on discovery of the drug which is used to treat many types of complex diseases. Virtual screening against a complex disease by general network estimation has become feasible with the development of network biology and system biology. More effective methods of computational estimation for the whole efficacy of a compound in a complex disease system are needed, given the distinct weightiness of the different target in a biological process and the standpoint that partial inhibition of several targets can be more efficient than the complete inhibition of a single target. METHODOLOGY: We developed a novel approach by integrating the affinity predictions from multi-target docking studies with biological network efficiency analysis to estimate the anticoagulant activities of compounds. From results of network efficiency calculation for human clotting cascade, factor Xa and thrombin were identified as the two most fragile enzymes, while the catalytic reaction mediated by complex IXa:VIIIa and the formation of the complex VIIIa:IXa were recognized as the two most fragile biological matter in the human clotting cascade system. Furthermore, the method which combined network efficiency with molecular docking scores was applied to estimate the anticoagulant activities of a serial of argatroban intermediates and eight natural products respectively. The better correlation (r = 0.671) between the experimental data and the decrease of the network deficiency suggests that the approach could be a promising computational systems biology tool to aid identification of anticoagulant activities of compounds in drug discovery. CONCLUSIONS: This article proposes a network-based multi-target computational estimation method for anticoagulant activities of compounds by combining network efficiency analysis with scoring function from molecular docking

Indentation Hardness Measurements at Macro-, Micro-, and Nanoscale: A Critical Overview

The Brinell, Vickers, Meyer, Rockwell, Shore, IHRD, Knoop, Buchholz, and nanoindentation methods used to measure the indentation hardness of materials at different scales are compared, and main issues and misconceptions in the understanding of these methods are comprehensively reviewed and discussed. Basic equations and parameters employed to calculate hardness are clearly explained, and the different international standards for each method are summarized. The limits for each scale are explored, and the different forms to calculate hardness in each method are compared and established. The influence of elasticity and plasticity of the material in each measurement method is reviewed, and the impact of the surface deformation around the indenter on hardness values is examined. The difficulties for practical conversions of hardness values measured by different methods are explained. Finally, main issues in the hardness interpretation at different scales are carefully discussed, like the influence of grain size in polycrystalline materials, indentation size effects at micro-and nanoscale, and the effect of the substrate when calculating thin films hardness. The paper improves the understanding of what hardness means and what hardness measurements imply at different scales.Funding Agencies|Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University ((Faculty Grant SFO Mat LiU) [2009 00971]</p

Genome-Wide Identification and Immune Response Analysis of Serine Protease Inhibitor Genes in the Silkworm, Bombyx mori

In most insect species, a variety of serine protease inhibitors (SPIs) have been found in multiple tissues, including integument, gonad, salivary gland, and hemolymph, and are required for preventing unwanted proteolysis. These SPIs belong to different families and have distinct inhibitory mechanisms. Herein, we predicted and characterized potential SPI genes based on the genome sequences of silkworm, Bombyx mori. As a result, a total of eighty SPI genes were identified in B. mori. These SPI genes contain 10 kinds of SPI domains, including serpin, Kunitz_BPTI, Kazal, TIL, amfpi, Bowman-Birk, Antistasin, WAP, Pacifastin, and alpha-macroglobulin. Sixty-three SPIs contain single SPI domain while the others have at least two inhibitor units. Some SPIs also contain non-inhibitor domains for protein-protein interactions, including EGF, ADAM_spacer, spondin_N, reeler, TSP_1 and other modules. Microarray analysis showed that fourteen SPI genes from lineage-specific TIL family and Group F of serpin family had enriched expression in the silk gland. The roles of SPIs in resisting pathogens were investigated in silkworms when they were infected by four pathogens. Microarray and qRT-PCR experiments revealed obvious up-regulation of 8, 4, 3 and 3 SPI genes after infection with Escherichia coli, Bacillus bombysepticus, Beauveria bassiana or B. mori nuclear polyhedrosis virus (BmNPV), respectively. On the contrary, 4, 11, 7 and 9 SPI genes were down-regulated after infection with E. coli, B. bombysepticus, B. bassiana or BmNPV, respectively. These results suggested that these SPI genes may be involved in resistance to pathogenic microorganisms. These findings may provide valuable information for further clarifying the roles of SPIs in the development, immune defence, and efficient synthesis of silk gland protein