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Articles 1 - 3 of 3
Full-Text Articles in Physical Sciences and Mathematics
Endothelial Cell Capture Of Heparin-Binding Growth Factors Under Flow, Bing Zhao, Changjiang Zhang, Kimberly Forsten-Williams, Jun Zhang, Michael Fannon
Endothelial Cell Capture Of Heparin-Binding Growth Factors Under Flow, Bing Zhao, Changjiang Zhang, Kimberly Forsten-Williams, Jun Zhang, Michael Fannon
Ophthalmology and Visual Science Faculty Publications
Circulation is an important delivery method for both natural and synthetic molecules, but microenvironment interactions, regulated by endothelial cells and critical to the molecule's fate, are difficult to interpret using traditional approaches. In this work, we analyzed and predicted growth factor capture under flow using computer modeling and a three-dimensional experimental approach that includes pertinent circulation characteristics such as pulsatile flow, competing binding interactions, and limited bioavailability. An understanding of the controlling features of this process was desired. The experimental module consisted of a bioreactor with synthetic endothelial-lined hollow fibers under flow. The physical design of the system was incorporated …
Mapsplice: Accurate Mapping Of Rna-Seq Reads For Splice Junction Discovery, Kai Wang, Darshan Singh, Zheng Zeng, Stephen J. Coleman, Yan Huang, Gleb L. Savich, Xiaping He, Piotr Mieczkowski, Sara A. Grimm, Charles M. Perou, James N. Macleod, Derek Y. Chiang, Jan F. Prins, Jinze Liu
Mapsplice: Accurate Mapping Of Rna-Seq Reads For Splice Junction Discovery, Kai Wang, Darshan Singh, Zheng Zeng, Stephen J. Coleman, Yan Huang, Gleb L. Savich, Xiaping He, Piotr Mieczkowski, Sara A. Grimm, Charles M. Perou, James N. Macleod, Derek Y. Chiang, Jan F. Prins, Jinze Liu
Computer Science Faculty Publications
The accurate mapping of reads that span splice junctions is a critical component of all analytic techniques that work with RNA-seq data. We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (≥75 bp). MapSplice is not dependent on splice site features or intron length, consequently it can detect novel canonical as well as non-canonical splices. MapSplice leverages the quality and diversity of read alignments of a given splice to increase accuracy. We demonstrate that MapSplice achieves higher sensitivity and specificity than TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support the accuracy of the algorithm. Splice junctions derived from eight breast cancer RNA-seq datasets recapitulated the extensiveness of alternative splicing on a global level as well as the differences between molecular subtypes of breast cancer. These combined results indicate that MapSplice is a highly accurate algorithm for the alignment of RNA-seq reads to splice junctions. Software download URL: http://www.netlab.uky.edu/p/bioinfo/MapSplice.
Scalable Object Recognition Using Hierarchical Quantization With A Vocabulary Tree, David Nistér, Henrik Stewénius
Scalable Object Recognition Using Hierarchical Quantization With A Vocabulary Tree, David Nistér, Henrik Stewénius
Center for Visualization and Virtual Environments Faculty Patents
An image retrieval technique employing a novel hierarchical feature/descriptor vector quantizer tool—‘vocabulary tree’, of sorts comprising hierarchically organized sets of feature vectors—that effectively partitions feature space in a hierarchical manner, creating a quantized space that is mapped to integer encoding. The computerized implementation of the new technique(s) employs subroutine components, such as: A trainer component of the tool generates a hierarchical quantizer, Q, for application/use in novel image-insertion and image-query stages. The hierarchical quantizer, Q, tool is generated by running k-means on the feature (a/k/a descriptor) space, recursively, on each of a plurality of nodes of a resulting quantization level …