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Pattern vectors from algebraic graph theory.

Graph structures have proven computationally cumbersome for pattern analysis. The reason for this is that, before graphs can be converted to pattern vectors, correspondences must be established between the nodes of structures which are potentially of different size. To overcome this problem, in this paper, we turn to the spectral decomposition of the Laplacian matrix. We show how the elements of the spectral matrix for the Laplacian can be used to construct symmetric polynomials that are permutation invariants. The coefficients of these polynomials can be used as graph features which can be encoded in a vectorial manner. We extend this representation to graphs in which there are unary attributes on the nodes and binary attributes on the edges by using the spectral decomposition of a Hermitian property matrix that can be viewed as a complex analogue of the Laplacian. To embed the graphs in a pattern space, we explore whether the vectors of invariants can be embedded in a low-dimensional space using a number of alternative strategies, including principal components analysis (PCA), multidimensional scaling (MDS), and locality preserving projection (LPP). Experimentally, we demonstrate that the embeddings result in well-defined graph clusters. Our experiments with the spectral representation involve both synthetic and real-world data. The experiments with synthetic data demonstrate that the distances between spectral feature vectors can be used to discriminate between graphs on the basis of their structure. The real-world experiments show that the method can be used to locate clusters of graphs.

Algorithms↗

A recombinant monocysteine mutant (Ser to Cys-155) of fast skeletal troponin T: identification by cross-linking of a domain involved in a physiologically relevant interaction with troponins C and I.

Troponin T (TnT), a subunit of the heterotrimeric troponin (Tn) complex, is essential for the Ca2+ regulation of vertebrate striated muscle contraction both in vivo and in vitro. With the exception of bovine cardiac TnT, all known vertebrate TnT isoforms lack a thiol group, a property which makes the wild-type proteins unsuitable as cross-linking substrate. We generated a mutant human fast skeletal TnT in which Ser155 was changed to Cys (TnT-Cys155). Mutation of this residue in TnT as well as in vitro expression in Escherichia coli and purification of the recombinant mutant protein did not affect its biological properties in terms of in vitro binding to troponin I (TnI), troponin C (TnC), actin-tropomyosin (actin-Tm), and actomyosin ATPase activity. TnT-Cys155 was labeled with 4-maleimidobenzophenone (BP-TnT155) and photo-cross-linked to TnI, TnC, Tm, and all of the thin filament proteins. BP-TnT155 did not cross-link to Tm and showed weak Ca2+/Mg2+-independent cross-linking with TnI in the binary complex and in the presence of all thin filament protein components. BP-TnT155 showed Ca2+/Mg2+-dependent cross-linking with TnC in the binary and ternary complexes and Ca2+-favored cross-linking with TnI in the ternary complex. Thus, residue 155 of TnT is within 10 A (the length of cross-linker) of TnC in the presence or absence of Ca2+ and comes within 10 A of both TnI and TnC in the presence of Ca2+. TnT residue 155 is in close proximity to or may even partly encompass the Tm binding site. These results suggest that TnT, in association with TnI, may participate in the "information transfer" mediated by the Ca2+ binding signal from TnC to Tm and the region around TnT residue 155 probably acts as a linker between troponin and actin-Tm in this signal transmission process. Our results also suggest that TnT contains at least one Ca2+/Mg2+-dependent TnC binding region located between its Tm and TnI binding regions. A recombinant truncated fragment of TnI, TnI96-181, containing amino acid residues 96-181 and labeled with BP at Cys-133, failed to cross-link with TnT, indicating that the region around Cys-133 of TnI is not involved in binary interaction with TnT.

Animals↗

A similarity learning approach to content-based image retrieval: application to digital mammography.

In this paper, we describe an approach to content-based retrieval of medical images from a database, and provide a preliminary demonstration of our approach as applied to retrieval of digital mammograms. Content-based image retrieval (CBIR) refers to the retrieval of images from a database using information derived from the images themselves, rather than solely from accompanying text indices. In the medical-imaging context, the ultimate aim of CBIR is to provide radiologists with a diagnostic aid in the form of a display of relevant past cases, along with proven pathology and other suitable information. CBIR may also be useful as a training tool for medical students and residents. The goal of information retrieval is to recall from a database information that is relevant to the user's query. The most challenging aspect of CBIR is the definition of relevance (similarity), which is used to guide the retrieval machine. In this paper, we pursue a new approach, in which similarity is learned from training examples provided by human observers. Specifically, we explore the use of neural networks and support vector machines to predict the user's notion of similarity. Within this framework we propose using a hierarchal learning approach, which consists of a cascade of a binary classifier and a regression module to optimize retrieval effectiveness and efficiency. We also explore how to incorporate online human interaction to achieve relevance feedback in this learning framework. Our experiments are based on a database consisting of 76 mammograms, all of which contain clustered microcalcifications (MCs). Our goal is to retrieve mammogram images containing similar MC clusters to that in a query. The performance of the retrieval system is evaluated using precision-recall curves computed using a cross-validation procedure. Our experimental results demonstrate that: 1) the learning framework can accurately predict the perceptual similarity reported by human observers, thereby serving as a basis for CBIR; 2) the learning-based framework can significantly outperform a simple distance-based similarity metric; 3) the use of the hierarchical two-stage network can improve retrieval performance; and 4) relevance feedback can be effectively incorporated into this learning framework to achieve improvement in retrieval precision based on online interaction with users; and 5) the retrieved images by the network can have predicting value for the disease condition of the query.

Algorithms↗

Face description with local binary patterns: application to face recognition.

This paper presents a novel and efficient facial image representation based on local binary pattern (LBP) texture features. The face image is divided into several regions from which the LBP feature distributions are extracted and concatenated into an enhanced feature vector to be used as a face descriptor. The performance of the proposed method is assessed in the face recognition problem under different challenges. Other applications and several extensions are also discussed.

Algorithms↗

A neural network classifier in experimental particle physics.

A classification problem in high energy physics has been solved on simulated data using a simple multilayer perceptron comprising binary units which was trained with the CHIR algorithm. The unstable training of such a network on a nonseparable set has been overcome by selecting those weight vectors with good performance while providing a flexible choice of the two types of classification errors. Specific features of the problem have been exploited in order to simplify and optimize the solution which has been compared to the popular backpropagation algorithm and found to perform on a similar level. Additional aspects of this work are the use of the CHIR algorithm on continuous input and incorporating the classic idea of a phi-machine in a multilayer perceptron.

Algorithms↗

Thoracic CT images: effect of lossy image compression on diagnostic accuracy.

PURPOSE: To evaluate the effects of lossy image (noninvertible) compression on diagnostic accuracy of thoracic computed tomographic images. MATERIALS AND METHODS: Sixty images from patients with mediastinal adenopathy and pulmonary nodules were compressed to six different levels with tree-structured vector quantization. Three radiologists then used the original and compressed images for diagnosis. Unlike many previous receiver operating characteristic-based studies that used confidence rankings and binary detection tasks, this study examined the sensitivity and predictive value positive scores from nonbinary detection tasks. RESULTS: At the 5% significance level, there was no statistically significant difference in diagnostic accuracy of image assessment at compression rates of up to 9:1. CONCLUSION: The techniques presented for evaluation of image quality do not depend on the specific compression algorithm and provide a useful approach to evaluation of the benefits of any lossy image processing technique.

Humans↗

Topical applications of pyrethroid and organophosphate mixtures revealed positive interactions against pyrethroid-resistant Anopheles gambiae.

The efficacy of a binary mixture of bifenthrin (pyrethroid) and chlorpyrifos-methyl (organophosphate) has been tested against susceptible and pyrethroid-resistant strains of Anopheles gambiae Giles, the major malaria vector in sub-Saharan Africa. Dose-mortality regression lines were determined for each insecticide alone and in mixtures by topical applications on adult female mosquitoes. A combination index (CI) was used to quantify the interactions occurring between the pyrethroid and organophosphate insecticides. The results revealed synergism at high doses against both susceptible (0.7 > CI > 0.3) and pyrethroid-resistant (0.9 > CI > 0.7) An. gambiae. These results suggest that insecticide mixtures may be an alternative strategy for vector control, especially in areas where mosquitoes are resistant to pyrethroids.

Animals↗

Prediction of protein structural classes using support vector machines.

The support vector machine, a machine-learning method, is used to predict the four structural classes, i.e. mainly alpha, mainly beta, alpha-beta and fss, from the topology-level of CATH protein structure database. For the binary classification, any two structural classes which do not share any secondary structure such as alpha and beta elements could be classified with as high as 90% accuracy. The accuracy, however, will decrease to less than 70% if the structural classes to be classified contain structure elements in common. Our study also shows that the dimensions of feature space 20(2) = 400 (for dipeptide) and 20(3) = 8 000 (for tripeptide) give nearly the same prediction accuracy. Among these 4 structural classes, multi-class classification gives an overall accuracy of about 52%, indicating that the multi-class classification technique in support of vector machines may still need to be further improved in future investigation.

Algorithms↗

Electron microscopical studies on the development of Babesia canis (Sporozoa) in the salivary glands of the vector tick Dermacentor reticulatus.

The formation of sporozoites of Babesia canis was studied by light- and electron microscopy in the salivary gland cells of adult female ticks from the 2nd day after attachment until 1 day after detachment. It was found that this process was initiated by the binary division of kinetes that had already entered or entered during the period examined. During division the kinetes (15 X 2.5 microns) lost their typical organelles, reduced their three-layered pellicle to a single membrane and became spherical. After nuclear division and a further time-lag cell division occurred, giving rise to two cells in which this process was repeated. After numerous binary divisions the parasites acquired more and more closely the shape of the later infectious, pyriform sporozoite. These sporozoites measured about 2.5 X 1.5 microns and also had a three-layered pellicle, with rhoptries and a few micronemes, but never contained "spherical bodies". The formation process needed about 2--3 days so that the transmission to the dog could be carried out while the tick engorges and this is probably the stimulation for the development. Finally the cytological features of this sporozoite formation were compared to those in the Theileria species studied by our group.

Animals↗

Automatic segmentation and quantification of electron micrographs: extracellular components.

Extracellular glycosaminoglycans when precipitated by tannic acid, appear in electron micrographs as amorphous reticulate masses or fragments sometimes finely beaded and often associated with collagen fibrils. An algorithm for automatic classification, segmentation, and quantification of the amount of tannic acid-precipitable material (TAPM) and collagen in electron microscopic images is presented. Small patches of a region are initially located and the patch boundaries are traced using a binary contour tracing algorithm. The patches are then grown out and merged together to form one large area. This area is classified using a two-dimensional feature vector into one of two classes: a region with TAPM and collagen, or one with cell bodies and/or processes. Once these areas are classified and segmented, the distribution of TAPM is measured. The algorithm was tested on several TAPM images displaying varying amounts and configurations of TAPM with good results. It may also be adapted to process other electron microscopic images containing elements of interest which have complex or amorphous form.

Animals↗

An automated image-registration technique based on multiple structure matching.

A new image-registration technique that matches multiple structures on complementary imaging data sets (e.g., CT and MRI) has been developed and tested with both phantom and patient data. The algorithm assumes a rigid-body transformation and is suitable for correlating structures within the cranium or at the skull base. The basic premise of the new technique is that an optimum transformation is achieved when the relative volume lying outside of the intersection between a structure and its transformed counterpart is a minimum. This relative volume is calculated numerically using a random sampling approach, and a binary searching algorithm was used to step through the nine-dimensional parameter space consisting of three rotation angles, three scaling factors and three components of a translation vector. For the nine tests using phantom data, the automated structure-matching technique was able to predict the correct rotation angles to within +/- 1 degree. The expected clinical performance of the new technique was assessed by comparing results obtained with the new method to those obtained using other techniques for 12 patients who were treated with charged particles at Lawrence Berkeley Laboratory (LBL) and who had image-registration studies performed as part of their treatment plan. For 9 of the 12 patients considered, the new structure-matching technique produced a significantly better registration than the older methods, as measured by the resultant average relative volume lying outside of the intersection between any structure and its transformed counterpart. For the other three patients, results were not significantly different for the new structure-matching method and the older techniques.

Algorithms↗

Crossover accelerates evolution in GAs with a Babel-like fitness landscape: mathematical analyses.

The effectiveness of crossover in accelerating evolution in genetic algorithms (GAs) is studied with a haploid finite population of bit sequences. A Babel-like fitness landscape is assumed. There is a single bit sequence (schema) that is significantly more advantageous than all the others. We study the time until domination of the advantageous schema (Τ&subd;). Evolution proceeds with appearance, spread, and domination of the advantageous schema. The most important process determining Τ&subd; is the appearance (creation) of the advantageous schema. Crossover helps this creation process and enhances the rate of evolution. To study this effect, we first establish an analytical method to estimate Τ&subd; with or without crossover. Then, we conduct a numerical analysis using the frequency vector representation of the population with the recurrence relations formulated after GA operations. Finally, we carry out direct computer simulations with simple GAs operating on a population of binary strings directly prepared in the computer memory to examine the performance of the two analytical methods. It is shown that Τ&subd; is reduced greatly by crossover with a mildly high rate when the mutation rate is adjusted to a moderate value and that an advantageous schema has a fairly larger order (the number of bits). From these observations, we can determine implementation criteria for GAs, which are useful when we are applying GAs to engineering problems having a conspicuously discontinuous fitness landscape.

Algorithms↗

Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure.

Classification models are generated to predict in vitro cytogenetic results for a diverse set of 383 organic compounds. Both k-nearest neighbor and support vector machine models are developed. They are based on calculated molecular structure descriptors. Endpoints used are the labels clastogenic or nonclastogenic according to an in vitro chromosomal aberration assay with Chinese hamster lung cells. Compounds that were tested with both a 24 and 48 h exposure are included. Each compound is represented by calculated molecular structure descriptors encoding the topological, electronic, geometrical, or polar surface area aspects of the structure. Subsets of informative descriptors are identified with genetic algorithm feature selection coupled to the appropriate classification algorithm. The overall classification success rate for a k-nearest neighbor classifier built with just six topological descriptors is 81.2% for the training set and 86.5% for an external prediction set. The overall classification success rate for a three-descriptor support vector machine model is 99.7% for the training set, 92.1% for the cross-validation set, and 83.8% for an external prediction set.

Algorithms↗

Vector solitons with an embedded domain wall.

We present a class of soliton solutions to a system of two coupled nonlinear Schrödinger equations, with an intrinsic domain wall (DW) which separates regions occupied by two different fields. The model describes a binary mixture of two Bose-Einstein condensates (BECs) with interspecies repulsion. For the attractive or repulsive interactions inside each species, we find solutions which are bright or dark solitons in each component, while for the opposite signs of the intraspecies interaction, a bright-dark soliton pair is found (each time, with the intrinsic DW). These solutions can arise in the context of discrete lattices, and most of them can be supported in continuum settings by an external parabolic trap. The stability of the solitons with intrinsic DWs is examined, and the evolution of unstable ones is analyzed. We also briefly discuss the possibility of generating such families of solutions in the presence of linear coupling between the components, and an application of the model to bimodal light propagation in nonlinear optics.

Biophysics↗

Design and in vivo characterization of self-inactivating human and non-human lentiviral expression vectors engineered for streptogramin-adjustable transgene expression.

Adjustable transgene expression is considered key for next-generation molecular interventions in gene therapy scenarios, therapeutic reprogramming of clinical cell phenotypes for tissue engineering and sophisticated gene-function analyses in the post-genomic era. We have designed a portfolio of latest generation self-inactivating human (HIV-derived) and non-human (EIAV-based) lentiviral expression vectors engineered for streptogramin-adjustable expression of reporter (AmyS(DeltaS), EYFP, SAMY, SEAP), differentiation-modulating (human C/EBP-alpha) and therapeutic (human VEGF) transgenes in a variety of rodent (CHO-K1, C2C12) and human cell lines (HT-1080, K-562), human and mouse primary cells (NHDF, PBMC, CD4+) as well as chicken embryos. Lentiviral design concepts include (i) binary systems harboring constitutive streptogramin-dependent transactivator (PIT) and PIT-responsive transgene expression units on separate lentivectors; (ii) streptogramin-responsive promoters (P(PIR8)) placed 5' of desired transgenes; (iii) within modified enhancer-free 3'-long terminal repeats; and (iv) bidirectional autoregulated configurations providing streptogramin-responsive transgene expression in a lentiviral one-vector format. Rigorous quantitative analysis revealed HIV-based direct P(PIR)-transgene configurations to provide optimal regulation performance for (i) adjustable expression of intracellular and secreted product proteins, (ii) regulated differential differentiation of muscle precursor cell lines into adipocytes or osteoblasts and (iii) conditional vascularization fine-tuning in chicken embryos. Similar performance could be achieved by engineering streptogramin-responsive transgene expression into an autoregulated one-vector format. Powerful transduction systems equipped with adjustable transcription modulation options are expected to greatly advance sophisticated molecular interventions in clinically and/or biotechnologically relevant primary cells and cell lines.

Adipocytes↗

Stacked Euler vector (SERVE): a gray-tone image feature based on bit-plane augmentation.

A new combinatorial feature called Stacked Euler Vector (SERVE) is introduced to characterize a gray-tone image. SERVE comprises a four-tuple, where each element is an integer representing the Euler number of the partial binary image formed by certain pixel overlap relations among the four most significant bit planes of the gray-tone image. Computation of SERVE is simple, fast, and does not involve any floating point operation. SERVE can be used to augment other features to improve the performance of image retrieval significantly. Experimental results on the COIL database are reported to demonstrate its performance.

Algorithms↗

Theoretical study of the local structure and Raman spectra of CaO-SiO2 binary melts.

A procedure for the Raman spectra calculation of vitreous and molten silicates was presented in this paper. It includes molecular dynamics MD simulation for the generation of equilibrium configurations, Wilson's GF matrix method for the calculations of eigenfrequencies and corresponding vectors, electro-optical parameters method (EOPM) for the Raman intensity calculations, and the bond polarizability model (BPM) for the determination of polarizability and polarizability derivative. One of the most important characteristics of this procedure is the achievement of the partial Raman spectra of five tetrahedral units, as well as the total spectral envelope. In this paper, the calculation was carried out for the vitreous and molten calcium silicates with different compositions and at various temperatures. It is worthwhile to note that the calculation is based on statistical configurations distribution in the space and so it is not needed to artificially adjust the full width at half maximum (FWHM) of spectra. It was also tested through the good agreement of the calculated spectra with the experimental, including some regularity of spectral properties. According to the calculation, the symmetrical stretching of whole tetrahedral units, to which the stretching of Si-O(nb) bond gives the main contribution to intensity, is proven to be the dominance in the high-frequency range (800-1200 cm(-1)) and the symmetrical bending of Si-O(b)-Si, to which the stretching of Si-O(b) bond exhibits the main contribution, is the dominance in the medium-frequency range (400-700 cm(-1)). As the first theoretical results, the Raman scattering coefficient of each Q(i) was found little change along with the variation of composition and temperature.

Journal Article↗

Quantitative genetics of vector competence for La Crosse virus and body size in Ochlerotatus hendersoni and Ochlerotatus triseriatus interspecific hybrids.

La Crosse virus is a leading cause of pediatric encephalitis in the United States. The mosquito Ochlerotatus triseriatus is an efficient vector for La Crosse virus, whereas the closely related O. hendersoni transmits only at very low rates. Quantitative trait loci (QTL) affecting the ability to orally transmit this virus and adult body size were identified in 164 F(2) female individuals from interspecific crosses of O. hendersoni females and O. triseriatus males using a combination of composite interval mapping (CIM), interval mapping (IM) for binary traits, and single-marker mapping. For oral transmission (OT), no genome locations exceeded the 95% experimentwise threshold for declaring a QTL using IM, but single-marker analysis identified four independent regions significantly associated with OT that we considered as tentative QTL. With two QTL, an increase in OT was associated with alleles from the refractory vector, O. hendersoni, and likely reflect epistatic interactions between genes that were uncovered by our interspecific crosses. For body size, two QTL were identified using CIM and a third tentative QTL was identified using single-marker analysis. The genome regions associated with body size also contain three QTL controlling OT, suggesting that these regions contain either single genes with pleiotropic effects or multiple linked genes independently determining each trait.

Animals↗