DYNAMIC ANALYSIS OF THE RIGID-FLEXIBLE EXCAVATOR MECHANISM BASED ON VIRTUAL PROTOTYPE

In this paper, the excavator’s dynamic performance is considered together with the study of its trajectory, stress distribution and vibration. Many researchers have focused their study on the kinematics principle while a few others focused their work on dynamic performance, especially the vibration analysis. Previous studies of dynamic performance analysis have ignored the vibration effects. To address these challenges, the rigid-flexible coupling model of the excavator attachment is established and carried out based on virtual prototyping in this study. The dipper handle, the boom and the hoist rope are modeled as a flexible multi-body system for structural strength. The other components are modeled as a rigid multi-body system to catch the dynamic characteristics. The results show that the number of flexible bodies has little effect on the excavation trajectory. The maximum stress determined for the dipper handle and the boom are 96.45 MPa and 212.24 MPa, respectively. The dynamic performance of the excavator is greatly influenced by the clearance and is characterized by two phases: as the clearance decreases, the dynamic response decreases at first and then increases

SVRMHC prediction server for MHC-binding peptides

BACKGROUND: The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. RESULTS: Recently, we demonstrated the appealing performance of SVRMHC, an SVR-based quantitative modeling method for peptide-MHC interactions, when applied to three mouse class I MHC molecules. Subsequently, we have greatly extended the construction of SVRMHC models and have established such models for more than 40 class I and class II MHC molecules. Here we present the SVRMHC web server for predicting peptide-MHC binding affinities using these models. Benchmarked percentile scores are provided for all predictions. The larger number of SVRMHC models available allowed for an updated evaluation of the performance of the SVRMHC method compared to other well- known linear modeling methods. CONCLUSION: SVRMHC is an accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. We believe it will prove to be a valuable resource for T cell epitope researchers

Integrated siRNA design based on surveying of features associated with high RNAi effectiveness

BACKGROUND: Short interfering RNAs have allowed the development of clean and easily regulated methods for disruption of gene expression. However, while these methods continue to grow in popularity, designing effective siRNA experiments can be challenging. The various existing siRNA design guidelines suffer from two problems: they differ considerably from each other, and they produce high levels of false-positive predictions when tested on data of independent origins. RESULTS: Using a distinctly large set of siRNA efficacy data assembled from a vast diversity of origins (the siRecords data, containing records of 3,277 siRNA experiments targeting 1,518 genes, derived from 1,417 independent studies), we conducted extensive analyses of all known features that have been implicated in increasing RNAi effectiveness. A number of features having positive impacts on siRNA efficacy were identified. By performing quantitative analyses on cooperative effects among these features, then applying a disjunctive rule merging (DRM) algorithm, we developed a bundle of siRNA design rule sets with the false positive problem well curbed. A comparison with 15 online siRNA design tools indicated that some of the rule sets we developed surpassed all of these design tools commonly used in siRNA design practice in positive predictive values (PPVs). CONCLUSION: The availability of the large and diverse siRNA dataset from siRecords and the approach we describe in this report have allowed the development of highly effective and generally applicable siRNA design rule sets. Together with ever improving RNAi lab techniques, these design rule sets are expected to make siRNAs a more useful tool for molecular genetics, functional genomics, and drug discovery studies

Bis{2,4-dibromo-6-[(2-phenyl­eth­yl)imino­meth­yl]phenolato-κ2 N,O}cobalt(II)

In the title complex, [Co(C15H12Br2NO)2], the CoII atom is four-coordinated by two N,O-bidentate chelate Schiff base ligands, displaying a flattened tetra­hedral coordination environment. The CoII atom occupies a special position on a twofold rotation axis. In the crystal, mol­ecules are linked via weak C—H⋯Br inter­actions

The enhancement of electrochemical capacitance of biomass-carbon by pyrolysis of extracted nanofibers

Biomass-derived carbons have been extensively researched as electrode material for energy storage and conversion recently. However, most of the previous works convert crude biomass directly into carbon and the electrochemical capacitances for the resultant carbons are quite often underestimated as well as large variations in capacitances exist in literatures due to the complex nature of biomass, which practically hinder their applications. In this work, polysaccharide nanofibers were extracted from an inexpensive natural fungus using a hydrothermal method and were converted to porous carbon nanofibers (CNFs) by potassium hydroxide activation. The porous carbons were assembled into symmetric supercapacitors using both potassium hydroxide and an ionic liquid (IL) as electrolytes. Solid state nuclear magnetic resonance characterization showed that the micropores of the as-prepared carbons are accessible to the IL electrolyte when uncharged and thus high capacitance is expected. It is found in both electrolytes the electrochemical capacitances of CNFs are significantly higher than those of the porous carbon derived directly from the crude fungus. Furthermore, the CNFs delivered an extraordinary energy density of 92.3 Wh kg−1 in the IL electrolyte, making it a promising candidate for electrode materials for supercapacitors.<br/

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information

<p>Abstract</p> <p>Background</p> <p>The zebrafish is a powerful model vertebrate amenable to high throughput <it>in vivo </it>genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies.</p> <p>Description</p> <p>The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced.</p> <p>Conclusion</p> <p>MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.</p