Description: Background: The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed. Results: A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform. Conclusions: IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at http://kyc.nenu.edu.cn/IVSPlat/.

Description: Author(s): Jie-Hui Huang, Zhang-Yang Chen, Tian-Bao Yu, Xin-Hua Deng, Jiang-Tao Liu, and Nian-Hua Liu The time evolution of residual entanglement in a three-qubit system embedded in a photonic crystal is investigated by using a modified conjugate gradient method. In the isotropic photonic crystal the phenomena of entanglement “sudden death” and entanglement “sudden birth” are found due to the decohe... [Phys. Rev. A 85, 014301] Published Tue Jan 17, 2012

Description: Author(s): Si-xue Qin, Lei Chang, Yu-xin Liu, Craig D. Roberts, and David J. Wilson Ground-state, radially excited, and exotic scalar, vector, and flavored-pseudoscalar mesons are studied in rainbow-ladder truncation using an interaction kernel that is consonant with modern Dyson-Schwinger equation and lattice-QCD results. The inability of this truncation to provide realistic predi... [Phys. Rev. C 85, 035202] Published Tue Mar 06, 2012

Description: Background: The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed. Results: A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform. Conclusions: IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at http://kyc.nenu.edu.cn/IVSPlat/.

Description: Author(s): Cheng-fu Mu, Yin Jiang, Peng-fei Zhuang, and Yu-xin Liu We study some properties of nucleons with a simplified version of a Faddeev equation at finite temperature and baryon chemical potential in the framework of the Nambu–Jona-Lasinio model. By taking diquark-quark bubble summation, we constructed the nucleon propagator and calculated the dynamical mass... [Phys. Rev. D 85, 014033] Published Fri Jan 27, 2012

Description: Using the finite element analysis program ABAQUS, a series of calculations on a cantilever beam, pile, and sheet pile wall were made to investigate the bending moment computational methods. The analyses demonstrated that the shear locking is not significant for the passive pile embedded in soil. Therefore, higher-order elements are not always necessary in the computation. The number of grids across the pile section is important for bending moment calculated with stress and less significant for that calculated with displacement. Although computing bending moment with displacement requires fewer grid numbers across the pile section, it sometimes results in variation of the results. For displacement calculation, a pile row can be suitably represented by an equivalent sheet pile wall, whereas the resulting bending moments may be different. Calculated results of bending moment may differ greatly with different grid partitions and computational methods. Therefore, a comparison of results is necessary when performing the analysis.

Description: Author(s): Li-jia Jiang (姜丽佳), Xian-yin Xin (辛现银), Kun-lun Wang (王昆仑), Si-xue Qin (秦思学), and Yu-xin Liu (刘玉鑫) We propose the 2+1 flavor chiral susceptibility criterion to identify the chiral phase transition of the 2+1 flavor quark system and take it to determine the phase boundary and the critical end point (CEP) in the Nambu-Jona-Lasinio model. We give explicitly the phase diagram of the 2+1 flavor quark ... [Phys. Rev. D 88, 016008] Published Fri Jul 19, 2013

Description: This paper presents a novel wavelet kernel neural network (WKNN) with wavelet kernel function. It is applicable in online learning with adaptive parameters and is applied on parameters tuning of fractional-order PID (FOPID) controller, which could handle time delay problem of the complex control system. Combining the wavelet function and the kernel function, the wavelet kernel function is adopted and validated the availability for neural network. Compared to the conservative wavelet neural network, the most innovative character of the WKNN is its rapid convergence and high precision in parameters updating process. Furthermore, the integrated pressurized water reactor (IPWR) system is established by RELAP5, and a novel control strategy combining WKNN and fuzzy logic rule is proposed for shortening controlling time and utilizing the experiential knowledge sufficiently. Finally, experiment results verify that the control strategy and controller proposed have the practicability and reliability in actual complicated system.

Description: Background: Dual anti-human epidermal growth factor receptor 2 (HER2) therapies have been shown to improve outcomes of HER2-positive breast cancer patients. We undertook a systematic review to compare treatment outcomes for patients who received single or combined anti-HER2 therapies. Methods: We identified randomized control trials that compared dual anti-HER2 therapy and anti-HER2 monotherapy in patients with HER2-positive breast cancer. Outcomes included pathologic complete response (pCR), overall survival (OS), progression-free survival (PFS), and adverse events. Included in the analysis were seven trials that recruited 2,609 patients. Results: In the neoadjuvant setting, the pooled pCR rate in the dual anti-HER2 therapy and monotherapy groups in combination with chemotherapy was 54.8% and 36%, respectively. This difference was statistically significant (relative risk, 1.56; 95% confidence interval (CI), 1.23-1.97; p 〈 0.001). In the metastatic setting, dual anti-HER2 therapy demonstrated significant benefits in both PFS (hazard ratio (HR), 0.71; 95% CI, 0.62-0.81; p 〈 0.001) and OS (HR, 0.68; 95% CI, 0.57-0.82; p 〈 0.001). Subgroup analyses indicated that the addition of chemotherapy to dual anti-HER2 therapy could greatly improve pCR in the neoadjuvant settings. However, in the metastatic setting, similar PFS and OS were found in patients receiving dual anti-HER2 therapy with or without chemotherapy. Dual anti-HER2 therapy was associated with more frequent adverse events than monotherapy, but no statistical differences were observed in cardiac toxicity. Conclusions: This systematic review provides a summary of all the data currently available, and confirms the benefits and risks of dual anti-HER2 therapy for HER2-positive breast cancer.

Description: Filter-based particle samples were simultaneously collected at 14 sites across 6 regions of China during the summer of 2012. These filters were analyzed for secondary organic aerosol (SOA) tracers from biogenic precursors (isoprene, monoterpenes and β-caryophyllene) and anthropogenic aromatics. The sum of all SOA tracers ranged from 29.9 to 371 ng m −3 with the majority from isoprene (123 ± 78.8 ng m −3 ), followed by monoterpenes (10.5 ± 6.64 ng m −3 ), β-caryophyllene (5.07 ± 3.99 ng m −3 ) and aromatics (2.90 ± 1.52 ng m −3 ). The highest levels of biogenic SOA tracers were observed in East China, whereas the highest concentrations of the aromatic SOA tracer, 2,3-dihydroxy-4-oxopentanoic acid (DHOPA), occurred in North China. All biogenic SOA tracers exhibited positive correlations with temperature, most likely resulting from enhanced biogenic volatile organic compounds (BVOCs) emissions and photochemistry in high-temperature regions. Among the isoprene SOA tracers, the low-NOx products 2-methyltetrols were the largest by mass concentration. However, at certain urban sites, the contribution of the high-NOx product 2-methylglyceric acid was significantly higher, implying a greater influence of NOx on isoprene SOA formation in urban areas. For the monoterpene SOA tracers, the ratio of the first-generation products (cis-pinonic acid plus pinic acid) to the high-generation product (3-methyl-1,2,3-butanetricarboxylic acid) exhibited a negative correlation with the amount of high-generation products, indicating that this ratio could serve as an indicator of the aging of monoterpene SOA. The ratio ranged from 0.89 to 21.0, with an average of 7.00 ± 6.02, among the observation sites, suggesting that monoterpene SOA was generally fresh over China during the summer. As a typical anthropogenic SOA tracer, DHOPA exhibited higher levels at urban sites than at remote sites. These SOA tracers were further used to attribute SOA origins via the SOA-tracer method. The total concentrations of secondary organic carbon (SOC) and SOA were estimated to be in the range of 0.37 to 2.47 μgC m −3 and 0.81 to 5.44 µg m −3 , respectively, with the highest levels observed in the eastern regions of China. Isoprene (46 ± 14%) and aromatics (27 ± 8%) were the two major contributors to SOC in every region. In North China, aromatics were the largest SOA contributor. Our ground-based observations suggest that anthropogenic aromatics are important SOA precursors in China.