Computational framework to integrate the effect of antigen recognition on disease epidemiology outcome: multi-scale approach

Human Leukocyte Antigen (HLA) plays an important role, in presenting foreign pathogens to our immune system, there by eliciting early immune responses. HLA genes are highly polymorphic, giving rise to diverse antigen presentation capability. An important factor contributing to enormous variations in individual responses to diseases is differences in their HLA profiles. The heterogeneity in allele specific disease responses decides the overall disease epidemiological outcome. Here we propose an agent based computational framework, capable of incorporating allele specific information, to analyze disease epidemiology. This framework assumes a SIR model to estimate average disease transmission and recovery rate. Using epitope prediction tool, it performs sequence based epitope detection for a given the pathogenic genome and derives an allele specific disease susceptibility index depending on the epitope detection efficiency. The allele specific disease transmission rate, that follows, is then fed to the agent based epidemiology model, to analyze the disease outcome. The methodology presented here has a potential use in understanding how a disease spreads and effective measures to control the disease.

The interaction of N-trifluoroacetylgalactosamine and its derivatives with winged bean (Psophocarpus tetragonolobus) basic agglutinin reveals differential mechanism of their recognition: a fluorine-19 nuclear magnetic resonance study

Here, we show the binding results of a leguminosae lectin, winged bean basic agglutinin (WBA I) to N-trifluoroacetylgalactosamine (NTFAGalN), methyl-alpha-N-trifluoroacetylgalactosamine (Me alpha NTFAGalN) and methyl-beta-tifluoroacetylgalactosamine (Me beta NTFAGalN) using (19) F NMR spectroscopy. No chemical shift difference between the free and bound states for NTFAGalN and Me beta NTFAGalN, and 0.01-ppm chemical shift change for Me alpha NTFAGalN, demonstrate that the Me alpha NTFAGalN has a sufficiently long residence time on the protein binding site as compared to Me beta NTFAGalN and the free anomers of NTFAGalN. The sugar anomers were found in slow exchange with the binding site of agglutinin. Consequently, we obtained their binding parameters to the protein using line shape analyses. Aforementioned analyses of the activation parameters for the interactions of these saccharides indicate that the binding of alpha and beta anomers of NTFAGalN and Me alpha NTFAGalN is controlled enthalpically, while that of Me beta NTFAGalN is controlled entropically. This asserts the sterically constrained nature of the interaction of the Me beta NTFAGalN with WBA I. These studies thus highlight a significant role of the conformation of the monosaccharide ligands for their recognition by WBA I.

Hierarchical sampling for metastable conformers determines biomolecular recognition: the case of malectin and diglucosylated N-glycan interactions

Structural information over the entire course of binding interactions based on the analyses of energy landscapes is described, which provides a framework to understand the events involved during biomolecular recognition. Conformational dynamics of malectin's exquisite selectivity for diglucosylated N-glycan (Dig-N-glycan), a highly flexible oligosaccharide comprising of numerous dihedral torsion angles, are described as an example. For this purpose, a novel approach based on hierarchical sampling for acquiring metastable molecular conformations constituting low-energy minima for understanding the structural features involved in a biologic recognition is proposed. For this purpose, four variants of principal component analysis were employed recursively in both Cartesian space and dihedral angles space that are characterized by free energy landscapes to select the most stable conformational substates. Subsequently, k-means clustering algorithm was implemented for geometric separation of the major native state to acquire a final ensemble of metastable conformers. A comparison of malectin complexes was then performed to characterize their conformational properties. Analyses of stereochemical metrics and other concerted binding events revealed surface complementarity, cooperative and bidentate hydrogen bonds, water-mediated hydrogen bonds, carbohydrate-aromatic interactions including CH-pi and stacking interactions involved in this recognition. Additionally, a striking structural transition from loop to beta-strands in malectin CRD upon specific binding to Dig-N-glycan is observed. The interplay of the above-mentioned binding events in malectin and Dig-N-glycan supports an extended conformational selection model as the underlying binding mechanism.

Sensory cues employed for the acquisition of familiarity-dependent recognition of a shoal of conspecifics by climbing perch (Anabas testudineus Bloch)

In this study we showed that a freshwater fish, the climbing perch (Anabas testudineus) is incapable of using chemical communication but employs visual cues to acquire familiarity and distinguish a familiar group of conspecifics from an unfamiliar one. Moreover, the isolation of olfactory signals from visual cues did not affect the recognition and preference for a familiar shoal in this species.

BIMODAL NANOINDENTATION RESPONSE OF THE (001) FACE IN CRYSTALLINE SODIUM SACCHARIN DIHYDRATE

The nanoindentation response of the (001) face of sodium saccharin dihydrate is examined. The structure can be demarcated into regular and irregular regions or domains. The regular domains have solid-like and the irregular ones have liquid-like characteristics. Therefore, these domains impart a microstructure to the crystal. The indent face (001) is prominently developed in this crystal and unambiguously presents the regular and irregular regions to nanoindention. Average values of elastic modulus and hardness show a distinct bimodal mechanical response. Such a response has been observed in the case of intergrown polymorphs of aspirin and felodipine. We examine two possible reasons as to why the responses could be for bimodal in this crystal. The first possibility could be that the two domains correspond to regions of the original dihydrate and a lower hydrate that is obtained by the loss of some water. The second possibility could be that these responses correspond to regular and irregular regions in the structure. Nanoindentation is a very useful technique in the characterization of molecular solids, as a complementary technique to X-ray crystallography, because it samples different length scales.

Human Action Recognition in Compressed Domain using PBL-McRBFN Approach

Large variations in human actions lead to major challenges in computer vision research. Several algorithms are designed to solve the challenges. Algorithms that stand apart, help in solving the challenge in addition to performing faster and efficient manner. In this paper, we propose a human cognition inspired projection based learning for person-independent human action recognition in the H.264/AVC compressed domain and demonstrate a PBL-McRBEN based approach to help take the machine learning algorithms to the next level. Here, we use gradient image based feature extraction process where the motion vectors and quantization parameters are extracted and these are studied temporally to form several Group of Pictures (GoP). The GoP is then considered individually for two different bench mark data sets and the results are classified using person independent human action recognition. The functional relationship is studied using Projection Based Learning algorithm of the Meta-cognitive Radial Basis Function Network (PBL-McRBFN) which has a cognitive and meta-cognitive component. The cognitive component is a radial basis function network while the Meta-Cognitive Component(MCC) employs self regulation. The McC emulates human cognition like learning to achieve better performance. Performance of the proposed approach can handle sparse information in compressed video domain and provides more accuracy than other pixel domain counterparts. Performance of the feature extraction process achieved more than 90% accuracy using the PTIL-McRBFN which catalyzes the speed of the proposed high speed action recognition algorithm. We have conducted twenty random trials to find the performance in GoP. The results are also compared with other well known classifiers in machine learning literature.

An Optical How Feature and McFIS Based Approach for 3-Dimensional Human Action Recognition

We propose to develop a 3-D optical flow features based human action recognition system. Optical flow based features are employed here since they can capture the apparent movement in object, by design. Moreover, they can represent information hierarchically from local pixel level to global object level. In this work, 3-D optical flow based features a re extracted by combining the 2-1) optical flow based features with the depth flow features obtained from depth camera. In order to develop an action recognition system, we employ a Meta-Cognitive Neuro-Fuzzy Inference System (McFIS). The m of McFIS is to find the decision boundary separating different classes based on their respective optical flow based features. McFIS consists of a neuro-fuzzy inference system (cognitive component) and a self-regulatory learning mechanism (meta-cognitive component). During the supervised learning, self-regulatory learning mechanism monitors the knowledge of the current sample with respect to the existing knowledge in the network and controls the learning by deciding on sample deletion, sample learning or sample reserve strategies. The performance of the proposed action recognition system was evaluated on a proprietary data set consisting of eight subjects. The performance evaluation with standard support vector machine classifier and extreme learning machine indicates improved performance of McFIS is recognizing actions based of 3-D optical flow based features.

Database Independent Human Emotion Recognition with Meta-Cognitive Neuro-Fuzzy Inference System

Facial emotions are the most expressive way to display emotions. Many algorithms have been proposed which employ a particular set of people (usually a database) to both train and test their model. This paper focuses on the challenging task of database independent emotion recognition, which is a generalized case of subject-independent emotion recognition. The emotion recognition system employed in this work is a Meta-Cognitive Neuro-Fuzzy Inference System (McFIS). McFIS has two components, a neuro-fuzzy inference system, which is the cognitive component and a self-regulatory learning mechanism, which is the meta-cognitive component. The meta-cognitive component, monitors the knowledge in the neuro-fuzzy inference system and decides on what-to-learn, when-to-learn and how-to-learn the training samples, efficiently. For each sample, the McFIS decides whether to delete the sample without being learnt, use it to add/prune or update the network parameter or reserve it for future use. This helps the network avoid over-training and as a result improve its generalization performance over untrained databases. In this study, we extract pixel based emotion features from well-known (Japanese Female Facial Expression) JAFFE and (Taiwanese Female Expression Image) TFEID database. Two sets of experiment are conducted. First, we study the individual performance of both databases on McFIS based on 5-fold cross validation study. Next, in order to study the generalization performance, McFIS trained on JAFFE database is tested on TFEID and vice-versa. The performance The performance comparison in both experiments against SVNI classifier gives promising results.

Action Recognition from Motion Capture Data using Meta-cognitive RBF Network Classifier

Action recognition plays an important role in various applications, including smart homes and personal assistive robotics. In this paper, we propose an algorithm for recognizing human actions using motion capture action data. Motion capture data provides accurate three dimensional positions of joints which constitute the human skeleton. We model the movement of the skeletal joints temporally in order to classify the action. The skeleton in each frame of an action sequence is represented as a 129 dimensional vector, of which each component is a 31) angle made by each joint with a fixed point on the skeleton. Finally, the video is represented as a histogram over a codebook obtained from all action sequences. Along with this, the temporal variance of the skeletal joints is used as additional feature. The actions are classified using Meta-Cognitive Radial Basis Function Network (McRBFN) and its Projection Based Learning (PBL) algorithm. We achieve over 97% recognition accuracy on the widely used Berkeley Multimodal Human Action Database (MHAD).

Human action recognition in H.264/AVC compressed domain using meta-cognitive radial basis function network

In this paper, we propose a H.264/AVC compressed domain human action recognition system with projection based metacognitive learning classifier (PBL-McRBFN). The features are extracted from the quantization parameters and the motion vectors of the compressed video stream for a time window and used as input to the classifier. Since compressed domain analysis is done with noisy, sparse compression parameters, it is a huge challenge to achieve performance comparable to pixel domain analysis. On the positive side, compressed domain allows rapid analysis of videos compared to pixel level analysis. The classification results are analyzed for different values of Group of Pictures (GOP) parameter, time window including full videos. The functional relationship between the features and action labels are established using PBL-McRBFN with a cognitive and meta-cognitive component. The cognitive component is a radial basis function, while the meta-cognitive component employs self-regulation to achieve better performance in subject independent action recognition task. The proposed approach is faster and shows comparable performance with respect to the state-of-the-art pixel domain counterparts. It employs partial decoding, which rules out the complexity of full decoding, and minimizes computational load and memory usage. This results in reduced hardware utilization and increased speed of classification. The results are compared with two benchmark datasets and show more than 90% accuracy using the PBL-McRBFN. The performance for various GOP parameters and group of frames are obtained with twenty random trials and compared with other well-known classifiers in machine learning literature. (C) 2015 Elsevier B.V. All rights reserved.

Compressed domain human action recognition in H.264/AVC video streams

This paper discusses a novel high-speed approach for human action recognition in H.264/AVC compressed domain. The proposed algorithm utilizes cues from quantization parameters and motion vectors extracted from the compressed video sequence for feature extraction and further classification using Support Vector Machines (SVM). The ultimate goal of the proposed work is to portray a much faster algorithm than pixel domain counterparts, with comparable accuracy, utilizing only the sparse information from compressed video. Partial decoding rules out the complexity of full decoding, and minimizes computational load and memory usage, which can result in reduced hardware utilization and faster recognition results. The proposed approach can handle illumination changes, scale, and appearance variations, and is robust to outdoor as well as indoor testing scenarios. We have evaluated the performance of the proposed method on two benchmark action datasets and achieved more than 85 % accuracy. The proposed algorithm classifies actions with speed (> 2,000 fps) approximately 100 times faster than existing state-of-the-art pixel-domain algorithms.

Digital image analysis around isotropic points for photoelastic pattern recognition

Fringe tracking and fringe order assignment have become the central topics of current research in digital photoelasticity. Isotropic points (IPs) appearing in low fringe order zones are often either overlooked or entirely missed in conventional as well as digital photoelasticity. We aim to highlight image processing for characterizing IPs in an isochromatic fringe field. By resorting to a global analytical solution of a circular disk, sensitivity of IPs to small changes in far-field loading on the disk is highlighted. A local theory supplements the global closed-form solutions of three-, four-, and six-point loading configurations of circular disk. The local theoretical concepts developed in this paper are demonstrated through digital image analysis of isochromatics in circular disks subjected to three-and four-point loads. (C) 2015 Society of Photo-Optical Instrumentation Engineers (SPIE)

Activity Recognition in Egocentric Life-Logging Videos

With the increasing availability of wearable cameras, research on first-person view videos (egocentric videos) has received much attention recently. While some effort has been devoted to collecting various egocentric video datasets, there has not been a focused effort in assembling one that could capture the diversity and complexity of activities related to life-logging, which is expected to be an important application for egocentric videos. In this work, we first conduct a comprehensive survey of existing egocentric video datasets. We observe that existing datasets do not emphasize activities relevant to the life-logging scenario. We build an egocentric video dataset dubbed LENA (Life-logging EgoceNtric Activities) (http://people.sutd.edu.sg/similar to 1000892/dataset) which includes egocentric videos of 13 fine-grained activity categories, recorded under diverse situations and environments using the Google Glass. Activities in LENA can also be grouped into 5 top-level categories to meet various needs and multiple demands for activities analysis research. We evaluate state-of-the-art activity recognition using LENA in detail and also analyze the performance of popular descriptors in egocentric activity recognition.