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    ABSTRACT: We propose a generic online multi-target track-before-detect (MT-TBD) that is applicable on confidence maps used as observations. The proposed tracker is based on particle filtering and automatically initializes tracks. The main novelty is the inclusion of the target ID in the particle state, enabling the algorithm to deal with unknown and large number of targets. To overcome the problem of mixing IDs of targets close to each other, we propose a probabilistic model of target birth and death based on a Markov Random Field (MRF) applied to the particle IDs. Each particle ID is managed using the information carried by neighboring particles. The assignment of the IDs to the targets is performed using Mean-Shift clustering and supported by a Gaussian Mixture Model. We also show that the computational complexity of MT-TBD is proportional only to the number of particles. To compare our method with recent state-of-the-art works, we include a postprocessing stage suited for multi-person tracking. We validate the method on real-world and crowded scenarios, and demonstrate its robustness in scenes presenting different perspective views and targets very close to each other.
    No preview · Article · Jan 2013 · Computer Vision and Image Understanding
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    ABSTRACT: Protein kinases have important functions in the control of cell biology and are implicated in several diseases including cancer. Here we describe a technique to quantify protein kinase activity in a global fashion and without preconception of the kinases that may be active in the cell or tissue under investigation. In Global Kinase Activity Profiling (GKAP), protein kinases present in experimental cell lysates phosphorylate endogenous substrates, also present in the lysate, under defined conditions. Reaction products are then quantified using standard phosphoproteomic techniques based on LC-MS/MS. The technique thus allows measuring the combined activities of kinases targeting common substrates, which are detected as phosphopeptides by LC-MS/MS. Almost four hundred kinase reactions could be quantified in a human epithelial cell line, 177 of which increased in response to EGF treatment while others decreased in cells exposed to the kinase inhibitors LY294002 or U0126. GKAP also detected marked differences in the patterns of kinase activities in human leukemia cell lines with different sensitivities to kinase inhibitors. These results reveal that GKAP detects and quantifies hundreds of kinase activities modulated by growth factors or pharmacological inhibitors, and that these activities correlate with the phenotypes of cancer cells and their responses to kinase inhibitors.
    No preview · Article · Oct 2012 · Journal of proteomics
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    ABSTRACT: Phosphoproteomics is increasingly used to address a wide range of biological questions. However, despite some success, techniques for phosphoproteomics are not without challenges. Phosphoproteins are present in cells in low abundance relative to their unphosphorylated counterparts; therefore phosphorylated proteins (or phosphopeptides after protein digestion) are rarely detected in standard shotgun proteomics experiments. Thus, extraction of phosphorylated polypeptides from complex mixtures is a critical step in the success of phosphoproteomics experiments. Intense research over the last decade has resulted in the development of powerful techniques for phosphopeptide enrichment prior to analysis by mass spectrometry. Here, we review how the development of IMAC, MOAC, chemical derivatization and antibody affinity purification and chromatography is contributing to the evolution of phosphoproteomics techniques. Although further developments are needed for the technology to reach maturity, current state-of-the-art techniques can already be used as powerful tools for biological research.
    No preview · Article · Jul 2012 · Amino Acids
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