Multivariate PLS Modeling of Apicomplexan FabD-Ligand Interaction Space for Mapping Target-Specific Chemical Space and Pharmacophore Fingerprints

Biomolecular recognition underlying drug-target interactions is determined by both binding affinity and specificity. Whilst, quantification of binding efficacy is possible, determining specificity remains a challenge, as it requires affinity data for multiple targets with the same ligand dataset. Thus, understanding the interaction space by mapping the target space to model its complementary chemical space through computational techniques are desirable. In this study, active site architecture of FabD drug target in two apicomplexan parasites viz. Plasmodium falciparum (PfFabD) and Toxoplasma gondii (TgFabD) is explored, followed by consensus docking calculations and identification of fifteen best hit compounds, most of which are found to be derivatives of natural products. Subsequently, machine learning techniques were applied on molecular descriptors of six FabD homologs and sixty ligands to induce distinct multivariate partial-least square models. The biological space of FabD mapped by the various chemical entities explain their interaction space in general. It also highlights the selective variations in FabD of apicomplexan parasites with that of the host. Furthermore, chemometric models revealed the principal chemical scaffolds in PfFabD and TgFabD as pyrrolidines and imidazoles, respectively, which render target specificity and improve binding affinity in combination with other functional descriptors conducive for the design and optimization of the leads.

Ac2PIM-responsive miR-150 and miR-143 Target Receptor-interacting Protein Kinase 2 and Transforming Growth Factor Beta-activated Kinase 1 to Suppress NOD2-induced Immunomodulators

Specific and coordinated regulation of innate immune receptor-driven signaling networks often determines the net outcome of the immune responses. Here, we investigated the cross-regulation of toll-like receptor (TLR)2 and nucleotide-binding oligomerization domain (NOD)2 pathways mediated by Ac2PIM, a tetra-acylated form of mycobacterial cell wall component and muramyl dipeptide (MDP), a peptidoglycan derivative respectively. While Ac2PIM treatment of macrophages compromised their ability to induce NOD2-dependent immunomodulators like cyclooxygenase (COX)-2, suppressor of cytokine signaling (SOCS)-3, and matrix metalloproteinase (MMP)-9, no change in the NOD2-responsive NO, TNF-alpha, VEGF-A, and IL-12 levels was observed. Further, genome-wide microRNA expression profiling identified Ac2PIM-responsive miR-150 and miR-143 to target NOD2 signaling adaptors, RIP2 and TAK1, respectively. Interestingly, Ac2PIM was found to activate the SRC-FAK-PYK2-CREB cascade via TLR2 to recruit CBP/P300 at the promoters of miR-150 and miR-143 and epigenetically induce their expression. Loss-of-function studies utilizing specific miRNA inhibitors establish that Ac2PIM, via the miRNAs, abrogate NOD2-induced PI3K-PKC delta-MAPK pathway to suppress beta-catenin-mediated expression of COX-2, SOCS-3, and MMP-9. Our investigation has thus underscored the negative regulatory role of Ac2PIM-TLR2 signaling on NOD2 pathway which could broaden our understanding on vaccine potential or adjuvant utilities of Ac2PIM and/or MDP.

Asparagine requirement in Plasmodium berghei as a target to prevent malaria transmission and liver infections

The proteins of Plasmodium, the malaria parasite, are strikingly rich in asparagine. Plasmodium depends primarily on host haemoglobin degradation for amino acids and has a rudimentary pathway for amino acid biosynthesis, but retains a gene encoding asparagine synthetase (AS). Here we show that deletion of AS in Plasmodium berghei (Pb) delays the asexual-and liver-stage development with substantial reduction in the formation of ookinetes, oocysts and sporozoites in mosquitoes. In the absence of asparagine synthesis, extracellular asparagine supports suboptimal survival of PbAS knockout (KO) parasites. Depletion of blood asparagine levels by treating PbASKO-infected mice with asparaginase completely prevents the development of liver stages, exflagellation of male gametocytes and the subsequent formation of sexual stages. In vivo supplementation of asparagine in mice restores the exflagellation of PbASKO parasites. Thus, the parasite life cycle has an absolute requirement for asparagine, which we propose could be targeted to prevent malaria transmission and liver infections.

Sound radiation from a perforated panel set in a baffle with a different perforation ratio

A finite flexible perforated panel set in a differently perforated rigid baffle is considered. The radiation efficiency from such a panel is derived using a 2-D wavenumber domain formulation. This generalization is later used to represent a more practical case of a perforated panel fixed in an unperforated baffle. The perforations are in the form of an array of uniformly distributed circular holes. A complex impedance model for the holes available in the literature is used. An averaged fluid particle velocity is derived using the continuity equation and the surface pressure is derived using an appropriate momentum equation. The discontinuity in the perforate impedance (due to different hole dimensions or perforation ratio) at the panel-baffle interface is carefully taken into account. It is found that there exists a `coupling' of different wavenumbers of the spatially mean fluid particle velocity field. The change in the resonance frequencies and the modeshapes of the panel due to the perforations is taken into account using the Receptance method. Analytical expressions for the radiated power and radiation efficiency are derived in an integral form and numerical results are presented. Several comparisons are made to understand the radiation efficiency curves. Since both the resistive and reactive components of the hole impedance are taken into account, the model is directly applicable to micro-perforated panels also. (C) 2016 Elsevier Ltd. All rights reserved.

Enhanced photocatalytic activity of ultra-high aspect ratio ZnO nanowires due to Cu induced defects

We report the synthesis of ZnO nanowires in ambient air at 650 degrees C by a single-step vapor transport method using two different sources Zn (ZnO nanowires-I) and Zn:Cu (ZnO nanowires-II). The Zn:Cu mixed source co-vaporize Zn with a small amount of Cu at temperatures where elemental Cu source does not vaporize. This method provides us a facile route for Cu doping into ZnO. The aspect ratio of the grown ZnO nanowires-II was found to be higher by more than five times compared ZnO nanowires-I. Photocatalytic activity was measured by using a solar simulator and its ultraviolet-filtered light. The ZnO nanowires-II shows higher catalytic activity due to increased aspect ratio and higher content of surface defects because of incorporation of Cu impurities.

Increasing Critical Sensitivity of the Load/Unload Response Ratio before Large Earthquakes with Identified Stress Acclumulation Pattern

The Load/Unload Response Ratio (LURR) method is proposed for short-to-intermediate-term earthquake prediction [Yin, X.C., Chen, X.Z., Song, Z.P., Yin, C., 1995. A New Approach to Earthquake Prediction — The Load/Unload Response Ratio (LURR) Theory, Pure Appl. Geophys., 145, 701–715]. This method is based on measuring the ratio between Benioff strains released during the time periods of loading and unloading, corresponding to the Coulomb Failure Stress change induced by Earth tides on optimally oriented faults. According to the method, the LURR time series usually climb to an anomalously high peak prior to occurrence of a large earthquake. Previous studies have indicated that the size of critical seismogenic region selected for LURR measurements has great influence on the evaluation of LURR. In this study, we replace the circular region usually adopted in LURR practice with an area within which the tectonic stress change would mostly affect the Coulomb stress on a potential seismogenic fault of a future event. The Coulomb stress change before a hypothetical earthquake is calculated based on a simple back-slip dislocation model of the event. This new algorithm, by combining the LURR method with our choice of identified area with increased Coulomb stress, is devised to improve the sensitivity of LURR to measure criticality of stress accumulation before a large earthquake. Retrospective tests of this algorithm on four large earthquakes occurred in California over the last two decades show remarkable enhancement of the LURR precursory anomalies. For some strong events of lesser magnitudes occurred in the same neighborhoods and during the same time periods, significant anomalies are found if circular areas are used, and are not found if increased Coulomb stress areas are used for LURR data selection. The unique feature of this algorithm may provide stronger constraints on forecasts of the size and location of future large events.

Load-Unload Response Ratio and Accelerating Moment/Energy Release Critical Region Scaling and Earthquake Prediction

The main idea of the Load-Unload Response Ratio (LURR) is that when a system is stable, its response to loading corresponds to its response to unloading, whereas when the system is approaching an unstable state, the response to loading and unloading becomes quite different. High LURR values and observations of Accelerating Moment/Energy Release (AMR/AER) prior to large earthquakes have led different research groups to suggest intermediate-term earthquake prediction is possible and imply that the LURR and AMR/AER observations may have a similar physical origin. To study this possibility, we conducted a retrospective examination of several Australian and Chinese earthquakes with magnitudes ranging from 5.0 to 7.9, including Australia's deadly Newcastle earthquake and the devastating Tangshan earthquake. Both LURR values and best-fit power-law time-to-failure functions were computed using data within a range of distances from the epicenter. Like the best-fit power-law fits in AMR/AER, the LURR value was optimal using data within a certain epicentral distance implying a critical region for LURR. Furthermore, LURR critical region size scales with mainshock magnitude and is similar to the AMR/AER critical region size. These results suggest a common physical origin for both the AMR/AER and LURR observations. Further research may provide clues that yield an understanding of this mechanism and help lead to a solid foundation for intermediate-term earthquake prediction.

Effect of Cold Rolling Ratio and Heating Rate of Batch Annealing on Textures of Micro-Carbon Steel Sheet

在四辊冷轧试验机和Gleeble-1500试验机上进行了热轧微碳钢板的冷轧和退火试验。用D/max-RC衍射仪测量了试样的,/”层织构,并用Roe软件进行了ODF分析。研究表明,所研究的热轧微碳深冲板压下率约为75%,退火升温速度为20-40℃/h时,试样为{111}织构特征；压下率较大(80%)时,退火织构为较弱的{111}组分。无论{111}织构还是非{111}织构都是在形核阶段开始形成,在晶粒长大优先长大,受到定向形核和选择生长双重机制的作用。

Influence of the thickness ratio of air layer to liquid layer on the onset of Benard-Marangoni convection

An experimental investigation of the onset of Benard-Marangoni convection has been performed in a liquid layer of rectangular configuration. The critical temperature difference was measured via the detections of both temperature field pattern (IR-imaging) on the free surface and fluid convection (PIV) in the liquid layer. The critical temperature difference or the critical Marangoni number was given. The experiments were performed for a fixed depth of air layer and a changeable depth of the liquid layer, and then the influence of the thickness ratio of the air layer to liquid layer on the Marangoni instability was studied.

Simulation of the Load-Unload Response Ratio and Critical Sensitivity in the Lattice Solid Model

The Load-Unload Response Ratio (LURR) method is an intermediate-term earthquake prediction approach that has shown considerable promise. It involves calculating the ratio of a specified energy release measure during loading and unloading where loading and unloading periods are determined from the earth tide induced perturbations in the Coulomb Failure Stress on optimally oriented faults. In the lead-up to large earthquakes, high LURR values are frequently observed a few months or years prior to the event. These signals may have a similar origin to the observed accelerating seismic moment release (AMR) prior to many large earthquakes or may be due to critical sensitivity of the crust when a large earthquake is imminent. As a first step towards studying the underlying physical mechanism for the LURR observations, numerical studies are conducted using the particle based lattice solid model (LSM) to determine whether LURR observations can be reproduced. The model is initialized as a heterogeneous 2-D block made up of random-sized particles bonded by elastic-brittle links. The system is subjected to uniaxial compression from rigid driving plates on the upper and lower edges of the model. Experiments are conducted using both strain and stress control to load the plates. A sinusoidal stress perturbation is added to the gradual compressional loading to simulate loading and unloading cycles and LURR is calculated. The results reproduce signals similar to those observed in earthquake prediction practice with a high LURR value followed by a sudden drop prior to macroscopic failure of the sample. The results suggest that LURR provides a good predictor for catastrophic failure in elastic-brittle systems and motivate further research to study the underlying physical mechanisms and statistical properties of high LURR values. The results provide encouragement for earthquake prediction research and the use of advanced simulation models to probe the physics of earthquakes.

Influences of the Fish-Mouth Project and the Groins on the Flow and Sediment Ratio of the Yangtze River Waterway

A depth-integrated two-dimensional numerical model of current, salinity and sediment transport was proposed and calibrated by the observation data in the Yangtze River Estuary. It was then applied to investigate the flow and sediment ratio of the navigati

A Semi-Empirical Equation of Penetration Depth on Concrete Target Impacted by Ogive-Nose Projectiles

In this paper, the penetration process of ogive-nose projectiles into the semi-infinite concrete target is investigated by the dimensional analysis method and FEM simulation. With the dimensional analysis, main non-dimensional parameters which control the penetration depth are obtained with some reasonable hypothesis. Then, a new semi-empirical equation is present based on the original work of Forrestal et al., has only two non-dimensional combined variables with definite physical meanings. To verify this equation, prediction results are compared with experiments in a wide variation region of velocity. Then, a commercial FEM code, LS-DYNA, is used to simulate the complex penetration process, that also show the novel semi-empirical equation is reasonable for determining the penetration depth in a concrete target.

High Aspect Ratio (L/D) Riser Viv Prediction Using Wake Oscillator Model

A two-dimensional (2-D) vortex-induced vibration (VIV) prediction model for high aspect ratio (LID) riser subjected to uniform and sheared flow is studied in this paper. The nonlinear structure equations are considered. The near wake dynamics describing the fluctuating nature of vortex shedding is modeled using classical van der Pol equation. A new approach was applied to calibrate the empirical parameters in the wake oscillator model. Compared the predicted results with the experimental data and computational fluid dynamic (CFD) results. Good agreements are observed. It can be concluded that the present model can be used as simple computational tool in predicting some aspects of VIV of long flexible structures. (C) 2008 Elsevier Ltd. All rights reserved.