The boundary contour method for magneto-electro-elastic media with quadratic boundary elements

AbstractThis paper presents a development of the boundary contour method (BCM) for magneto-electro-elastic media. First, the divergence-free of the integrand of the magneto-electro-elastic boundary element is proved. Second, the boundary contour method formulations are obtained by introducing quadratic shape functions and Green’s functions [Ding, H.J., Jiang, A.M., 2004. A boundary integral formulation and solution for 2D problems in magneto-electro-elastic media. Computers and Structures, 82 (20–21), 1599–1607] for magneto-electro-elastic media and using the rigid body motion solution to regularize the BCM and avoid computation of the corner tensor. The BCM is applied to the problem of magneto-electro-elastic media. Finally, numerical solutions for illustrative examples are compared with exact ones. The numerical results of the BCM coincide very well with the exact solution, and the feasibility and efficiency of the method are verified

Elucidating the Evolutionary Relationships among Bos taurus Digestive Organs Using Unigene Expression Data

Although the nature of ruminant evolution is still disputed, current theory based on physiology and genetic analysis suggests that the abomasum is the evolutionarily oldest stomach compartment, the rumen evolved some time after the abomasum, and the omasum is the evolutionarily youngest stomach compartment. In addition, there is some evidence of relaxed selective constraint in the stomach-like organ and the foregut shortly after the foregut formation event. Along with the assumption of a mean, stochastic rate of evolution, analysis of differences in genetic profiles among digestive body organs can give clues to the relationships among these organs. The presence of large numbers of uniquely expressed entries in the abomasum and rumen indicates either a period of relaxed selective constraint or greater evolutionary age. Additionally, differences in expression profiles indicate that the abomasum, rumen, and intestine are more closely related to each other, while the reticulum and omasum are more closely related to the rumen. Functional analysis using Gene Ontology (GO) categories also supports the proposed evolutionary relationships by identifying shared functions, such as muscle activity and development, lipid transport, and urea metabolism, between all sections of the digestive tract investigated

Efficacy of autologous bone marrow buffy coat grafting combined with core decompression in patients with avascular necrosis of femoral head: a prospective, double-blinded, randomized, controlled study

Introduction Avascular necrosis of femoral head (ANFH) is a progressive disease that often leads to hip joint dysfunction and even disability in young patients. Although the standard treatment, which is core decompression, has the advantage of minimal invasion, the efficacy is variable. Recent studies have shown that implantation of bone marrow containing osteogenic precursors into necrotic lesion of ANFH may be promising for the treatment of ANFH. Methods A prospective, double-blinded, randomized controlled trial was conducted to examine the effect of bone-marrow buffy coat (BBC) grafting combined with core decompression for the treatment of ANFH. Forty-five patients (53 hips) with Ficat stage I to III ANFH were recruited. The hips were allocated to the control group (core decompression + autologous bone graft) or treatment group (core decompression + autologous bone graft with BBC). Both patients and assessors were blinded to the treatment options. The clinical symptoms and disease progression were assessed as the primary and secondary outcomes. Results At the final follow-up (24 months), there was a significant relief in pain (P \u3c0.05) and clinical joint symptoms as measured by the Lequesne index (P \u3c0.05) and Western Ontario and McMaster Universities Arthritis Index (P \u3c0.05) in the treatment group. In addition, 33.3% of the hips in the control group have deteriorated to the next stage after 24 months post-procedure, whereas only 8% in the treatment group had further deterioration (P \u3c0.05). More importantly, the non-progression rates for stage I/II hips were 100% in the treatment group and 66.7% in the control group. Conclusion Implantation of the autologous BBC grafting combined with core decompression is effective to prevent further progression for the early stages of ANFH. Trial registration ClinicalTrials.gov identifier NCT01613612. Registered 13 December 2011

Experimental study on fracture plugging effect of irregular-shaped lost circulation materials

Using micro-visualization experimental device for the formation of fracture plugging zone, the plugging behavior of irregular-shaped lost circulation materials (LCMs) with different types and concentrations in fractures was experimentally analyzed. The results show that the sealing time decreases significantly with the increase of material concentration. When the concentration is 20%, the sealing times of materials LCM-1∼LCM-5 are 6s, 7s, 5s, 6s, 4s, respectively. The formation of fracture plugging zone includes two stages, and the main factors affecting the formation of fracture plugging zone are flatness, roundness, convexity and concentrations. Flatness affects the retention stage of LCMs through the matching degree between particle size and fracture width. Convexity and roundness affect the retention stage by increasing the friction coefficient between particles. The high-efficiency retention ability of irregular LCMs is characterized by strong matching to fracture width, and strong friction and sliding resistance between particles. It is recommended that the optimized geometric parameters of high-efficiency retention materials should meet the requirements of “low flatness, low roundness and low convexity” (flatness \u3c0.6, roundness \u3c0.6 and convexity \u3c0.8), which can improve the plugging effect significantly

Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

<p>Abstract</p> <p>Background</p> <p>Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA), we have developed a conformational generation method called Cyndi in the previous study. In this work, in addition to Tripos force field in the previous version, Cyndi was updated by incorporation of MMFF94 force field to assess the conformational energy more rationally. With two force fields against a larger dataset of 742 bioactive conformations of small ligands extracted from PDB, a comparative analysis was performed between pure force field based method (FFBM) and multiple empirical criteria based method (MECBM) hybrided with different force fields.</p> <p>Results</p> <p>Our analysis reveals that incorporating multiple empirical rules can significantly improve the accuracy of conformational generation. MECBM, which takes both empirical and force field criteria as the objective functions, can reproduce about 54% (within 1Å RMSD) of the bioactive conformations in the 742-molecule testset, much higher than that of pure force field method (FFBM, about 37%). On the other hand, MECBM achieved a more complete and efficient sampling of the conformational space because the average size of unique conformations ensemble per molecule is about 6 times larger than that of FFBM, while the time scale for conformational generation is nearly the same as FFBM. Furthermore, as a complementary comparison study between the methods with and without empirical biases, we also tested the performance of the three conformational generation methods in MacroModel in combination with different force fields. Compared with the methods in MacroModel, MECBM is more competitive in retrieving the bioactive conformations in light of accuracy but has much lower computational cost.</p> <p>Conclusions</p> <p>By incorporating different energy terms with several empirical criteria, the MECBM method can produce more reasonable conformational ensemble with high accuracy but approximately the same computational cost in comparison with FFBM method. Our analysis also reveals that the performance of conformational generation is irrelevant to the types of force field adopted in characterization of conformational accessibility. Moreover, post energy minimization is not necessary and may even undermine the diversity of conformational ensemble. All the results guide us to explore more empirical criteria like geometric restraints during the conformational process, which may improve the performance of conformational generation in combination with energetic accessibility, regardless of force field types adopted.</p

Unshifted Metastable He I* Mini-Broad Absorption Line System in the Narrow Line Type 1 Quasar SDSS J080248.18++551328.9

We report the identification of an unusual absorption line system in the quasar SDSS J080248.18$+$551328.9 and present a detailed study of the system, incorporating follow-up optical and NIR spectroscopy. A few tens of absorption lines are detected, including He I*, Fe II* and Ni II* that arise from metastable or excited levels, as well as resonant lines in Mg I, Mg II, Fe II, Mn II, and Ca II. All of the isolated absorption lines show the same profile of width $\Delta v\sim 1,500$km s$^{-1}$ centered at a common redshift as that of the quasar emission lines, such as [O II], [S II], and hydrogen Paschen and Balmer series. With narrow Balmer lines, strong optical Fe II multiplets, and weak [O III] doublets, its emission line spectrum is typical for that of a narrow-line Seyfert 1 galaxy (NLS1). We have derived reliable measurements of the gas-phase column densities of the absorbing ions/levels. Photoionization modeling indicates that the absorber has a density of $n_{\rm H} \sim (1.0-2.5)\times 10^5~ {\rm cm}^{-3}$ and a column density of $N_{\rm H} \sim (1.0-3.2)\times 10^{21} \sim {\rm cm}^{-2}$, and is located at $R\sim100-250$ pc from the central super-massive black hole. The location of the absorber, the symmetric profile of the absorption lines, and the coincidence of the absorption and emission line centroid jointly suggest that the absorption gas is originated from the host galaxy and is plausibly accelerated by stellar processes, such as stellar winds \zhy{and/or} supernova explosions. The implications for the detection of such a peculiar absorption line system in an NLS1 are discussed in the context of co-evolution between super-massive black hole growth and host galaxy build-up.Comment: 28 pages, 16 figures; accepted for publication in Astrophysical Journa

Mechanics of Channel Gating of the Nicotinic Acetylcholine Receptor

The nicotinic acetylcholine receptor (nAChR) is a key molecule involved in the propagation of signals in the central nervous system and peripheral synapses. Although numerous computational and experimental studies have been performed on this receptor, the structural dynamics of the receptor underlying the gating mechanism is still unclear. To address the mechanical fundamentals of nAChR gating, both conventional molecular dynamics (CMD) and steered rotation molecular dynamics (SRMD) simulations have been conducted on the cryo-electron microscopy (cryo-EM) structure of nAChR embedded in a dipalmitoylphosphatidylcholine (DPPC) bilayer and water molecules. A 30-ns CMD simulation revealed a collective motion amongst C-loops, M1, and M2 helices. The inward movement of C-loops accompanying the shrinking of acetylcholine (ACh) binding pockets induced an inward and upward motion of the outer β-sheet composed of β9 and β10 strands, which in turn causes M1 and M2 to undergo anticlockwise motions around the pore axis. Rotational motion of the entire receptor around the pore axis and twisting motions among extracellular (EC), transmembrane (TM), and intracellular MA domains were also detected by the CMD simulation. Moreover, M2 helices undergo a local twisting motion synthesized by their bending vibration and rotation. The hinge of either twisting motion or bending vibration is located at the middle of M2, possibly the gate of the receptor. A complementary twisting-to-open motion throughout the receptor was detected by a normal mode analysis (NMA). To mimic the pulsive action of ACh binding, nonequilibrium MD simulations were performed by using the SRMD method developed in one of our laboratories. The result confirmed all the motions derived from the CMD simulation and NMA. In addition, the SRMD simulation indicated that the channel may undergo an open-close (O ↔ C) motion. The present MD simulations explore the structural dynamics of the receptor under its gating process and provide a new insight into the gating mechanism of nAChR at the atomic level

PDTD: a web-accessible protein database for drug target identification

<p>Abstract</p> <p>Background</p> <p>Target identification is important for modern drug discovery. With the advances in the development of molecular docking, potential binding proteins may be discovered by docking a small molecule to a repository of proteins with three-dimensional (3D) structures. To complete this task, a reverse docking program and a drug target database with 3D structures are necessary. To this end, we have developed a web server tool, TarFisDock (<it>Tar</it>get <it>Fis</it>hing <it>Dock</it>ing) <url>http://www.dddc.ac.cn/tarfisdock</url>, which has been used widely by others. Recently, we have constructed a protein target database, <it>P</it>otential <it>D</it>rug <it>T</it>arget <it>D</it>atabase (PDTD), and have integrated PDTD with TarFisDock. This combination aims to assist target identification and validation.</p> <p>Description</p> <p>PDTD is a web-accessible protein database for <it>in silico </it>target identification. It currently contains >1100 protein entries with 3D structures presented in the Protein Data Bank. The data are extracted from the literatures and several online databases such as TTD, DrugBank and Thomson Pharma. The database covers diverse information of >830 known or potential drug targets, including protein and active sites structures in both PDB and mol2 formats, related diseases, biological functions as well as associated regulating (signaling) pathways. Each target is categorized by both nosology and biochemical function. PDTD supports keyword search function, such as PDB ID, target name, and disease name. Data set generated by PDTD can be viewed with the plug-in of molecular visualization tools and also can be downloaded freely. Remarkably, PDTD is specially designed for target identification. In conjunction with TarFisDock, PDTD can be used to identify binding proteins for small molecules. The results can be downloaded in the form of mol2 file with the binding pose of the probe compound and a list of potential binding targets according to their ranking scores.</p> <p>Conclusion</p> <p>PDTD serves as a comprehensive and unique repository of drug targets. Integrated with TarFisDock, PDTD is a useful resource to identify binding proteins for active compounds or existing drugs. Its potential applications include <it>in silico </it>drug target identification, virtual screening, and the discovery of the secondary effects of an old drug (i.e. new pharmacological usage) or an existing target (i.e. new pharmacological or toxic relevance), thus it may be a valuable platform for the pharmaceutical researchers. PDTD is available online at <url>http://www.dddc.ac.cn/pdtd/</url>.</p

Green synthesis of biogenetic Te(0) nanoparticles by high tellurite tolerance fungus Mortierella sp. AB1 with antibacterial activity

Tellurite [Te(IV)] is a high-toxicity metalloid. In this study, a fungus with high Te(IV) resistance was isolated. Strain AB1 could efficiently reduce highly toxic Te(IV) to less toxic Te(0). The reduced products formed rod-shaped biogenetic Te(0) nanoparticles (Bio-TeNPs) intracellularly. Further TEM-element mapping, FTIR, and XPS analysis showed that the extracted Bio-TeNPs ranged from 100 to 500 nm and consisted of Te(0), proteins, lipids, aromatic compounds, and carbohydrates. Moreover, Bio-TeNPs exhibited excellent antibacterial ability against Shigella dysenteriae, Escherichia coli, Enterobacter sakazakii, and Salmonella typhimurium according to inhibition zone tests. Further growth and live/dead staining experiments showed that E. coli and S. typhimurium were significantly inhibited by Bio-TeNPs, and cells were broken or shriveled after treatment with Bio-TeNPs based on SEM observation. Additionally, the antioxidant and cytotoxicity tests showed that the Bio-TeNPs exhibited excellent antioxidant capacity with no cytotoxicity. All these results suggested that strain AB1 showed great potential in bioremediation and Bio-TeNPs were excellent antibacterial nanomaterials with no cytotoxicity.Peer reviewe