Efficient hydrolysis of raw starch and ethanol fermentation: a novel raw starch-digesting glucoamylase from Penicillium oxalicum

Additional file 3: Figure S2. SDS-PAGE analysis of the recombinant rPoGA15A and native PoGA15A. Lane 1, protein molecular weight marker; lane 2, the purified recombinant rPoGA15A; lane 3, the native PoGA15A

Achieving Covert Communication With A Probabilistic Jamming Strategy

In this work, we consider a covert communication scenario, where a transmitter Alice communicates to a receiver Bob with the aid of a probabilistic and uninformed jammer against an adversary warden's detection. The transmission status and power of the jammer are random and follow some priori probabilities. We first analyze the warden's detection performance as a function of the jammer's transmission probability, transmit power distribution, and Alice's transmit power. We then maximize the covert throughput from Alice to Bob subject to a covertness constraint, by designing the covert communication strategies from three different perspectives: Alice's perspective, the jammer's perspective, and the global perspective. Our analysis reveals that the minimum jamming power should not always be zero in the probabilistic jamming strategy, which is different from that in the continuous jamming strategy presented in the literature. In addition, we prove that the minimum jamming power should be the same as Alice's covert transmit power, depending on the covertness and average jamming power constraints. Furthermore, our results show that the probabilistic jamming can outperform the continuous jamming in terms of achieving a higher covert throughput under the same covertness and average jamming power constraints

3D Structure Determination of an Unstable Transient Enzyme Intermediate by Paramagnetic NMR Spectroscopy

Enzyme catalysis relies on conformational plasticity, but structural information on transient intermediates is difficult to obtain. We show that the three-dimensional (3D) structure of an unstable, low-abundance enzymatic intermediate can be determined by nuclear magnetic resonance (NMR) spectroscopy. The approach is demonstrated for Staphylococcus aureus sortase A (SrtA), which is an established drug target and biotechnological reagent. SrtA is a transpeptidase that converts an amide bond of a substrate peptide into a thioester. By measuring pseudocontact shifts (PCSs) generated by a site-specific cysteine-reactive paramagnetic tag that does not react with the active-site residue Cys184, a sufficient number of restraints were collected to determine the 3D structure of the unstable thioester intermediate of SrtA that is present only as a minor species under non-equilibrium conditions. The 3D structure reveals structural changes that protect the thioester intermediate against hydrolysis

Isolation, Identification and Determination of Six Nucleosides and Two Amino Acids from Bamboo Shoots of Gramineae Phyllostachys prominens (W Y Xiong)

Purpose: To develop a method to identify and quantify the compounds in the shoots of four Phyllostachys bamboo species (Gramineae Phyllostachys prominens W. Y. Xiong, Gramineae Phyllostachys iridescins C. Y. Yao Gramineae Phyllostachys pubescens (Carr.) Mitford, Gramineae Phyllostachys praecox C. D. Chu et C. S. Chao. ).Methods: The compounds in bamboo shoots were isolated and identified by ultraviolet (UV) spectroscopy, mass spectrometry (MS), and nuclear magnetic resonance (NMR). Quantitative analysis was performed by reversed-phase high performance liquid chromatography (RP-HPLC) using a C18 column and a mixture (1:1ratio) of acetonitrile and 15 mM ammonium acetate (pH 6.0) as mobile phase. This method was validated for its reproducibility, chemical stability, and recovery.Results: Six nucleosides and two amino acids were isolated from bamboo shoots, including guanosine, 2’-deoxyguanosine, adenosine, thymidine, uridine, cytidine, tryptophan, and phenylalanine. The HPLC method was rapid and reproducible. The intraday and interday concentrations of the eight identified compounds showed good linearity in the range of 0.22 - 60.00 μg/mL. The relative standard deviation (RSD) for intraday and interday precision for reproducibility and stability was < 3 %. The validated method was successfully applied to determine the content of the eight compounds in four different Phyllostachys species.Conclusion: Adenosine was isolated from bamboo shoots previously, but the isolation of the other seven compounds are reported here for the first time. The method proposed is sensitive and reproducible, and would facilitate studies of nutritional/medicinal compounds in bamboo shoot.Keywords: Bamboo shoots, Phyllostachys prominens, Guanosine, 2’ Deoxyguanosine, Adenosine, Thymidine, Uridine, Cytidine, Tryptophan, Phenylalanin

GPU-Monte Carlo based fast IMRT plan optimization

Purpose: Intensity-modulated radiation treatment (IMRT) plan optimization needs pre-calculated beamlet dose distribution. Pencil-beam or superposition/convolution type algorithms are typically used because of high computation speed. However, inaccurate beamlet dose distributions, particularly in cases with high levels of inhomogeneity, may mislead optimization, hindering the resulting plan quality. It is desire to use Monte Carlo (MC) methods for beamlet dose calculations. Yet, the long computational time from repeated dose calculations for a number of beamlets prevents this application. It is our objective to integrate a GPU-based MC dose engine in lung IMRT optimization using a novel two-steps workflow.Methods: A GPU-based MC code gDPM is used. Each particle is tagged with an index of a beamlet where the source particle is from. Deposit dose are stored separately for beamlets based on the index. Due to limited GPU memory size, a pyramid space is allocated for each beamlet, and dose outside the space is neglected. A two-steps optimization workflow is proposed for fast MC-based optimization. At first step, a rough dose calculation is conducted with only a few number of particle per beamlet. Plan optimization is followed to get an approximated fluence map. In the second step, more accurate beamlet doses are calculated, where sampled number of particles for a beamlet is proportional to the intensity determined previously. A second-round optimization is conducted, yielding the final result.Results: For a lung case with 5317 beamlets, 105 particles per beamlet in the first round, and 108 particles per beam in the second round are enough to get a good plan quality. The total simulation time is 96.4 sec.Conclusion: A fast GPU-based MC dose calculation method along with a novel two-step optimization workflow are developed. The high efficiency allows the use of MC for IMRT optimizations.--------------------------------Cite this article as: Li Y, Tian Z, Shi F, Jiang S, Jia X. GPU-Monte Carlo based fast IMRT plan optimization. Int J Cancer Ther Oncol 2014; 2(2):020244. DOI: 10.14319/ijcto.0202.4