Discriminant Feature Extraction by Generalized Difference Subspace.

In this paper, we reveal the discriminant capacity of orthogonal data projection onto the generalized difference subspace (GDS), both theoretically and experimentally. In our previous work, we demonstrated that the GDS projection works as a quasi-orthogonalization of class subspaces, which is an effective feature extraction for subspace based classifiers. Here, we further show that GDS projection also works as a discriminant feature extraction through a similar mechanism to the Fisher discriminant analysis (FDA). A direct proof of the connection between GDS projection and FDA is difficult due to the significant difference in their formulations. To circumvent the complication, we first introduce geometrical Fisher discriminant analysis (gFDA) based on a simplified Fisher criterion. It is derived from a heuristic yet practically plausible assumption: the direction of the sample mean vector of a class is largely aligned to the first principal component vector of the class, given that the principal component analysis (PCA) is applied without data centering. gFDA works stably even under few samples, bypassing the small sample size (SSS) problem of FDA. We then prove that gFDA is equivalent to GDS projection with a small correction term. This equivalence ensures GDS projection to inherit the discriminant ability from FDA via gFDA. Furthermore, we discuss two useful extensions of these methods, 1) a nonlinear extension by kernel trick, 2) a combination with CNN features. The equivalence and the effectiveness of the extensions have been verified through extensive experiments on the extended Yale B+, CMU face database, ALOI, ETH80, MNIST, and CIFAR10, mainly focusing on image recognition under small samples.

A Novel Separating Hyperplane Classification Framework to Unify Nearest-Class-Model Methods for High-Dimensional Data.

In this article, we establish a novel separating hyperplane classification (SHC) framework to unify three nearest-class-model methods for high-dimensional data: the nearest subspace method (NSM), the nearest convex hull method (NCHM), and the nearest convex cone method (NCCM). Nearest-class-model methods are an important paradigm for the classification of high-dimensional data. We first introduce the three nearest-class-model methods and then conduct dual analysis for theoretically investigating them, to understand deeply their underlying classification mechanisms. A new theorem for the dual analysis of NCCM is proposed in this article by discovering the relationship between a convex cone and its polar cone. We then establish the new SHC framework to unify the nearest-class-model methods based on the theoretical results. One important application of this new SHC framework is to help explain empirical classification results: why one class model has a better performance than others on certain data sets. Finally, we propose a new nearest-class-model method, the soft NCCM, under the novel SHC framework to solve the overlapping class model problem. For illustrative purposes, we empirically demonstrate the significance of our SHC framework and the soft NCCM through two types of typical real-world high-dimensional data: the spectroscopic data and the face image data.

Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images.

Computing similarity or dissimilarity between protein structures is an important task in structural biology. A conventional method to compute protein structure dissimilarity requires structural alignment of the proteins. However, defining one best alignment is difficult, especially when the structures are very different. In this paper, we propose a new similarity measure for protein structure comparisons using a set of multi-view 2D images of 3D protein structures. In this approach, each protein structure is represented by a subspace from the image set. The similarity between two protein structures is then characterized by the canonical angles between the two subspaces. The primary advantage of our method is that precise alignment is not needed. We employed Grassmann Discriminant Analysis (GDA) as the subspace-based learning in the classification framework. We applied our method for the classification problem of seven SCOP structural classes of protein 3D structures. The proposed method outperformed the k-nearest neighbor method (k-NN) based on conventional alignment-based methods CE, FATCAT, and TM-align. Our method was also applied to the classification of SCOP folds of membrane proteins, where the proposed method could recognize the fold HEM-binding four-helical bundle (f.21) much better than TM-Align.

Matched Shrunken Cone Detector (MSCD): Bayesian Derivations and Case Studies for Hyperspectral Target Detection.

Hyperspectral images (HSIs) possess non-negative properties for both hyperspectral signatures and abundance coefficients, which can be naturally modeled using cone-based representation. However, in hyperspectral target detection, cone-based methods are barely studied. In this paper, we propose a new regularized cone-based representation approach to hyperspectral target detection, as well as its two working models by incorporating into the cone representation l2-norm and l1-norm regularizations, respectively. We call the new approach the matched shrunken cone detector (MSCD). Also important, we provide principled derivations of the proposed MSCD from the Bayesian perspective: we show that MSCD can be derived by assuming a multivariate half-Gaussian distribution or a multivariate half-Laplace distribution as the prior distribution of the coefficients of the models. In the experimental studies, we compare the proposed MSCD with the subspace methods and the sparse representation-based methods for HSI target detection. Two real hyperspectral data sets are used for evaluating the detection performances on sub-pixel targets and full-pixel targets, respectively. Results show that the proposed MSCD can outperform other methods in both cases, demonstrating the competitiveness of the regularized cone-based representation.

Difference subspace and its generalization for subspace-based methods.

Subspace-based methods are known to provide a practical solution for image set-based object recognition. Based on the insight that local shape differences between objects offer a sensitive cue for recognition, this paper addresses the problem of extracting a subspace representing the difference components between class subspaces generated from each set of object images independently of each other. We first introduce the difference subspace (DS), a novel geometric concept between two subspaces as an extension of a difference vector between two vectors, and describe its effectiveness in analyzing shape differences. We then generalize it to the generalized difference subspace (GDS) for multi-class subspaces, and show the benefit of applying this to subspace and mutual subspace methods, in terms of recognition capability. Furthermore, we extend these methods to kernel DS (KDS) and kernel GDS (KGDS) by a nonlinear kernel mapping to deal with cases involving larger changes in viewing direction. In summary, the contributions of this paper are as follows: 1) a DS/KDS between two class subspaces characterizes shape differences between the two respectively corresponding objects, 2) the projection of an input vector onto a DS/KDS realizes selective visualization of shape differences between objects, and 3) the projection of an input vector or subspace onto a GDS/KGDS is extremely effective at extracting differences between multiple subspaces, and therefore improves object recognition performance. We demonstrate validity through shape analysis on synthetic and real images of 3D objects as well as extensive comparison of performance on classification tests with several related methods; we study the performance in face image classification on the Yale face database B+ and the CMU Multi-PIE database, and hand shape classification of multi-view images.

Kinetics of dextran-independent α-(1→3)-glucan synthesis by Streptococcus sobrinus glucosyltransferase I.

Glucosyltransferase (GTF)-I from cariogenic Streptococcus sobrinus elongates the α-(1→3)-linked glucose polymer branches on the primer dextran bound to the C-terminal glucan-binding domain. We investigated the GTF-I-catalyzed glucan synthesis reaction in the absence of the primer dextran. The time course of saccharide production during dextran-independent glucan synthesis from sucrose was analyzed. Fructose and glucose were first produced by the sucrose hydrolysis. Leucrose was subsequently produced, followed by insoluble glucan [α-(1→3)-linked glucose polymers] after a lag phase. High levels of intermediate nigerooligosaccharide series accumulation were characteristically not observed during the lag phase. The results from the enzymatic activity of the acceptor reaction for the nigerooligosaccharide with a degree of polymerization of 2-6 and methyl α-D-glucopyranoside as a glucose analog indicate that the activity increased with an increase in the degree of polymerization. The production of insoluble glucan was numerically simulated using the fourth-order Runge-Kutta method with the kinetic parameters estimated from the enzyme assay. The simulated time course provided a profile similar to that of experimental data. These results define the relationship between the kinetic properties of GTF-I and the time course of saccharide production. These results are discussed with respect to a mechanism that underlies efficient glucan synthesis.

Subspace-based support vector machines for pattern classification.

In this paper, we discuss subspace-based support vector machines (SS-SVMs), in which an input vector is classified into the class with the maximum similarity. Namely, for each class we define the weighted similarity measure using the vectors called dictionaries that represent the class, and optimize the weights so that the margin between classes is maximized. Because the similarity measure is defined for each class, for a data sample the similarity measure to which the data sample belongs needs to be the largest among all the similarity measures. Introducing slack variables, we define these constraints either by equality constraints or inequality constraints. As a result we obtain subspace-based least squares SVMs (SSLS-SVMs) and subspace-based linear programming SVMs (SSLP-SVMs). To speedup training of SSLS-SVMs, which are similar to LS-SVMs by all-at-once formulation, we also propose SSLS-SVMs by one-against-all formulation, which optimize each similarity measure separately. Using two-class problems, we clarify the difference of SSLS-SVMs and SSLP-SVMs and evaluate the effectiveness of the proposed methods over the conventional methods with equal weights and with weights equal to eigenvalues.

Dural arteriovenous fistula in the anterior cranial fossa: four case reports.

Three of 4 cases of dural arteriovenous fistulas (DAVFs) in the anterior cranial fossa were detected incidentally by magnetic resonance (MR) imaging, and one case manifested as intracerebral hemorrhage. Cerebral angiography revealed fistulas located in the anterior cranial fossa. Three patients underwent surgery, and the fistulas were successfully obliterated. One patient with nonruptured DAVF requested conservative medical management. Incidental detection of asymptomatic or nonruptured DAVFs in the anterior cranial fossa has increased with the wider use of MR imaging. Increase in the size of a venous varix is the indicator for aggressive therapeutic intervention in a patient receiving conservative medical management for asymptomatic or nonruptured DAVFs in the anterior cranial fossa.

Deformation of mesh type stainless palatal plate of maxillary complete denture and the growth of microorganisms.

PATIENT: An 83-year-old woman visited the hospital for new complete dentures. A mesh type stainless palatal plate (Trutissu plate) was selected, because it enables the patient to experience the taste and temperature of food. Twenty one months after insertion, the patient returned complaining of pain on mucosa under the mandibular denture base. On clinical examination, a small swollen area was observed on the palatine rugae region of the mesh plate. By making a small hole in the swollen part, a creamy mass of dark brown color was discharged from the swollen space between the laminated structure of the Trutissu plate. Three months after the first deformation was corrected, further deformation of the Trutissu plate was observed. The patient admitted that she had not used the ultrasonic cleansing apparatus. A candidiasis-like lesion was observed on the palatal mucosa. DISCUSSION: The formation of Candida biofilms on dentures may assist survival of fungal cells and contribute to the disease process in patients with denture stomatitis. In this case, the patient did not use ultrasonic cleaner, thus resulting in microbial accumulation and morphological change of the laminated mesh plate. However, this is rare in the clinical use of the Trutissu mesh plate, and the only case reported in 20 years. Ultrasonic cleansing was effective in removing microorganisms from the denture. CONCLUSION: Routine ultrasonic cleansing should be performed to avoid the possible accumulation of microorganisms in the laminated mesh structure.

Rapid and simple detection of eight major periodontal pathogens by the loop-mediated isothermal amplification method.

Loop-mediated isothermal amplification (LAMP) was applied to develop a rapid and simple detection system for eight periodontal pathogens: Aggregatibacter (Actinobacillus) actinomycetemcomitans, Campylobacter rectus, Eikenella corrodens, Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia, Treponema denticola and Tannerella forsythia. Primers were designed from the 16S ribosomal RNA gene for each pathogen, and the LAMP amplified the targets specifically and efficiently under isothermal condition at 64 degrees C. To simplify the manipulation of LAMP examination, boiled cells and intact cells suspended in phosphate-buffered saline (PBS) were tested as templates besides extracted DNA template. The detection limits were 1-10 cells per tube using extracted DNA template. However, LAMP methods using boiled cells and intact cells required 10-100 and 100-1000 cells per tube, respectively. LAMPs for A. actinomycetemcomitans, P. gingivalis and P. intermedia were then applied to clinical plaque samples, and the method demonstrated equal or higher sensitivity compared with the conventional real-time PCR method. These findings suggest the usefulness of the LAMP method for the rapid and simple microbiological diagnosis of periodontitis, and the possibility of LAMP examination without the DNA extraction step.

Inhibition of swarming motility of Pseudomonas aeruginosa by branched-chain fatty acids.

Pseudomonas aeruginosa is capable of moving by swimming, swarming, and twitching motilities. In this study, we investigated the effects of fatty acids on Pseudomonas aeruginosa PAO1 motilities. A branched-chain fatty acid (BCFA)--12-methyltetradecanoic acid (anteiso-C15:0)--has slightly repressed flagella-driven swimming motility and completely inhibited a more complex type of surface motility, i.e. swarming, at a concentration of 10 microg mL(-1). In contrast, anteiso-C15:0 exhibited no effect on pili-mediated twitching motility. Other BCFAs and unsaturated fatty acids tested in this study showed similar inhibitory effects on swarming motility, although the level of inhibition differed between these fatty acids. These fatty acids caused no significant growth inhibition in liquid cultures. Straight-chain saturated fatty acids such as palmitic acid were less effective in swarming inhibition. The wetness of the PAO1 colony was significantly reduced by the addition of anteiso-C15:0; however, the production of rhamnolipids as a surface-active agent was not affected by the fatty acid. In addition to motility repression, anteiso-C15:0 caused 31% repression of biofilm formation by PAO1, suggesting that BCFA could affect the multiple cellular activities of Pseudomonas aeruginosa.

Thermodynamics of the binding of the C-terminal repeat domain of Streptococcus sobrinus glucosyltransferase-I to dextran.

Glucosyltransferases (GTFs) secreted by mutans streptococci and some other lactic acid bacteria catalyze glucan synthesis from sucrose, and possess a C-terminal glucan-binding domain (GBD) containing homologous, directly repeating units. We prepared a series of C-terminal truncated forms of the GBD of Streptococcus sobrinus GTF-I and studied their binding to dextran by isothermal titration calorimetry. The binding of all truncates was strongly exothermic. Their titration curves were analyzed assuming that the GBD recognizes and binds to a stretch of dextran chain, not to a whole dextran molecule. Both the number of glucose units constituting the dextran stretch (n) and the accompanying enthalpy change (DeltaH degrees ) are proportional to the molecular mass of the GBD truncate, with which the Gibbs energy change calculated by the relation DeltaG degrees = -RT ln K (R, the gas constant; T, the absolute temperature; K, the binding constant of a truncate for a dextran stretch of n glucose units) also increases linearly. For the full-length GBD (508 amino acid residues), n = 33.9, K = 4.88 x 10(7) M-1, and DeltaH degrees = -289 kJ mol-1 at 25 degrees C. These results suggest that identical, independent glucose-binding subsites, each comprising 14 amino acid residues on average, are arranged consecutively from the GBD N-terminus. Thus, the GBD binds tightly to a stretch of dextran chain through the adding up of individually weak subsite/glucose interactions. Furthermore, the entropy change accompanying the GBD/dextran interaction as given by the relation DeltaS degrees = (DeltaG degrees - DeltaH degrees)/T has a very large negative value, probably because of a loss of the conformational freedom of dextran and GBD after binding.

Depletion of O6-methylguanine-DNA methyltransferase by O6-benzylguanine enhances 5-FU cytotoxicity in colon and oral cancer cell lines.

O6-methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme whose expression is controlled by its promoter methylation. A cell that expresses a low amount of MGMT is known to be more sensitive to the antiproliferative effects of alkylating agents. We have previously shown that the colorectal cancer patients treated with 5-fluorouracil (5-FU) as adjuvant chemotherapy had a better prognosis when the tumor revealed hypermethylation in its MGMT promoter. Therefore, we sought to investigate the relationship between the expression levels of MGMT and the anti-tumor effect of 5-FU in vitro by using two colon adenocarcinoma and four oral cancer cell lines with a variety of MGMT expression. We also investigated the effects of MGMT depletion by O6-benzylguanine (O6-BG), a potent inhibitor of MGMT. The 5-FU treatment uniformly depleted protein and mRNA expression of MGMT in all cell lines examined. Cell lines expressing low levels of MGMT were sensitive to 5-FU. On the other hand, cells expressing high levels of MGMT were less sensitive to 5-FU. The 5-FU treatment exhibited a better antiproliferative effect on the cells expressing high levels of MGMT by the pretreatment of O6-BG. Depletion of MGMT by O6-BG enhanced the anti-tumor effect of 5-FU. Assessment of the levels of MGMT expression in cancer cells and the control of its expression could contribute to the effective chemotherapy by 5-FU especially in patients who previously were considered as low-responsive individuals whose tumors have high levels of MGMT.

Genome-wide screening of genes required for swarming motility in Escherichia coli K-12.

Escherichia coli K-12 has the ability to migrate on semisolid media by means of swarming motility. A systematic and comprehensive collection of gene-disrupted E. coli K-12 mutants (the Keio collection) was used to identify the genes involved in the swarming motility of this bacterium. Of the 3,985 nonessential gene mutants, 294 were found to exhibit a strongly repressed-swarming phenotype. Further, 216 of the 294 mutants displayed no significant defects in swimming motility; therefore, the 216 genes were considered to be specifically associated with the swarming phenotype. The swarming-associated genes were classified into various functional categories, indicating that swarming is a specialized form of motility that requires a wide variety of cellular activities. These genes include genes for tricarboxylic acid cycle and glucose metabolism, iron acquisition, chaperones and protein-folding catalysts, signal transduction, and biosynthesis of cell surface components, such as lipopolysaccharide, the enterobacterial common antigen, and type 1 fimbriae. Lipopolysaccharide and the enterobacterial common antigen may be important surface-acting components that contribute to the reduction of surface tension, thereby facilitating the swarm migration in the E. coli K-12 strain.

Colloid (enterogenous) cyst in the frontal lobe.

A 60-year-old man presented with a left frontal mass lesion incidentally detected at a health check without apparent symptoms. Computed tomography revealed the lesion as homogeneous high density and magnetic resonance (MR) imaging showed the lesion as hyperintense on T(1)-weighted images, isointense on T(2)-weighted images, and hypointense on diffusion-weighted images. T(1)-weighted MR images with gadolinium showed no enhancement of the mass lesion. Cerebral angiography revealed an avascular area around the left frontal lesion. Total removal of the lesion was achieved through a craniotomy without complications. Histological, immunohistochemical, and electron microscopy examinations established the definite diagnosis of colloid cyst.

Composition of the bacterial flora in tonsilloliths.

Tonsilloliths are a potential cause of oral malodor. In this study, microbial profiles and composition of tonsilloliths were determined using culture-independent molecular methods and scanning electron microscopy. 16S ribosomal RNA bacterial genes (16S rDNAs) isolated from tonsilloliths of 6 individuals were amplified by PCR and cloned into Escherichia coli. Partial 16S rDNA sequences of approximately 600 bases of cloned inserts were used to determine species identity by comparison with sequences of known species. Characteristics of bacteria on the surface and inside the tonsillolith were analyzed using scanning electron microscopy. Anaerobic bacteria detected in tonsilloliths belonged to the genera Eubacterium, Fusobacterium, Megasphaera, Porphyromonas, Prevotella, Selenomonas and Tannerella, all of which appear to be associated with production of volatile sulfur compounds. Electron microscopy revealed cocci and rods on the surface and rods predominating inside the tonsilloliths. These results support the tonsillolith as an origin of oral malodor.

Role of O6-methylguanine-DNA methyltransferase and effect of O6-benzylguanine on the anti-tumor activity of cis-diaminedichloroplatinum(II) in oral cancer cell lines.

The DNA repair enzyme O6-methylguanine-DNA methyltransferase (MGMT) modulates the effectiveness of alkylating agents. However, the relationship between MGMT and the sensitivities to other agents has not been explored. In the present study, the association between MGMT expression and the cellular sensitivity to the platinum agent, CDDP was examined in four human oral cancer cell lines. CDDP depleted MGMT protein and mRNA levels in all four cell lines. Two cell lines with low MGMT expression were sensitive to an alkylating agent, N-methyl-N'-nitro-N-nitrosoguanidine and CDDP, whereas two other cell lines with high MGMT expression were resistant to both agents. Furthermore, the addition of the MGMT inhibitor, O6-benzylguanine (O6-BG), invariably enhanced CDDP sensitivity. CDDP depleted MGMT expression, and CDDP sensitivity was enhanced by O6-BG. These results provide valuable information about the relationship between MGMT expression and CDDP sensitivity in oral cancer chemotherapy.

Biofilm formation by a fimbriae-deficient mutant of Actinobacillus actinomycetemcomitans.

Actinobacillus actinomycetemcomitans strain 310-TR produces fimbriae and forms a tight biofilm in broth cultures, without turbid growth. The fimbriae-deficient mutant 310-DF, constructed in this study, was grown as a relatively fragile biofilm at the bottom of a culture vessel. Scanning electron microscopy revealed that on glass coverslips, 310-TR formed tight and spherical microcolonies, while 310-DF produced looser ones. These findings suggest that fimbriae are not essential for the surface-adherent growth but are required for enhancing cell-to-surface and cell-to-cell interactions to stabilize the biofilm. Treatment of the 310-DF biofilm with either sodium metaperiodate or DNase resulted in significant desorption of cells from glass surfaces, indicating that both carbohydrate residues and DNA molecules present on the cell surface are also involved in the biofilm formation.

Induction of L-form-like cell shape change of Bacillus subtilis under microculture conditions.

A remarkable cell shape change was observed in Bacillus subtilis strain 168 under microculture conditions on CI agar medium (Spizizen's minimal medium supplemented with a trace amount of yeast extract and Casamino acids). Cells cultured under a cover glass changed in form from rod-shaped to spherical, large and irregular shapes that closely resembled L-form cells. The cell shape change was observed only with CI medium, not with Spizizen's minimum medium alone or other rich media. The whole-cell protein profile of cells grown under cover glass and cells grown on CI agar plates differed in several respects. Tandem mass analysis of nine gel bands which differed in protein expression between the two conditions showed that proteins related to nitrate respiration and fermentation were expressed in the shape-changed cells grown under cover glass. The cell shape change of CI cultures was repressed when excess KNO3 was added to the medium. Whole-cell protein analysis of the normal rod-shaped cells grown with 0.1% KNO3 and the shape-changed cells grown without KNO3 revealed that the expression of the branched-chain alpha-keto acid dehydrogenase complex (coded by the bfmB gene locus) was elevated in the shape-changed cells. Inactivation of the bfmB locus resulted in the repression of cell shape change, and cells in which bfmB expression was induced by IPTG did show changes in shape. Transmission electron microscopy of ultrathin sections demonstrated that the shape-changed cells had thin walls, and plasmolysis of cells fixed with a solution including 0.1 M sucrose was observed. Clarifying the mechanism of thinning of the cell wall may lead to the development of a new type of cell wall biosynthetic inhibitor.