A Subspace Projection Methodology for Nonlinear Manifold Based Face Recognition

A novel feature extraction method that utilizes nonlinear mapping from the original data space to the feature space is presented in this dissertation. Feature extraction methods aim to find compact representations of data that are easy to classify. Measurements with similar values are grouped to same category, while those with differing values are deemed to be of separate categories. For most practical systems, the meaningful features of a pattern class lie in a low dimensional nonlinear constraint region (manifold) within the high dimensional data space. A learning algorithm to model this nonlinear region and to project patterns to this feature space is developed. Least squares estimation approach that utilizes interdependency between points in training patterns is used to form the nonlinear region. The proposed feature extraction strategy is employed to improve face recognition accuracy under varying illumination conditions and facial expressions. Though the face features show variations under these conditions, the features of one individual tend to cluster together and can be considered as a neighborhood. Low dimensional representations of face patterns in the feature space may lie in a nonlinear constraint region, which when modeled leads to efficient pattern classification. A feature space encompassing multiple pattern classes can be trained by modeling a separate constraint region for each pattern class and obtaining a mean constraint region by averaging all the individual regions. Unlike most other nonlinear techniques, the proposed method provides an easy intuitive way to place new points onto a nonlinear region in the feature space. The proposed feature extraction and classification method results in improved accuracy when compared to the classical linear representations. Face recognition accuracy is further improved by introducing the concepts of modularity, discriminant analysis and phase congruency into the proposed method. In the modular approach, feature components are extracted from different sub-modules of the images and concatenated to make a single vector to represent a face region. By doing this we are able to extract features that are more representative of the local features of the face. When projected onto an arbitrary line, samples from well formed clusters could produce a confused mixture of samples from all the classes leading to poor recognition. Discriminant analysis aims to find an optimal line orientation for which the data classes are well separated. Experiments performed on various databases to evaluate the performance of the proposed face recognition technique have shown improvement in recognition accuracy, especially under varying illumination conditions and facial expressions. This shows that the integration of multiple subspaces, each representing a part of a higher order nonlinear function, could represent a pattern with variability. Research work is progressing to investigate the effectiveness of subspace projection methodology for building manifolds with other nonlinear functions and to identify the optimum nonlinear function from an object classification perspective

Attention and Pooling based Sigmoid Colon Segmentation in 3D CT images

Segmentation of the sigmoid colon is a crucial aspect of treating diverticulitis. It enables accurate identification and localisation of inflammation, which in turn helps healthcare professionals make informed decisions about the most appropriate treatment options. This research presents a novel deep learning architecture for segmenting the sigmoid colon from Computed Tomography (CT) images using a modified 3D U-Net architecture. Several variations of the 3D U-Net model with modified hyper-parameters were examined in this study. Pyramid pooling (PyP) and channel-spatial Squeeze and Excitation (csSE) were also used to improve the model performance. The networks were trained using manually annotated sigmoid colon. A five-fold cross-validation procedure was used on a test dataset to evaluate the network's performance. As indicated by the maximum Dice similarity coefficient (DSC) of 56.92+/-1.42%, the application of PyP and csSE techniques improves segmentation precision. We explored ensemble methods including averaging, weighted averaging, majority voting, and max ensemble. The results show that average and majority voting approaches with a threshold value of 0.5 and consistent weight distribution among the top three models produced comparable and optimal results with DSC of 88.11+/-3.52%. The results indicate that the application of a modified 3D U-Net architecture is effective for segmenting the sigmoid colon in Computed Tomography (CT) images. In addition, the study highlights the potential benefits of integrating ensemble methods to improve segmentation precision.Comment: 8 Pages, 6 figures, Accepted at IEEE DICTA 202

Structural Annotation of Mycobacterium tuberculosis Proteome

Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for ∼2877 ORFs, covering ∼70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Blood cells play essential roles in human health, underpinning physiological processes such as immunity, oxygen transport, and clotting, which when perturbed cause a significant global health burden. Here we integrate data from UK Biobank and a large-scale international collaborative effort, including data for 563,085 European ancestry participants, and discover 5,106 new genetic variants independently associated with 29 blood cell phenotypes covering a range of variation impacting hematopoiesis. We holistically characterize the genetic architecture of hematopoiesis, assess the relevance of the omnigenic model to blood cell phenotypes, delineate relevant hematopoietic cell states influenced by regulatory genetic variants and gene networks, identify novel splice-altering variants mediating the associations, and assess the polygenic prediction potential for blood traits and clinical disorders at the interface of complex and Mendelian genetics. These results show the power of large-scale blood cell trait GWAS to interrogate clinically meaningful variants across a wide allelic spectrum of human variation. Analysis of blood cell traits in the UK Biobank and other cohorts illuminates the full genetic architecture of hematopoietic phenotypes, with evidence supporting the omnigenic model for complex traits and linking polygenic burden with monogenic blood diseases

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Blood cells play essential roles in human health, underpinning physiological processes such as immunity, oxygen transport, and clotting, which when perturbed cause a significant global health burden. Here we integrate data from UK Biobank and a large-scale international collaborative effort, including data for 563,085 European ancestry participants, and discover 5,106 new genetic variants independently associated with 29 blood cell phenotypes covering a range of variation impacting hematopoiesis. We holistically characterize the genetic architecture of hematopoiesis, assess the relevance of the omnigenic model to blood cell phenotypes, delineate relevant hematopoietic cell states influenced by regulatory genetic variants and gene networks, identify novel splice-altering variants mediating the associations, and assess the polygenic prediction potential for blood traits and clinical disorders at the interface of complex and Mendelian genetics. These results show the power of large-scale blood cell trait GWAS to interrogate clinically meaningful variants across a wide allelic spectrum of human variation.</p

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

Most loci identified by GWASs have been found in populations of European ancestry (EUR). In trans-ethnic meta-analyses for 15 hematological traits in 746,667 participants, including 184,535 non-EUR individuals, we identified 5,552 trait-variant associations at p &lt; 5 × 10−9, including 71 novel associations not found in EUR populations. We also identified 28 additional novel variants in ancestry-specific, non-EUR meta-analyses, including an IL7 missense variant in South Asians associated with lymphocyte count in vivo and IL-7 secretion levels in vitro. Fine-mapping prioritized variants annotated as functional and generated 95% credible sets that were 30% smaller when using the trans-ethnic as opposed to the EUR-only results. We explored the clinical significance and predictive value of trans-ethnic variants in multiple populations and compared genetic architecture and the effect of natural selection on these blood phenotypes between populations. Altogether, our results for hematological traits highlight the value of a more global representation of populations in genetic studies. Delineation of the genetic architecture of hematological traits in a multi-ethnic dataset allows identification of rare variants with strong effects specific to non-European populations and improved fine mapping of GWAS variants using the trans-ethnic approach

Perinatal Hypophosphatasia in a Premature Infant.

A premature male infant was delivered at 32 weeks' gestation due to category-2 fetal tracing after preterm labor. The physical exam showed shortened and bowed long bones, with calvarium felt in small area of the head. Serum alkaline phosphatase was very low on admission. Extensive metaphyseal abnormalities, bowing of long bones, and poor ossification of all bones were noted on skeletal survey (radiography). Based on ultrasound evidence of "bowing" and long bone fractures at 26 weeks, amniocentesis was performed that later diagnosed hypophosphatasia by genetic testing while ruling out osteogenesis imperfecta. Although ventilated initially, the infant gradually improved with enzyme replacement therapy (ERT) and was extubated to noninvasive ventilation for 6 weeks. Following clinical deterioration with hypoxic respiratory failure secondary to sepsis at 4 months of age, he succumbed to severe pulmonary hypertension, likely secondary to chronic lung disease and prolonged ventilation. Early diagnosis allowed timely initiation of appropriate therapy. Radiological improvement with the therapy showed promising results in this rare disease. Despite specific novel therapy being available, variability in presentation dictates prognosis in this previously universally fatal condition. The potential unknown effects of ERT on pulmonary vascular remodeling need further investigation

Perinatal Hypophosphatasia in a Premature Infant.

A premature male infant was delivered at 32 weeks' gestation due to category-2 fetal tracing after preterm labor. The physical exam showed shortened and bowed long bones, with calvarium felt in small area of the head. Serum alkaline phosphatase was very low on admission. Extensive metaphyseal abnormalities, bowing of long bones, and poor ossification of all bones were noted on skeletal survey (radiography). Based on ultrasound evidence of "bowing" and long bone fractures at 26 weeks, amniocentesis was performed that later diagnosed hypophosphatasia by genetic testing while ruling out osteogenesis imperfecta. Although ventilated initially, the infant gradually improved with enzyme replacement therapy (ERT) and was extubated to noninvasive ventilation for 6 weeks. Following clinical deterioration with hypoxic respiratory failure secondary to sepsis at 4 months of age, he succumbed to severe pulmonary hypertension, likely secondary to chronic lung disease and prolonged ventilation. Early diagnosis allowed timely initiation of appropriate therapy. Radiological improvement with the therapy showed promising results in this rare disease. Despite specific novel therapy being available, variability in presentation dictates prognosis in this previously universally fatal condition. The potential unknown effects of ERT on pulmonary vascular remodeling need further investigation

Imidazole Functionalized Polyaniline: Synthesis, Characterization, and Cu (II) Coordination Studies

Polyaniline functionalized with imidazole as strategically designed receptor group in its backbone was synthesized for copper binding. The synthesized polymer has been characterized using FTIR, NMR, and UV-Vis spectroscopic techniques. The addition of copper (II) to the polymer distinctly changes the properties such as crystallinity, molecular weight, aggregation, and electronic properties. XRD, DLS, SEM, and four-point probe techniques have been used for study of these changes. It is observed that the secondary ion generated as a result of copper coordination results in the doping of the polyaniline backbone, which enhances the conductivity by one order of magnitude. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci 123: 526-534, 201

Analysis of Cr(VI) Bioremediation by <em>Citrobacter freundii</em> Using Synchrotron Soft X-ray Scanning Transmission X-ray Microscopy

Scanning transmission X-ray microscopy (STXM) was utilized for analysing the bioremediation of Cr(VI) by Citrobacter freundii, a species of gram-negative bacteria. The biosorption and bioreduction processes were analysed by the chemical mapping of cells biosorbed at different concentrations of Cr(VI). STXM spectromicroscopy images were recorded at O K-edge and Cr L-edge. A thorough analysis of the X-ray absorption features corresponding to different oxidation states of Cr in the biosorbed cell indicated the coexistence of Cr(III) and Cr(VI) at higher concentrations. This signifies the presence of partially reduced Cr(VI) in addition to biosorbed Cr(VI). In addition, the Cr(III) signal is intense compared with Cr(VI) at different regions of the cell indicating excess of reduced Cr. Speciation of adsorbed Cr was analysed for the spectral features of biosorbed cell and comparison with Cr standards. Analysis of absorption onset, L3/L2 ratio and absorption fine structure concludes that adsorbed Cr is predominantly present as Cr(III) hydroxide or oxyhydroxide. The evolution of absorption features in the duration of biosorption process was also studied. These time lapse studies depict the gradual decrement in Cr(VI) signal as biosorption proceeds. A strong evidence of interaction of Cr with the cell material was also observed. The obtained results provide insights into the biosorption process and chemical speciation of Cr on the cells