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PubMed2006

Generalized Haar DWT and transformations between decision trees and neural networks.

The core contribution of this paper is a three-fold improvement of the Haar discrete wavelet transform (DWT). It is modified to efficiently transform a multiclass- (rather than numerical-) valued function over a multidimensional (rather than low dimensional) domain, or transform a multiclass-valued decision tree into another useful representation. We prove that this multidimensional, multiclass DWT uses dynamic programming to minimize (within its framework) the number of nontrivial wavelet coefficients needed to summarize a training set or decision tree. It is a spatially localized algorithm that takes linear time in the number of training samples, after a sort. Convergence of the DWT to benchmark training sets seems to degrade with rising dimension in this test of high dimensional wavelets, which have been seen as difficult to implement. This multiclass multidimensional DWT has tightly coupled applications from learning "dyadic" decision trees directly from training data, rebalancing or converting preexisting decision trees to fixed depth boolean or threshold neural networks (in effect parallelizing the evaluation of the trees), or learning rule/exception sets represented as a new form of tree called an "E-tree", which could greatly help interpretation/visualization of a dataset.

Journal Article↗
PubMed2006

Exploiting discriminant information in nonnegative matrix factorization with application to frontal face verification.

In this paper, two supervised methods for enhancing the classification accuracy of the Nonnegative Matrix Factorization (NMF) algorithm are presented. The idea is to extend the NMF algorithm in order to extract features that enforce not only the spatial locality, but also the separability between classes in a discriminant manner. The first method employs discriminant analysis in the features derived from NMF. In this way, a two-phase discriminant feature extraction procedure is implemented, namely NMF plus Linear Discriminant Analysis (LDA). The second method incorporates the discriminant constraints inside the NMF decomposition. Thus, a decomposition of a face to its discriminant parts is obtained and new update rules for both the weights and the basis images are derived. The introduced methods have been applied to the problem of frontal face verification using the well-known XM2VTS database. Both methods greatly enhance the performance of NMF for frontal face verification.

Algorithms↗
PubMed2004

Gabor-based kernel PCA with fractional power polynomial models for face recognition.

This paper presents a novel Gabor-based kernel Principal Component Analysis (PCA) method by integrating the Gabor wavelet representation of face images and the kernel PCA method for face recognition. Gabor wavelets first derive desirable facial features characterized by spatial frequency, spatial locality, and orientation selectivity to cope with the variations due to illumination and facial expression changes. The kernel PCA method is then extended to include fractional power polynomial models for enhanced face recognition performance. A fractional power polynomial, however, does not necessarily define a kernel function, as it might not define a positive semidefinite Gram matrix. Note that the sigmoid kernels, one of the three classes of widely used kernel functions (polynomial kernels, Gaussian kernels, and sigmoid kernels), do not actually define a positive semidefinite Gram matrix either. Nevertheless, the sigmoid kernels have been successfully used in practice, such as in building support vector machines. In order to derive real kernel PCA features, we apply only those kernel PCA eigenvectors that are associated with positive eigenvalues. The feasibility of the Gabor-based kernel PCA method with fractional power polynomial models has been successfully tested on both frontal and pose-angled face recognition, using two data sets from the FERET database and the CMU PIE database, respectively. The FERET data set contains 600 frontal face images of 200 subjects, while the PIE data set consists of 680 images across five poses (left and right profiles, left and right half profiles, and frontal view) with two different facial expressions (neutral and smiling) of 68 subjects. The effectiveness of the Gabor-based kernel PCA method with fractional power polynomial models is shown in terms of both absolute performance indices and comparative performance against the PCA method, the kernel PCA method with polynomial kernels, the kernel PCA method with fractional power polynomial models, the Gabor wavelet-based PCA method, and the Gabor wavelet-based kernel PCA method with polynomial kernels.

Algorithms↗
PubMed2006

Capitalize on dimensionality increasing techniques for improving Face Recognition Grand Challenge performance.

This paper presents a novel pattern recognition framework by capitalizing on dimensionality increasing techniques. In particular, the framework integrates Gabor image representation, a novel multiclass Kernel Fisher Analysis (KFA) method, and fractional power polynomial models for improving pattern recognition performance. Gabor image representation, which increases dimensionality by incorporating Gabor filters with different scales and orientations, is characterized by spatial frequency, spatial locality, and orientational selectivity for coping with image variabilities such as illumination variations. The KFA method first performs nonlinear mapping from the input space to a high-dimensional feature space, and then implements the multiclass Fisher discriminant analysis in the feature space. The significance of the nonlinear mapping is that it increases the discriminating power of the KFA method, which is linear in the feature space but nonlinear in the input space. The novelty of the KFA method comes from the fact that 1) it extends the two-class kernel Fisher methods by addressing multiclass pattern classification problems and 2) it improves upon the traditional Generalized Discriminant Analysis (GDA) method by deriving a unique solution (compared to the GDA solution, which is not unique). The fractional power polynomial models further improve performance of the proposed pattern recognition framework. Experiments on face recognition using both the FERET database and the FRGC (Face Recognition Grand Challenge) databases show the feasibility of the proposed framework. In particular, experimental results using the FERET database show that the KFA method performs better than the GDA method and the fractional power polynomial models help both the KFA method and the GDA method improve their face recognition performance. Experimental results using the FRGC databases show that the proposed pattern recognition framework improves face recognition performance upon the BEE baseline algorithm and the LDA-based baseline algorithm by large margins.

Algorithms↗
PubMed2003

Application of ultrasound-based velocity estimate statistics to strain-rate estimation.

Quantification of the relative myocardial deformation rate, or strain rate, is an emerging capability to aid a cardiologist in assessing myocardial function. Ultrasound Doppler techniques can be used to compute tissue motion relative to a transducer. The myocardial strain rate can be computed as the localized spatial derivative of the tissue velocity. Such a strain-rate estimate is typically numerically noisy. We present the relevant speckle statistics to faciliate the computation of the strain rate based on a weighted least squares regression, with statistically appropriate weights.

Child↗
PubMed2006

A structural rationale for SV40 Vp1 temperature-sensitive mutants and their complementation.

Two groups of temperature-sensitive (ts) mutants, termed ts B and ts C, have mutations in the major capsid protein of SV40, Vp1. These mutants have virion assembly defects at the nonpermissive temperature, but can complement one another when two mutants, one from each group, coinfect a cell. A third group of mutants, termed ts BC, have related phenotypes, but do not complement other mutants. We found that the mutations fall into two structural and functional classes. All ts C and one ts BC mutations map to the region close to the Ca2+ binding sites, and are predicted to disrupt the insertion of the distal part of the C-terminal invading arm (C-arm) into the receiving clamp. They share a severe defect in assembly at the nonpermissive temperature, with few capsid proteins attached to the viral minichromosome. By contrast, all ts B and most ts BC mutations map to a contiguous region including acceptor sites for the proximal part of the C-arm and intrapentamer contacts. These mutants form assembly intermediates that carry substantial capsid proteins on the minichromosome. Thus, accurate virion assembly is prevented by mutations that disrupt interactions between the receiving pentamer and both the proximal and distal parts of the C-arms, with the latter having a greater effect. The distinct spatial localization and assembly defects of the two classes of mutants provide a rationale for their intracistronic complementation and suggest models of capsid assembly.

Binding Sites↗
PubMed1993

Mast cell degranulation upregulates alpha 6 integrins on epidermal Langerhans cells.

The expression of the alpha 6 beta 4 and alpha 6 beta 1 integrins on epidermal Langerhans cells (LC) before and after mast cell degranulation was studied in cultured human neonatal foreskin by immunohistochemistry. Twenty-four hours after addition of mast cell secretagogues, morphine sulfate, or substance P, solitary mid-epidermal cells showed staining for the integrin subunits alpha 6, beta 4, and beta 1. This expression was not observed in cultured control explants, and immunostained cells were confirmed to be non-epithelial, dendritic cells by immuno-electron microscopy. The identity of these cells as LC was further established by coincident staining for alpha 6 and CD1a using double immunofluorescence labeling. Addition of tumor necrosis factor-alpha (TNF alpha), the predominant cytokine in mast cell granules, also induced LC to express alpha 6 integrins. Furthermore, preincubation of skin organ cultures with anti-TNF alpha antibodies or the mast cell inhibitor cromolyn sodium abrogated the ability to induce alpha 6 integrins on LC consequent to experimental mast cell degranulation by substance P. These data implicate a role for mast cell-derived TNF alpha in the regulation of the integrins alpha 6 beta 4 and alpha 6 beta 1 on LC. These findings may have important implications relevant to mechanisms for spatial localization of LC within the cutaneous compartments during immune responses.

Cell Degranulation↗
PubMed2006

Tenascin-C patterns and splice variants in actinic keratosis and cutaneous squamous cell carcinoma.

BACKGROUND: Tenascin-C (Tn-C) is an extracellular matrix protein with multiple functions that is present at low levels in normal tissues, but which is highly present in various tumours. The mRNA expression and protein level of Tn-C including its various isoforms have not been investigated comprehensively so far in cutaneous squamous cell carcinoma (SCC) and the precursor lesion actinic keratosis (AK). OBJECTIVES: To assess the dysregulated expression and splice variants of Tn-C in cutaneous squamous cell dysplasia and carcinoma. METHODS: Biopsies from 66 patients (or representative subsets) that comprised 25 specimens from normal skin, 19 AK and 22 cutaneous SCC were analysed for Tn-C splice variants using splice-specific primers. The amount of Tn-C mRNA was investigated by quantitative real-time reverse transcription-polymerase chain reaction. In addition, the presence of Tn-C protein was analysed in sections of paraffin-embedded tissues using immunohistochemistry. RESULTS: The large Tn-C splice variant was present in only 5% of normal skin samples, in comparison with 63% of AK (P < 0.001) and 88% of SCC (P < 0.001). Tn-C mRNA expression was significantly increased in AK and SCC compared with normal skin (P < 0.001). The corresponding proteins were rarely detected in cells of the vascular epithelial layers and perifollicular layers of some normal skin specimens, and their spatial localization expanded into the papillary dermis of AK. The largest amount and the widest distribution were found in samples of SCC, in which Tn-C was located in the basal cells at the tumour invasion front and additionally in the papillary dermis and reticular dermis. CONCLUSIONS: Tn-C is present in the dermis, its expression is increased during skin cancer development, and the large splice variant is characteristic for AK and SCC, which may prove useful for diagnostic approaches in cutaneous SCC.

Aged↗
PubMed2006

Spatial expression of two anti-inflammatory mediators, annexin 1 and galectin-1, in nasal polyposis.

BACKGROUND: There is renewed interest in the role played by specific counter-regulatory mechanisms to control the inflammatory host response, poorly investigated in human pathology. Here, we monitored the expression of two anti-inflammatory mediators, annexin 1 and galectin-1, and assessed their potential link to glucocorticoids' (GCs) effective control of nasal polyposis (NP). METHODS: Total patterns of mRNA and protein expression were analysed by quantitative real-time PCR (qPCR) and Western blotting analyses, whereas ultrastructural immunocytochemistry was used for spatial localization and quantification of each mediator, focusing on mast cells, eosinophils and epithelial cells. RESULTS: Up-regulation of the annexin 1 gene, and down-regulation of galectin-1 gene, was detected in polypoid tissue compared with nasal mucosa. Patient treatment with betamethasone augmented galectin-1 protein expression in polyps. At the cellular level, control mast cells and eosinophils displayed higher annexin 1 expression, whereas marked galectin-1 immunolabelling was detected in the granule matrix of mast cells. Cells of glandular duct epithelium also displayed expression of both annexin 1 and galectin-1, augmented after treatment. CONCLUSION: Mast cells and epithelial cells appeared to be pivotal cell types involved in the expression of both annexin 1 and galectin-1. It is possible that annexin 1 and galectin-1 could be functionally associated with a specific mechanism in NP and that GC exert at least part of their beneficial effects on the airway mucosa by up-regulating, in a specific cell target fashion, these anti-inflammatory agonists.

Adult↗
PubMed1984

Histomorphological study of cellular interactions between stromal and haemopoietic stem cells in normal and leukaemic bone marrow.

The interactions between haemopoietic and stromal elements are crucial for stem cell proliferation and differentiation. The bulk of this evidence is derived from experiments in rodents and in-vitro culture studies. We have studied the spatial relationships between the stromal and haemopoietic components and their cellular composition in histological sections of bone marrow (BM) from seven healthy fetuses, 10 normal adults and over 60 patients with acute myeloid leukaemia (AML) and chronic granulocytic leukaemia (CGL) at different stages of the disease. During the early developmental stage (16-18 weeks) fetal BM showed focal haemopoiesis with a characteristic spatial localization of haemopoiesis near bony trabeculae and around small blood vessels. In AML following the treatment-induced hypoplasia, large uniform unilocular fat cells arranged in groups designated 'structured fat' developed from scattered multilocular precursor fat cells. Early foci of haemopoietic regeneration were present almost exclusively in areas of structured fat. In the marrow of patients with CGL in blast transformation (BT) treated by intensive therapy and autografting with cryopreserved haemopoietic stem cells, the haemopoiesis was focal. Clusters of regenerating erythroid precursors or of megakaryocytes were seen in intimate contact with marrow sinusoids and granulopoietic precursors in intimate association with small blood vessels and also in close contact with the endosteal surface of bony trabeculae. We conclude that the endosteal cells, fat cells and the vascular endothelial cells comprise the critical non-haemopoietic stromal elements of human BM. The close associations observed between the regenerating haemopoietic cells and the stromal cells provide strong evidence in support of the existence of a permissive haemopoietic micro-environment in man and emphasize the structural and functional interrelationships that exists between bone, fat, the microvascular system and haemopoiesis in human bone marrow.

Adult↗
PubMed2004

Fluctuation analysis of mitochondrial NADH fluorescence signals in confocal and two-photon microscopy images of living cardiac myocytes.

A fluctuation analysis was performed on the reduced nicotine adenine dinucleotide (NADH) fluorescence signal from resting rabbit myocytes using confocal and two-photon microscopy. The purpose of this study was to establish whether any co-ordinated biochemical processes, such as binding, metabolism and inner mitochondrial membrane potential, were contributing to NADH signal fluctuations above background instrument noise. After a basic characterization of the instrument noise, time series of cellular NADH fluorescence images were collected and compared with an internal standard composed of NADH in the bathing medium. The coefficient of variation as a function of mean signal amplitude of cellular NADH fluorescence and bathing media NADH was identical even as a function of temperature. These data suggest that the fluctuations in cellular NADH fluorescence in resting myocytes are dominated by sampling noise of these instruments and not significantly modified by biological processes. Further analysis revealed no significant spatial correlations within the cell, and Fourier analysis revealed no coherent frequency information. These data suggest that the impact of biochemical processes, which might affect cellular NADH fluorescence emission, are either too small in magnitude, occurring in the wrong temporal scale or too highly spatially localized for detection using these standard optical microscopy approaches.

Animals↗
PubMed1989

The role of the sporulation gene spoIIIE in the regulation of prespore-specific gene expression in Bacillus subtilis.

The spoIIIG gene encodes a sigma factor that determines prespore-specific gene expression during sporulation in Bacillus subtilis. Correct spatial and temporal expression of the spoIIIG gene depends on a number of other sporulation (spo) genes, but only one of these genes, spoIIIE, has a specific effect on spoIIIG expression and not on gene expression in the other differentiating cell, the mother cell. However, the spoIIIE gene is expressed predominantly before differentiation begins. Thus, its product must play an important role in sensing or determining the spatial localization of prespore-specific gene expression in this system.

Amino Acid Sequence↗
PubMed1978

Characterisation of a local structure in the synthetic parathyroid hormone fragment 1--34 by 1H nuclear-magnetic-resonance techniques.

Previous studies had shown that the molecular conformation of the synthetic human parathyroid hormone fragment 1--34 in dilute aqueous solution contained a local non-random structure formed by the four consecutive residues--Val-21--GIn-22--Trp-23--Leu-24--. This paper gives a detailed description of this local spatial structure obtained from high resolution 1H NMR studies at 360 MHZ of several peptide analogs of the partial sequence 20--24. The most important spectral parameters were high-field shifts of the alpha and gamma protons of Val-21, the spin-spin coupling constants related to the rotamer populations of the side-chains of Val-21 and Trp-23, and pH titration shifts of the amide proton resonances. It was found that the backbone fragment 20--24 is so arranged that the side-chain of Val-21 is located next to the indole ring plane of Trp-23; evidence is presented that this non-random structure is mainly stabilized by hydrophobic interactions between the side-chains of Val-21 and Trp-23. The thermal population of the observed molecular structure at room temperature was estimated from the nuclear magnetic resonance data to be approximately 20%.

Amino Acid Sequence↗
PubMed2005

Three-dimensional reconstruction of the equine ovary.

The equine ovary has a very unique structure in terms of its extreme large size, the presence of the ovulation fossa and the inverted location of its cortex and medulla. In the previous study, it was recognized that the application of three-dimensional internal structure microscopy (3D-ISM) to observe the mare ovary is very effective. Three-dimensional reconstruction of serially sliced images made by 3D-ISM was successful in this study with the aid of the sophisticated image processing technique. The rotation of the reconstructed ovary has been carried out with and without the application of the transparency technique in the ovarian stromal region. The spatial localization of follicles and corpus luteum was clearly visualized by rotating the reconstructed image of the ovary. The extraction of the images of follicles and corpus luteum was also available and gave a quantifiable understanding of their structure.

Animals↗
PubMed2003

Context-specific acquisition of location discrimination by hippocampal place cells.

The spatially localized firing of rodent hippocampal place cells is strongly determined by the local geometry of the environment. Over time, however, the cells can acquire additional inputs, including inputs from more distal cues. This is manifest as a change in firing pattern ('remapping') when the new inputs are manipulated. Place cells also reorganize their firing in response to non-geometric changes in 'context', such as a change in the colour or odour of the environment. The present study investigated whether the new inputs acquired by place cells in one context were still available to the cells when they expressed their altered firing patterns in a new context. We found that the acquired information did not transfer to the new context, suggesting that the context inputs and the acquired inputs must interact somewhere upstream of the place cells themselves. We present a model of one possible such interaction, and of how such an interaction could be modified by experience in a Hebbian manner, thus explaining the context specificity of the new learning.

Action Potentials↗
PubMed2006

daime, a novel image analysis program for microbial ecology and biofilm research.

Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime (digital image analysis in microbial ecology), a new computer program integrating 2-D and 3-D image analysis and visualization functionality, which has previously not been available in a single open-source software package. For example, daime automatically finds 2-D and 3-D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with '3D-FISH', which preserves the 3-D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms.

Biofilms↗
PubMed2006

Spatial separation of endothelial small- and intermediate-conductance calcium-activated potassium channels (K(Ca)) and connexins: possible relationship to vasodilator function?

Activation of endothelial cell small- (S) and intermediate- (I) conductance calcium-activated potassium channels (K(Ca)) and current or molecular transfer via myoendothelial gap junctions underlies endothelium-derived hyperpolarization leading to vasodilation. The mechanism underlying the K(Ca) component of vasodilator activity and the characteristics of gap junctions are targets for the selective control of vascular function. In the rat mesenteric artery, where myoendothelial gap junctions and connexin (Cx) 40 are critical for the transmission of the endothelial cell hyperpolarization to the smooth muscle, SK(Ca) and IK(Ca) provide different facets of the endothelium-derived hyperpolarization response, being critical for the hyperpolarization and repolarization phases, respectively. The present study addressed the question of whether this functional separation of responses may be related to the spatial localization of the associated channels? The distribution of endothelial SK(Ca) and IK(Ca) and Cx subtype(s) were examined in the rat mesenteric artery using conventional confocal and high-resolution ultrastructural immunohistochemistry. At the internal elastic lamina-smooth muscle cell interface at internal elastic lamina holes (as potential myoendothelial gap junction sites), strong punctate IK(Ca), Cx37 and Cx40 expression was present. SK(Ca), Cx37, Cx40 and Cx43 were localized to adjacent endothelial cell gap junctions. High-resolution immunohistochemistry demonstrated IK(Ca) and Cx37-conjugated gold to myoendothelial gap junction-associated endothelial cell projections. Clear co-localization of K(Ca) and Cxs suggests a causal relationship between their activity and the previously described differential functional activation of SK(Ca) and IK(Ca). Such precise localizations may represent a selective target for control of vasodilator function and vascular tone.

Animals↗
PubMed2006

Evidence that GAD65 mediates increased GABA synthesis during intense neuronal activity in vivo.

In this study we tested the hypothesis that the 65-kDa isoform of glutamate decarboxylase (GAD(65)) mediates activity-dependent GABA synthesis as invoked by seizures in anesthetized rats. GABA synthesis was measured following acute GABA-transaminase inhibition by gabaculine using spatially localized (1)H NMR spectroscopy before and after bicuculline-induced seizures. Experiments were conducted with animals pre-treated with vigabatrin 24 h earlier in order to reduce GAD(67) protein and also with non-treated controls. GAD isoform content was quantified by immunoblotting. GABA was higher in vigabatrin-treated rats compared to non-treated controls. In vigabatrin-treated animals, GABA synthesis was 28% lower compared to controls [p < 0.05; vigabatrin-treated, 0.043 +/- 0.011 micromol/(g min); non-treated, 0.060 +/- 0.014 micromol/(g min)] and GAD(67) was 60% lower. No difference between groups was observed for GAD(65). Seizures increased GABA synthesis in both control [174%; control, 0.060 +/- 0.014 micromol/(g min) vs. seizures, 0.105 +/- 0.043 micromol/(g min)] and vigabatrin-treated rats [214%; control, 0.043 +/- 0.011 micromol/(g min); seizures, 0.092 +/- 0.018 micromol/(g min)]. GAD(67) could account for at least half of basal GABA synthesis but only 20% of the two-fold increase observed in vigabatrin-treated rats during seizures. The seizure-induced activation of GAD(65) in control cortex occurs concomitantly with a 2.3-fold increase in inorganic phosphate, known to be a potent activator of apoGAD(65)in vitro. Our results are consistent with a major role for GAD(65) in activity-dependent GABA synthesis.

4-Aminobutyrate Transaminase↗