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Pitigala S.,Center for Computational science | Li C.,MTSU
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2014

PubMed is the most comprehensive citation database in the field of biomedicine. It contains over 23 million citations from MEDLINE, life science journals and books. However, retrieving relevant information from PubMed is challenging due to its size and rapid growth. Keyword based information retrieval is not adequate in PubMed. Many tools have been developed to enhance the quality of information retrieval from PubMed. PubMed Related Article (PMRA) feature is one approach developed to help the users retrieve information efficiently. It finds highly related citations to a given citation. This study focuses on extending the PMRA feature to multiple citations in the context of personalized information retrieval. Our experimental results show that the extended PMRA feature using the words appearing in two or more citations is able to find more relevant articles than using the PMRA feature on individual PubMed citations. © 2014 Springer International Publishing Switzerland.

Staaterman E.,University of Miami | Paris C.B.,University of Miami | Helgers J.,Center for Computational science
Journal of Theoretical Biology | Year: 2012

Larval reef fish possess considerable swimming and sensory abilities, which could enable navigation towards settlement habitat from the open ocean. Due to their small size and relatively low survival, tagging individual larvae is not a viable option, but numerical modeling studies have proven useful for understanding the role of orientation throughout ontogeny. Here we combined the theoretical framework of the biased correlated random walk model with a very high resolution three-dimensional coupled biophysical model to investigate the role of orientation behavior in fish larvae. Virtual larvae of the bicolor damselfish (Stegastes partitus) were released daily during their peak spawning period from two locations in the Florida Keys Reef Tract, a region of complex eddy fields bounded by the strong Florida Current. The larvae began orientation behavior either before or during flexion, and only larvae that were within a given maximum detection distance from the reef were allowed to orient. They were subjected to ontogenetic vertical migration, increased their swimming speed during ontogeny, and settled on reefs within a flexible window of 24 to 32 days of pelagic duration. Early orientation, as well as a large maximum detection distance, increased settlement, implying that the early use of large-scale cues increases survival. Orientation behavior also increased the number of larvae that settled near their home reef, providing evidence that orientation is a mechanism driving self-recruitment. This study demonstrates that despite the low swimming abilities of the earliest larval stages, orientation during this "critical period" would have remarkable demographic consequences. © 2012 Elsevier Ltd.

Mansour N.N.,NASA | Panerai F.,University of Kentucky | Panerai F.,NASA | Martin A.,University of Kentucky | And 8 more authors.
44th AIAA Thermophysics Conference | Year: 2013

The morphology characteristics and ablation behavior of a highly porous carbon fiber preform are studied using a combined experimental/numerical approach. Morphological characterization of the three-dimensional structure of the material is performed by hard X-rays synchrotron micro-tomography at the Advanced Light Source of Lawrence Berkeley National Laboratory. The resulting micro-tomography voxels are used to compute geometrical properties of the carbon preform, like porosity, specific surface area and tortuosity, that are otherwise indirectly measured through experimental techniques. The reconstructed volumes are used to build a computational grid for numerical simulations of the fibers' ablation. By modeling the diffusion of oxygen through the porous medium using Lagrangian methods, and the oxidation at the carbon fibers' surface using a reactivity model, the ablation of the carbon fibers are simulated for a range of Thiele numbers. It is shown that in the diffusion limited regime (large Thiele number), the ablation of the fibers occurs at the surface of the material. In the reaction limited regime (low Thiele number), the oxygen penetrates into the fibers, resulting in volumetric ablation and high material spallation.

Martin A.,University of Kentucky | Martin A.,Center for Computational science | Boyd I.D.,University of Michigan
Journal of Spacecraft and Rockets | Year: 2015

The steps necessary to achieve the strong coupling between a flowfield solver and a material response solver are presented. This type of coupling is required to accurately capture the complex aerothermodynamic physics occurring during hypersonic atmospheric entries. A blowing boundary condition for the flowfield solver is proposed. This allows the ablating gas calculated by the material response solver to be correctly injected in the boundary layer. A moving mesh algorithm for the flowfield solver that implicitly enforces the geometric conservation law is presented. Using that capability, a mesh movement procedure for surface recession and for accurate shock capturing is proposed. The entire technique is tested using a material response solver with surface ablation and pyrolysis coupled to a hypersonic solver for weakly ionized flows in thermochemical nonequilibrium. Results using the reentry trajectory of the IRV-2 test vehicle are presented, showing that the surface heat fluxes remain accurate as the vehicle geometry and freestream conditions change. Copyright © 2014 by Alexandre Martin and Iain D. Boyd.

Hunter P.,University of Auckland | Hunter P.,University of Oxford | Coveney P.V.,Center for Computational science | De Bono B.,European Bioinformatics Institute | And 22 more authors.
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2010

European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE. © 2010 The Royal Society.

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