Characterization and classification of tumor lesions using computerized fractal-based texture analysis and support vector machines in digital mammograms

Objective: This paper presents a detailed study of fractal-based methods for texture characterization of mammographic mass lesions and architectural distortion. The purpose of this study is to explore the use of fractal and lacunarity analysis for the characterization and classification of both tumor lesions and normal breast parenchyma in mammography. Materials and methods: We conducted comparative evaluations of five popular fractal dimension estimation methods for the characterization of the texture of mass lesions and architectural distortion. We applied the concept of lacunarity to the description of the spatial distribution of the pixel intensities in mammographic images. These methods were tested with a set of 57 breast masses and 60 normal breast parenchyma (dataset1), and with another set of 19 architectural distortions and 41 normal breast parenchyma (dataset2). Support vector machines (SVM) were used as a pattern classification method for tumor classification. Results: Experimental results showed that the fractal dimension of region of interest (ROIs) depicting mass lesions and architectural distortion was statistically significantly lower than that of normal breast parenchyma for all five methods. Receiver operating characteristic (ROC) analysis showed that fractional Brownian motion (FBM) method generated the highest area under ROC curve (A z = 0.839 for dataset1, 0.828 for dataset2, respectively) among five methods for both datasets. Lacunarity analysis showed that the ROIs depicting mass lesions and architectural distortion had higher lacunarities than those of ROIs depicting normal breast parenchyma. The combination of FBM fractal dimension and lacunarity yielded the highest A z value (0.903 and 0.875, respectively) than those based on single feature alone for both given datasets. The application of the SVM improved the performance of the fractal-based features in differentiating tumor lesions from normal breast parenchyma by generating higher A z value. Conclusion: FBM texture model is the most appropriate model for characterizing mammographic images due to self-affinity assumption of the method being a better approximation. Lacunarity is an effective counterpart measure of the fractal dimension in texture feature extraction in mammographic images. The classification results obtained in this work suggest that the SVM is an effective method with great potential for classification in mammographic image analysis.

Hamiltonian constraint analysis of vector field theories with spontaneous Lorentz symmetry breaking

Recent investigations of various quantum-gravity theories have revealed a variety of possible mechanisms that lead to Lorentz violation. One of the more elegant of these mechanisms is known as Spontaneous Lorentz Symmetry Breaking (SLSB), where a vector or tensor field acquires a nonzero vacuum expectation value. As a consequence of this symmetry breaking, massless Nambu-Goldstone modes appear with properties similar to the photon in Electromagnetism. This thesis considers the most general class of vector field theories that exhibit spontaneous Lorentz violation-known as bumblebee models-and examines their candidacy as potential alternative explanations of E&M, offering the possibility that Einstein-Maxwell theory could emerge as a result of SLSB rather than of local U(1) gauge invariance. With this aim we employ Dirac's Hamiltonian Constraint Analysis procedure to examine the constraint structures and degrees of freedom inherent in three candidate bumblebee models, each with a different potential function, and compare these results to those of Electromagnetism. We find that none of these models share similar constraint structures to that of E&M, and that the number of degrees of freedom for each model exceeds that of Electromagnetism by at least two, pointing to the potential existence of massive modes or propagating ghost modes in the bumblebee theories.

Identification of concurrent control chart patterns with singular spectrum analysis and learning vector quantization

Identification of unnatural control chart patterns (CCPs) from manufacturing process measurements is a critical task in quality control as these patterns indicate that the manufacturing process is out-of-control. Recently, there have been numerous efforts in developing pattern recognition and classification methods based on artificial neural network to automatically recognize unnatural patterns. Most of them assume that a single type of unnatural pattern exists in process data. Due to this restrictive assumption, severe performance degradations are observed in these methods when unnatural concurrent CCPs present in process data. To address this problem, this paper proposes a novel approach based on singular spectrum analysis (SSA) and learning vector quantization network to identify concurrent CCPs. The main advantage of the proposed method is that it can be applied to the identification of concurrent CCPs in univariate manufacturing processes. Moreover, there are no permutation and scaling ambiguities in the CCPs recovered by the SSA. These desirable features make the proposed algorithm an attractive alternative for the identification of concurrent CCPs. Computer simulations and a real application for aluminium smelting processes confirm the superior performance of proposed algorithm for sets of typical concurrent CCPs.

Support vector machine (SVM) based multiclass prediction with basic statistical analysis of plasminogen activators

Plasminogen (Pg), the precursor of the proteolytic and fibrinolytic enzyme of blood, is converted to the active enzyme plasmin (Pm) by different plasminogen activators (tissue plasminogen activators and urokinase), including the bacterial activators streptokinase and staphylokinase, which activate Pg to Pm and thus are used clinically for thrombolysis. The identification of Pg-activators is therefore an important step in understanding their functional mechanism and derives new therapies.

The Vampirome: Transcriptome and proteome analysis of the principal and accessory submaxillary glands of the vampire bat Desmodus rotundus, a vector of human rabies

Vampire bats are notorious for being the sole mammals that strictly feed on fresh blood for their survival. While their saliva has been historically associated with anticoagulants, only one antihemostatic (plasminogen activator) has been molecularly and functionally characterized. Here, RNAs from both principal and accessory submaxillary (submandibular) salivary glands of Desmodus rotundus were extracted, and ~. 200. million reads were sequenced by Illumina. The principal gland was enriched with plasminogen activators with fibrinolytic properties, members of lipocalin and secretoglobin families, which bind prohemostatic prostaglandins, and endonucleases, which cleave neutrophil-derived procoagulant NETs. Anticoagulant (tissue factor pathway inhibitor, TFPI), vasodilators (PACAP and C-natriuretic peptide), and metalloproteases (ADAMTS-1) were also abundantly expressed. Members of the TSG-6 (anti-inflammatory), antigen 5/CRISP, and CCL28-like (antimicrobial) protein families were also sequenced. Apyrases (which remove platelet agonist ADP), phosphatases (which degrade procoagulant polyphosphates), and sphingomyelinase were found at lower transcriptional levels. Accessory glands were enriched with antimicrobials (lysozyme, defensin, lactotransferrin) and protease inhibitors (TIL-domain, cystatin, Kazal). Mucins, heme-oxygenase, and IgG chains were present in both glands. Proteome analysis by nano LC-MS/MS confirmed that several transcripts are expressed in the glands. The database presented herein is accessible online at http://exon.niaid.nih.gov/transcriptome/D_rotundus/Supplemental-web.xlsx. These results reveal that bat saliva emerges as a novel source of modulators of vascular biology. Biological significance: Vampire bat saliva emerges as a novel source of antihemostatics which modulate several aspects of vascular biology. © 2013.

Entoepidemiology of Chagas disease in northwest Sao Paulo and cytogenetic analysis of its main vector, Triatoma sordida (Hemiptera: Triatominae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Vector Mode Analysis of Ring-Core Fibers: Design Tools for Spatial Division Multiplexing

Design tools have existed for decades for standard step-index fibers, with analytical expressions for cutoff conditions as a function of core size, refractive indexes, and wavelength. We present analytical expressions for cutoff conditions for fibers with a ring-shaped propagation region. We validate our analytical expressions against numerical solutions, as well as via asymptotic analysis yielding the existing solutions for standard step-index fiber. We demonstrate the utility of our solutions for optimizing fibers supporting specific eigenmode behaviors of interest for spatial division multiplexing. In particular, we address large mode separation for orbital angular momentum modes and fibers supporting only modes with a single intensity ring.

A simulation tool for transient stability analysis on vector computers

This paper deals with transient stability analysis based on time domain simulation on vector processing. This approach requires the solution of a set of differential equations in conjunction of another set of algebraic equations. The solution of the algebraic equations has presented a scalar as sequential set of tasks, and the solution of these equations, on vector computers, has required much more investigations to speedup the simulations. Therefore, the main objective of this paper has been to present methods to solve the algebraic equations using vector processing. The results, using a GRAY computer, have shown that on-line transient stability assessment is feasible.

A comparative analysis of the relative efficacy of vector-control strategies against dengue fever

Dengue is considered one of the most important vector-borne infection, affecting almost half of the world population with 50 to 100 million cases every year. In this paper, we present one of the simplest models that can encapsulate all the important variables related to vector control of dengue fever. The model considers the human population, the adult mosquito population and the population of immature stages, which includes eggs, larvae and pupae. The model also considers the vertical transmission of dengue in the mosquitoes and the seasonal variation in the mosquito population. From this basic model describing the dynamics of dengue infection, we deduce thresholds for avoiding the introduction of the disease and for the elimination of the disease. In particular, we deduce a Basic Reproduction Number for dengue that includes parameters related to the immature stages of the mosquito. By neglecting seasonal variation, we calculate the equilibrium values of the model’s variables. We also present a sensitivity analysis of the impact of four vector-control strategies on the Basic Reproduction Number, on the Force of Infection and on the human prevalence of dengue. Each of the strategies was studied separately from the others. The analysis presented allows us to conclude that of the available vector control strategies, adulticide application is the most effective, followed by the reduction of the exposure to mosquito bites, locating and destroying breeding places and, finally, larvicides. Current vector-control methods are concentrated on mechanical destruction of mosquitoes’ breeding places. Our results suggest that reducing the contact between vector and hosts (biting rates) is as efficient as the logistically difficult but very efficient adult mosquito’s control.

Knowledge-based analysis of microarray gene expression data by using support vector machines

We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). SVMs are considered a supervised computer learning method because they exploit prior knowledge of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and self-organizing maps. SVMs have many mathematical features that make them attractive for gene expression analysis, including their flexibility in choosing a similarity function, sparseness of solution when dealing with large data sets, the ability to handle large feature spaces, and the ability to identify outliers. We test several SVMs that use different similarity metrics, as well as some other supervised learning methods, and find that the SVMs best identify sets of genes with a common function using expression data. Finally, we use SVMs to predict functional roles for uncharacterized yeast ORFs based on their expression data.

NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Molecular analysis of complex modular structures, such as promoter regions or multi-domain proteins, often requires the creation of families of experimental DNA constructs having altered composition, order, or spacing of individual modules. Generally, creation of every individual construct of such a family uses a specific combination of restriction sites. However, convenient sites are not always available and the alternatives, such as chemical resynthesis of the experimental constructs or engineering of different restriction sites onto the ends of DNA fragments, are costly and time consuming. A general cloning strategy (nucleic acid ordered assembly with directionality, NOMAD; WWW resource locator http:@Lmb1.bios.uic.edu/NOMAD/NOMAD.htm l) is proposed that overcomes these limitations. Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments. NOMAD manipulates DNA fragments in the form of "modules" having a standardized cohesive end structure. Specially designed "assembly vectors" allow for sequential and directional insertion of any number of modules in an arbitrary predetermined order, using the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequences. Studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMAD.

Better prediction of protein contact number using a support vector regression analysis of amino acid sequence

Background: Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C-beta atoms in other residues within a sphere around the C-beta atom of the residue of interest. Contact number is partly conserved between protein folds and thus is useful for protein fold and structure prediction. In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. In this study, we provide a more accurate contact number prediction method from protein primary sequence. Results: We predict contact number from protein sequence using a novel support vector regression algorithm. Using protein local sequences with multiple sequence alignments (PSI-BLAST profiles), we demonstrate a correlation coefficient between predicted and observed contact numbers of 0.70, which outperforms previously achieved accuracies. Including additional information about sequence weight and amino acid composition further improves prediction accuracies significantly with the correlation coefficient reaching 0.73. If residues are classified as being either contacted or non-contacted, the prediction accuracies are all greater than 77%, regardless of the choice of classification thresholds. Conclusion: The successful application of support vector regression to the prediction of protein contact number reported here, together with previous applications of this approach to the prediction of protein accessible surface area and B-factor profile, suggests that a support vector regression approach may be very useful for determining the structure-function relation between primary sequence and higher order consecutive protein structural and functional properties.