Design of a grid service-based platform for in silico protein-ligand screenings

Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound "drug-like" subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.     

Dynamic changes in the use of online advice in response to task success or failure

A range of responsible gambling systems have been developed, but they are not necessarily used by consumers. This requires an understanding of factors (e.g. risk and loss) influencing response to advice. Therefore, an experiment examined the use of decisional support in response to induced success or failure. A total of 21 university students played computer Blackjack at two levels of risk, and were informed as to whether the odds were in their favour (‘card count’), and were given online advice as to card selection (Basic). Winning streaks led to overconfidence, as indicated by larger mean bets, more Basic errors, and a failure to adjust wagering upon cessation of the winning streak. Participants were more cautious in response to losses, betting less, and were more likely to comply with advice. Participants attended and complied with advice earlier at low risk, but at high risk noticed advice later and did not comply. Induced emotional states (e.g. winning or losing) are important as they influence the likelihood that people will listen to online advice. Designers of Behaviour Change Support Systems should consider methods of contingently implementing advice.     

Evaluation of terrain and canopy height products in central African tropical forests

Since the introduction of space-based altimetry data into the science community, global products associated with elevation and vegetation metrics have been heavily utilized for a variety of ecological applications. Satellite remote sensing enables the collection of global (or near-global), standardized data sets, which can be used in their original form or used as inputs along with other data sets in generating new products. Recent effort has focused on using available data to generate maps of tree heights at a global scale in the service of a better understanding of above ground biomass distribution and its effects on global carbon storage. However, global data sets, while validated at a global scale, often display local and regional variations in accuracy which must be quantified before applying those data sets to smaller scale studies. This work addresses the need for a better understanding of the quality of the Shuttle Radar Topography Mission (SRTM) 90 m digital elevation model and a global 1 km canopy height model in the dense tropical forests of Gabon by using a small-footprint airborne lidar survey and large-footprint, space-based waveform lidar data from teh National Air and Space Administration’s Ice, Cloud, and land Elevation Satellite (ICESat) for validation. As expected, the study found SRTM elevations to be heavily biased by vegetation in this biome, with elevations consistently located within the canopy volume. In addition, the global canopy height model consistently underestimates maximum canopy height at both local and regional scales.     

Examining the predictive relationship between personality and emotion traits and students’ agent-directed emotions: towards emotionally-adaptive agent-based learning environments

The current study examined the relationships between learners’ (\(N = 123\)) personality traits, the emotions they typically experience while studying (trait studying emotions), and the emotions they reported experiencing as a result of interacting with four pedagogical agents (agent-directed emotions) in MetaTutor, an advanced multi-agent learning environment. Overall, significant relationships between a subset of trait emotions (trait anger, trait anxiety) and personality traits (agreeableness, conscientiousness, and neuroticism) were found for four agent-directed emotions (enjoyment, pride, boredom, and neutral) though the relationships differed between pedagogical agents. These results demonstrate that some trait emotions and personality traits can be used to predict learners’ emotions directed toward specific pedagogical agents (with different roles). Results provide suggestions for adapting pedagogical agents to support learners’ (with certain characteristics; e.g., high in neuroticism or agreeableness) experience of adaptive emotions (e.g., enjoyment) and minimize their experience on non-adaptive emotions (e.g., boredom). Such an approach presents a scalable and easily implementable method for creating emotionally-adaptive, agent-based learning environments, and improving learner-pedagogical agent interactions in order to support learning.     

The spring paradigm in tracking control of simple mechanical systems

An intrinsic formulation of geometric proportional–derivative tracking control for fully actuated mechanical systems is developed. The region of stability is determined directly from the size of the system’s injectivity radius and, for a restricted set of control problems, the system’s locus of cut points about a desired reference point. Exponential stability is obtained under certain boundedness conditions. For controlled motion along a geodesic, the proffered scheme yields a particularly simple and elegant manifestation of the underlying use of the mass–spring–damper paradigm in the control design methodology.     

Indirect augmented reality

Developing augmented reality (AR) applications for mobile devices and outdoor environments has historically required a number of technical trade-offs related to tracking. One approach is to rely on computer vision which provides very accurate tracking, but can be brittle, and limits the generality of the application. Another approach is to rely on sensor-based tracking which enables widespread use, but at the cost of generally poor tracking performance. In this paper we present and evaluate a new approach, which we call Indirect AR, that enables perfect alignment of virtual content in a much greater number of application scenarios.To achieve this improved performance we replace the live camera view used in video see through AR with a previously captured panoramic image. By doing this we improve the perceived quality of the tracking while still maintaining a similar overall experience. There are some limitations of this technique, however, related to the use of panoramas. We evaluate these boundaries conditions on both a performance and experiential basis through two user studies. The result of these studies indicates that users preferred Indirect AR over traditional AR in most conditions, and when conditions do degrade to the point the experience changes, Indirect AR can still be a very useful tool in many outdoor application scenarios.     

Localized coarsening of conforming all-hexahedral meshes

Finite element mesh adaptation methods can be used to improve the efficiency and accuracy of solutions to computational modeling problems. In many applications involving hexahedral meshes, localized modifications which preserve a conforming all-hexahedral mesh are desired. Effective hexahedral refinement methods that satisfy these criteria have recently become available; however, due to hexahedral mesh topology constraints, little progress has been made in the area of hexahedral coarsening. This paper presents a new method to locally coarsen conforming all-hexahedral meshes. The method works on both structured and unstructured meshes and is not based on undoing previous refinement. Building upon recent developments in quadrilateral coarsening, the method utilizes hexahedral sheet and column operations, including pillowing, column collapsing, and sheet extraction. A general algorithm for automated coarsening is presented and examples of models that have been coarsened with this new algorithm are shown. While results are promising, further work is needed to improve the automated process.     

超越华硕的信心：三星与捷波共同签定采购备忘录

2008年2月26日,春节过后的喜庆气氛依然笼罩在街头。深圳作为我国南方经济增长最快和最有活力的城市。也迎来了全新的一年。IT行业在这个快速发展的城市中也占据了重要的位置。而就在这一天．捷波资讯股份有限公司与三星电子公司在三星深圳办事处签定了采购备忘录。     

Human pathogenic streptococcal proteomics and vaccine development

Gram-positive streptococci are non-motile, chain-forming bacteria commonly found in the normal oral and bowel flora of warm-blooded animals. Over the past decade, a proteomic approach combining 2-DE and MS has been used to systematically map the cellular, surface-associated and secreted proteins of human pathogenic streptococcal species. The public availability of complete streptococcal genomic sequences and the amalgamation of proteomic, genomic and bioinformatic technologies have recently facilitated the identification of novel streptococcal vaccine candidate antigens and therapeutic agents. The objective of this review is to examine the constituents of the streptococcal cell wall and secreted proteome, the mechanisms of transport of surface and secreted proteins, and describe the current methodologies employed for the identification of novel surface-displayed proteins and potential vaccine antigens.     

A bayesian approach to deformed pattern matching of iris images

We describe a general probabilistic framework for matching patterns that experience in-plane nonlinear deformations, such as iris patterns. Given a pair of images, we derive a maximum a posteriori probability (MAP) estimate of the parameters of the relative deformation between them. Our estimation process accomplishes two things simultaneously: it normalizes for pattern warping and it returns a distortion-tolerant similarity metric which can be used for matching two nonlinearly deformed image patterns. The prior probability of the deformation parameters is specific to the pattern-type and, therefore, should result in more accurate matching than an arbitrary general distribution. We show that the proposed method is very well suited for handling iris biometrics, applying it to two databases of iris images which contain real instances of warped patterns. We demonstrate a significant improvement in matching accuracy using the proposed deformed Bayesian matching methodology. We also show that the additional computation required to estimate the deformation is relatively inexpensive, making it suitable for real-time applications