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"abstract": "Mutation hotspots are either solitary amino acid residues or stretches of amino acids that show elevated mutation frequency in cancer-related genes, but their prevalence and biological relevance are not completely understood. Here, we developed a Smith-Waterman algorithm-based mutation hotspot discovery method, MutClustSW, to identify mutation hotspots of either single or clustered amino acid residues. We identified 181 missense mutation hotspots from COSMIC and TCGA mutation databases. In addition to 77 single amino acid residue hotspots (42.5 percent) including well-known mutation hotspots such as IDH1 (p.R132) and BRAF (p.V600), we identified 104 mutation hotspots (57.5 percent) as clusters or stretches of multiple amino acids, and the hotspots on MUC2, EPPK1, KMT2C, and TP53 were larger than 50 amino acids. Twelve of 27 nonsense mutation hotspots (44.4 percent) were observed in four cancer-related genes, TP53, ARID1A, CDKN2A, and PTEN, suggesting that truncating mutations on some tumor suppressor genes are not randomly distributed as previously assumed. We also show that hotspot mutations have higher mutation allele frequency than non-hotspots, and the hotspot information can be used to prioritize the cancer drivers. Together, the proposed algorithm and the mutation hotspot information can serve as valuable resources in the selection of functional driver mutations and associated genes.",
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"content": "Mutation hotspots are either solitary amino acid residues or stretches of amino acids that show elevated mutation frequency in cancer-related genes, but their prevalence and biological relevance are not completely understood. Here, we developed a Smith-Waterman algorithm-based mutation hotspot discovery method, MutClustSW, to identify mutation hotspots of either single or clustered amino acid residues. We identified 181 missense mutation hotspots from COSMIC and TCGA mutation databases. In addition to 77 single amino acid residue hotspots (42.5 percent) including well-known mutation hotspots such as IDH1 (p.R132) and BRAF (p.V600), we identified 104 mutation hotspots (57.5 percent) as clusters or stretches of multiple amino acids, and the hotspots on MUC2, EPPK1, KMT2C, and TP53 were larger than 50 amino acids. Twelve of 27 nonsense mutation hotspots (44.4 percent) were observed in four cancer-related genes, TP53, ARID1A, CDKN2A, and PTEN, suggesting that truncating mutations on some tumor suppressor genes are not randomly distributed as previously assumed. We also show that hotspot mutations have higher mutation allele frequency than non-hotspots, and the hotspot information can be used to prioritize the cancer drivers. Together, the proposed algorithm and the mutation hotspot information can serve as valuable resources in the selection of functional driver mutations and associated genes.",
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"affiliation": "Department of Medical Informatics, Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea",
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"abstract": "Remote homology detection represents a central problem in bioinformatics, where the challenge is to detect functionally related proteins when their sequence similarity is low. Recent solutions employ representations derived from the sequence profile, obtained by replacing each amino acid of the sequence by the corresponding most probable amino acid in the profile. However, the information contained in the profile could be exploited more deeply, provided that there is a representation able to capture and properly model such crucial evolutionary information. In this paper, we propose a novel profile-based representation for sequences, called soft Ngram. This representation, which extends the traditional Ngram scheme (obtained by grouping N consecutive amino acids), permits considering all of the evolutionary information in the profile: this is achieved by extracting Ngrams from the whole profile, equipping them with a weight directly computed from the corresponding evolutionary frequencies. We illustrate two different approaches to model the proposed representation and to derive a feature vector, which can be effectively used for classification using a support vector machine (SVM). A thorough evaluation on three benchmarks demonstrates that the new approach outperforms other Ngram-based methods, and shows very promising results also in comparison with a broader spectrum of techniques.",
"abstracts": [
{
"abstractType": "Regular",
"content": "Remote homology detection represents a central problem in bioinformatics, where the challenge is to detect functionally related proteins when their sequence similarity is low. Recent solutions employ representations derived from the sequence profile, obtained by replacing each amino acid of the sequence by the corresponding most probable amino acid in the profile. However, the information contained in the profile could be exploited more deeply, provided that there is a representation able to capture and properly model such crucial evolutionary information. In this paper, we propose a novel profile-based representation for sequences, called soft Ngram. This representation, which extends the traditional Ngram scheme (obtained by grouping N consecutive amino acids), permits considering all of the evolutionary information in the profile: this is achieved by extracting Ngrams from the whole profile, equipping them with a weight directly computed from the corresponding evolutionary frequencies. We illustrate two different approaches to model the proposed representation and to derive a feature vector, which can be effectively used for classification using a support vector machine (SVM). A thorough evaluation on three benchmarks demonstrates that the new approach outperforms other Ngram-based methods, and shows very promising results also in comparison with a broader spectrum of techniques.",
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"abstract": "With a structural bioinformatic approach, we have explored amino acid compositions at PISA defined interfaces between small molecules and proteins that are contained in an optimized subset of 11,351 PDB files. The use of a series of restrictions, to prevent redundancy and biases from interactions between amino acids with charged side chains and ions, yielded a final data set of 45,230 protein-small molecule interfaces. We have compared occurrences of natural amino acids in surface exposed regions and binding sites for all the proteins of our data set. From our structural bioinformatic survey, the most relevant signal arose from the unexpected Gly abundance at enzyme catalytic sites. This finding suggested that Gly must have a fundamental role in stabilizing concave protein surface moieties. Subsequently, we have tried to predict the effect of <italic>in silico</italic> Gly mutations in hen egg white lysozyme to optimize those conditions that can reshape the protein surface with the appearance of new pockets. Replacing amino acids having bulky side chains with Gly in specific protein regions seems a feasible way for designing proteins with additional surface pockets, which can alter protein surface dynamics, therefore, representing controllable switches for protein activity.",
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"content": "With a structural bioinformatic approach, we have explored amino acid compositions at PISA defined interfaces between small molecules and proteins that are contained in an optimized subset of 11,351 PDB files. The use of a series of restrictions, to prevent redundancy and biases from interactions between amino acids with charged side chains and ions, yielded a final data set of 45,230 protein-small molecule interfaces. We have compared occurrences of natural amino acids in surface exposed regions and binding sites for all the proteins of our data set. From our structural bioinformatic survey, the most relevant signal arose from the unexpected Gly abundance at enzyme catalytic sites. This finding suggested that Gly must have a fundamental role in stabilizing concave protein surface moieties. Subsequently, we have tried to predict the effect of <italic>in silico</italic> Gly mutations in hen egg white lysozyme to optimize those conditions that can reshape the protein surface with the appearance of new pockets. Replacing amino acids having bulky side chains with Gly in specific protein regions seems a feasible way for designing proteins with additional surface pockets, which can alter protein surface dynamics, therefore, representing controllable switches for protein activity.",
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"abstract": "Abstract—Classification of texture images, especially those with different orientation and scale changes, is a challenging and important problem in image analysis and classification. This paper proposes an effective scheme for rotation and scale invariant texture classification using log-polar wavelet signatures. The rotation and scale invariant feature extraction for a given image involves applying a log-polar transform to eliminate the rotation and scale effects, but at same time produce a row shifted log-polar image, which is then passed to an adaptive row shift invariant wavelet packet transform to eliminate the row shift effects. So, the output wavelet coefficients are rotation and scale invariant. The adaptive row shift invariant wavelet packet transform is quite efficient with only O (n \\cdot log n) complexity. A feature vector of the most dominant log-polar wavelet energy signatures extracted from each subband of wavelet coefficients is constructed for rotation and scale invariant texture classification. In the experiments, we employed a Mahalanobis classifier to classify a set of 25 distinct natural textures selected from the Brodatz album. The experimental results, based on different testing data sets for images with different orientations and scales, show that the proposed classification scheme using log-polar wavelet signatures outperforms two other texture classification methods, its overall accuracy rate for joint rotation and scale invariance being 90.8 percent, demonstrating that the extracted energy signatures are effective rotation and scale invariant features. Concerning its robustness to noise, the classification scheme also performs better than the other methods.",
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"abstract": "Shared-control haptic guidance is a common form of robot-mediated training used to teach novice subjects to perform dynamic tasks. Shared-control guidance is distinct from more traditional guidance controllers, such as virtual fixtures, in that it provides novices with real-time visual and haptic feedback from a real or virtual expert. Previous studies have shown varying levels of training efficacy using shared-control guidance paradigms; it is hypothesized that these mixed results are due to interactions between specific guidance implementations (“paradigms”) and tasks. This work proposes a novel guidance paradigm taxonomy intended to help classify and compare the multitude of implementations in the literature, as well as a revised proxy rendering model to allow for the implementation of more complex guidance paradigms. The efficacies of four common paradigms are compared in a controlled study with 50 healthy subjects and two dynamic tasks. The results show that guidance paradigms must be matched to a task's dynamic characteristics to elicit effective training and low workload. Based on these results, we provide suggestions for the future development of improved haptic guidance paradigms.",
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"content": "Shared-control haptic guidance is a common form of robot-mediated training used to teach novice subjects to perform dynamic tasks. Shared-control guidance is distinct from more traditional guidance controllers, such as virtual fixtures, in that it provides novices with real-time visual and haptic feedback from a real or virtual expert. Previous studies have shown varying levels of training efficacy using shared-control guidance paradigms; it is hypothesized that these mixed results are due to interactions between specific guidance implementations (“paradigms”) and tasks. This work proposes a novel guidance paradigm taxonomy intended to help classify and compare the multitude of implementations in the literature, as well as a revised proxy rendering model to allow for the implementation of more complex guidance paradigms. The efficacies of four common paradigms are compared in a controlled study with 50 healthy subjects and two dynamic tasks. The results show that guidance paradigms must be matched to a task's dynamic characteristics to elicit effective training and low workload. Based on these results, we provide suggestions for the future development of improved haptic guidance paradigms.",
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