Mutual Similarity Research Articles

The integrated and local estimations of instability for a class of autonomous delay systems

Abstract The Lyapunov stability of a partly nonlinear delay system is investigated both analytically and numerically for the sake of calculation of (i) integrated and (ii) local estimates. The improvement of numerical scheme for calculation of characteristic exponents is achieved within the integrated analysis and the properties of mutual similarity of the internal product are proved. At the local instabilities investigation, two kinds of instability for the delay system with high-power nonlinearity are detected. The intermittency of the chaotic behavior is also explored numerically and analogy with hydrodynamic turbulence is shown.

Characterization of Stowaway MITEs in pea (Pisum sativum L.) and identification of their potential master elements.

We have investigated miniature inverted-repeat transposable elements (MITEs) of the Stowaway family and corresponding Mariner-like master elements that could potentially facilitate their mobilization in the genome of the garden pea (Pisum sativum L.). The population of pea Stowaway MITEs consists of 103-104 copies dispersed in the genome. Judging from a sequence analysis of 17 isolated Stowaway elements and their flanking genomic regions, the elements are relatively uniform in size and sequence and occur in the vicinity of genes as well as within repetitive sequences. Insertional polymorphism of several elements was detected among various Pisum accessions, suggesting they were still transpositionally active during diversification of these taxa. The identification of several Mariner-like elements (MLEs) harboring intact open reading frames, capable of encoding a transposase, further supports a recent mobilization of the Stowaway elements. Using transposase-coding sequences as a hybridization probe, we estimated that there are about 50 MLE sequences in the pea genome. Among the 5 elements sequenced, 3 distinct subfamilies showing mutual similarities within their transposase-coding regions, but otherwise diverged in sequence, were distinguished and designated as Psmar-1 to Psmar-3. The terminal inverted repeats (TIRs) of these MLE subfamilies differed in their homology to the TIRs of Stowaway MITEs. The homlogy ranged from 9 bp in Psmar-3 to 30 bp in Psmar-1, which corresponds to the complete Stowaway TIR sequence. Based on this feature, the Psmar-1 elements are believed to be the most likely candidates for the master elements of the Stowaway MITEs in pea.

Centralized data analysis of a large interlaboratory proteomics project: A feasibility study

The human Plasma Proteome Project (PPP) is a large-scale collaboration between many laboratories. One of the most demanding tasks in the PPP involved the analysis of very large amounts of raw MS/MS data produced by the participants. The main approach for managing this task was letting the participants analyze their own data and submit the results to the central PPP repository as lists of identified proteins and peptides. To complement this distributed approach, we also performed centralized analysis of the raw MS/MS data provided by the participants. Due to the data redundancy inherent in such a project, centralized analysis has the potential to reduce the computational effort by reducing redundancy before the analysis. Centralized analysis can also unify the process and take advantage of data sharing among laboratories to improve protein identification and validation. The process we employed included removing low-quality spectra, clustering spectra by mutual similarity, and applying uniform peptide and protein identification procedures. To demonstrate the process, we analyzed 5.28 million MS/MS spectra derived by eight laboratories from tryptic peptides of serum and plasma proteins.

Influence of atmosphere kind on temperature programmed decomposition of noble metal chlorides

The hydrated chlorides of noble metals located in the 8–10 groups of Periodic System were used in this work: Ru, Rh, Pd, Ir and Pt. The common mechanism of chloride compounds decomposition in oxidative, inert and reductive atmospheres was postulated and mutual similarities and differences were discussed. These compounds play a significant role in heterogeneous catalysis, as starting materials for metal/oxide catalysts, and also in analytical chemistry and industry.

Efficient multi-modal dense field non-rigid registration: alignment of histological and section images

We describe a new algorithm for non-rigid registration capable of estimating a constrained dense displacement field from multi-modal image data. We applied this algorithm to capture non-rigid deformation between digital images of histological slides and digital flat-bed scanned images of cryotomed sections of the larynx, and carried out validation experiments to measure the effectiveness of the algorithm. The implementation was carried out by extending the open-source Insight ToolKit software. In diagnostic imaging of cancer of the larynx, imaging modalities sensitive to both anatomy (such as MRI and CT) and function (PET) are valuable. However, these modalities differ in their capability to discriminate the margins of tumor. Gold standard tumor margins can be obtained from histological images from cryotomed sections of the larynx. Unfortunately, the process of freezing, fixation, cryotoming and staining the tissue to create histological images introduces non-rigid deformations and significant contrast changes. We demonstrate that the non-rigid registration algorithm we present is able to capture these deformations and the algorithm allows us to align histological images with scanned images of the larynx. Our non-rigid registration algorithm constructs a deformation field to warp one image onto another. The algorithm measures image similarity using a mutual information similarity criterion, and avoids spurious deformations due to noise by constraining the estimated deformation field with a linear elastic regularization term. The finite element method is used to represent the deformation field, and our implementation enables us to assign inhomogeneous material characteristics so that hard regions resist internal deformation whereas soft regions are more pliant. A gradient descent optimization strategy is used and this has enabled rapid and accurate convergence to the desired estimate of the deformation field. A further acceleration in speed without cost of accuracy is achieved by using an adaptive mesh refinement strategy.

Dual market structures and the likelihood of repeated ties – evidence from pharmaceutical biotechnology

This paper analyses the role of repeated ties in the high-tech pharmaceutical biotechnology industry, a sector that is characterized by a strong dual market structure. Our most important finding is that previous ties in pairs of large pharmaceutical companies and small biotechnology firms have a negative effect on their subsequent partnering. An explanation for this result is found in the context of understanding the specifics of large-small coalitions in a high-tech dual market structure. Unlike what is known about repeated ties in many other industries, this high-tech dual market structure indicates that R&D partnerships between a small number of very large companies and a large group of dependent, small firms are not characterized by mutual dependence, similarity, or equality.

Translocation of a 190-kb mitochondrial fragment into rice chromosome 12 followed by the integration of four retrotransposons

A 190-kb mitochondrial DNA sequence interrupted by seven foreign DNA segments was identified in rice chromosome 12. This fragment is the largest mitochondrial fragment translocated into the rice nuclear genome. The sequence is composed of a 190-kb segment of mitochondrial origin corresponding to 38.79% of the mitochondrial genome, 45 kb comprising four segments of retrotransposon origin, and 13 kb comprising three segments of unknown origin. The 190-kb sequence shows more than 99.68% similarity to the current mitochondrial sequence, suggesting that its integration into the nucleus was quite recent. Several sequences in the 190-kb segment have been rearranged relative to the current mitochondrial sequence, suggesting that the past and present arrangements of the mitochondrial genome differ. The four retrotransposons show no mutual sequence similarity and are integrated into different locations, suggesting that their integration events were independent, frequent, and quite recent. A fragment of the mitochondrial genome present in the nuclear genome, such as the 248-kb sequence characterized in this study, is a good relic with which to investigate the past mitochondrial genome structure and the behavior of independent retrotransposons during evolution.

Two structurally different defensin genes, one of them encoding a novel defensin isoform, are expressed in honeybee Apis mellifera

Two defensins showing high mutual similarity have previously been characterized in honeybee Apis mellifera: royalisin, a peptide isolated from the royal jelly, and defensin, found in the hemolymph of bacterially infected bees. Here we show that both these peptides are encoded by the same polymorphic gene, which we termed defensin1. Besides this gene, we identified an additional defensin gene coding for a novel honeybee defensin designated defensin2. The pre-pro-peptide sequence of defensin 2 was inferred from its cDNA. Mature defensin 2 peptide shows 55.8% identity with defensin 1. Sequences of genomic loci of the two defensin genes revealed their different structure. Defensin1 possesses an exon–intron structure unique among arthropoda defensin genes. Its second intron splits exactly the common structural module of defensins from a short amidated C-terminal extension found only in hymenopteran defensins. Transcription of defensin genes in some nurse honeybees tissues was studied by RT–PCR. Both defensins are expressed in heads and thoraces. Defensin1 but not defensin2 mRNA was detected in hyphopharyngeal, mandibular and thoracic salivary glands. Immune response elements were identified by computer analysis of the promoter regions of defensin genes. Their different representation in these genes reflects presumably observed tissue-specific expression of defensins.

The Circular Bacteriocins Gassericin A and Circularin A

Gassericin A, a bacteriocin produced by Lactobacillus gasseri LA39, shows antibacterial activity against a number of Gram-positive food-borne pathogenic bacteria. Circularin A produced by Clostridium beijerinckii ATCC25752 is active against C. tyrobutyricum, a known cheese-spoilage bacterium. Both bacteriocins were purified to homogeneity from culture supernatants by reverse-phase chromatography and the subsequently determined amino acid sequences were used to clone the bacteriocin structural genes. Mature gassericin A and circularin A are class V circular bacteriocins comprised of 58 and 69 amino acid residues, respectively. Both bacteriocins are resistant to several peptidases and proteases, as are other cyclic bacteriocins. Heterologous expression of gassericin A in Escherichia coli was used to produce a non-cyclic mature peptide, which was shown to have a specific activity 173-fold lower than the circular molecule. The minimal region for production and secretion of active circularin A is comprised of five genes, as was deduced by heterologous gene expression in Enterococcus faecalis. Gassericin A and circularin A have limited mutual similarity in their primary sequences. Unlike most bacteriocins, including gassericin A, circularin A has a three-amino-acid-leader sequence.

A program to perform Ward's clustering method on several regionalized variables

There are many statistical techniques that allow finding similarities or differences among data and variables. Cluster analysis encompasses many diverse techniques for discovering structure within complex sets of data. The objective of cluster analysis is to group either the data or the variables into clusters such that the elements within a cluster have a high degree of “natural association” among themselves while clusters are “relatively distinct” from one another. To do so, many criteria have been described: partitioning methods, arbitrary origin methods, mutual similarity procedures and hierarchical clustering techniques. One of the most widespread hierarchical clustering methods is the Ward's method. Earth science studies deal in general with multivariate and regionalized observations which may be compositional, i.e. data such as percentages, concentrations, mg/kg (ppm). Sometimes, it is interesting to know whether these data have to be divided into different subpopulations. This problem cannot be studied with traditional Ward's method because samples are not independent. In that case, an extension of Ward's clustering method to spatially dependent samples can be used. This methodology is based on a generalized Mahalanobis distance, which uses the covariance and cross-covariance (or variogram and cross-variogram) matrices. This paper describes a refinement of this method previously defined, which was iterative and tedious, as it was necessary to re-estimate the spatial covariance structure at each step. In this paper, we stay within the same theoretical framework, but we improve the methodology using the fast fourier Transform method to find the covariance structure. Thus, we obtain a generalization to several variables of adapted Ward's clustering method.

An Approach to Multimodal Biomedical Image Registration Utilizing Particle Swarm Optimization

Biomedical image registration, or geometric alignment of two-dimensional and/or three-dimensional (3D) image data, is becoming increasingly important in diagnosis, treatment planning, functional studies, computer-guided therapies, and in biomedical research. Registration based on intensity values usually requires optimization of some similarity metric between the images. Local optimization techniques frequently fail because functions of these metrics with respect to transformation parameters are generally nonconvex and irregular and, therefore, global methods are often required. In this paper, a new evolutionary approach, particle swarm optimization, is adapted for single-slice 3D-to-3D biomedical image registration. A new hybrid particle swarm technique is proposed that incorporates initial user guidance. Multimodal registrations with initial orientations far from the ground truth were performed on three volumes from different modalities. Results of optimizing the normalized mutual information similarity metric were compared with various evolutionary strategies. The hybrid particle swarm technique produced more accurate registrations than the evolutionary strategies in many cases, with comparable convergence. These results demonstrate that particle swarm approaches, along with evolutionary techniques and local methods, are useful in image registration, and emphasize the need for hybrid approaches for difficult registration problems.

Multivalued type proximity measure and concept of mutual similarity value useful for clustering symbolic patterns

In this paper, a novel similarity measure for estimating the degree of similarity between two patterns (described by interval type data) is proposed. The proposed measure computes the degree of similarity between two patterns and approximates the computed similarity value by a multivalued type data. Unlike conventional proximity matrices, the proximity matrix obtained through the application of the proposed similarity measure is not necessarily symmetric. Based on this unconventional similarity matrix a modified agglomerative method by introducing the concept of mutual similarity value (MSV) for clustering symbolic patterns is also presented. Experiments on various data sets have been conducted in order to study the efficacy of the proposed methodology.

Visualization and User-Modeling for Browsing Personal Photo Libraries

We present a user-centric system for visualization and layout for content-based image retrieval. Image features (visual and/or semantic) are used to display retrievals as thumbnails in a 2-D spatial layout or “configuration” which conveys all pair-wise mutual similarities. A graphical optimization technique is used to provide maximally uncluttered and informative layouts. Moreover, a novel subspace feature weighting technique can be used to modify 2-D layouts in a variety of context-dependent ways. An efficient computational technique for subspace weighting and re-estimation leads to a simple user-modeling framework whereby the system can learn to display query results based on layout examples (or relevance feedback) provided by the user. The resulting retrieval, browsing and visualization can adapt to the user's (time-varying) notions of content, context and preferences in style and interactive navigation. Monte Carlo simulations with machine-generated layouts as well as pilot user studies have demonstrated the ability of this framework to model or “mimic” users, by automatically generating layouts according to their preferences.

AN APPROACH TO NATURAL STROKE EXTRACTION FOR OFF-LINE LOOSELY-CONSTRAINED HANDWRITTEN CHINESE CHARACTERS

This paper proposes a new approach to extracting natural strokes from the skeletons of loosely-constrained, off-line handwritten Chinese characters. It admits the output substrokes from a previously proposed fuzzy substroke extractor as its inputs. By identifying a number of expected ambiguities which include mutual similarities, unstable touches and joint/cross distortions, fuzzy stroke models are constructed and a "hit-all" fuzzy stroke matching strategy is pursued. Fuzzy partitioning technique is used to generate a ranked list of consistent stroke sets from the set of fuzzy strokes being identified. With this approach, a maximum of 20 distinct natural stroke classes can be extracted from each input character, together with an estimate on the actual count of strokes which compose the character. Our system offers a number of performance tuning capabilities such as the computation of the fuzzy scores of each extracted stroke, the adjustment on the fuzzy stroke model parameters, and the potential of incorporating one's personal writing styles into our methodology.

Performance of mutual information similarity measure for registration of multitemporal remote sensing images

Accurate registration of multitemporal remote sensing images is essential for various change detection applications. Mutual information has recently been used as a similarity measure for registration of medical images because of its generality and high accuracy. Its application in remote sensing is relatively new. There are a number of algorithms for the estimation of joint histograms to compute mutual information, but they may suffer from interpolation-induced artifacts under certain conditions. In this paper, we investigate the use of a new joint histogram estimation algorithm called generalized partial volume estimation (GPVE) for computing mutual information to register multitemporal remote sensing images. The experimental results show that higher order GPVE algorithms have the ability to significantly reduce interpolation-induced artifacts. In addition, mutual-information-based image registration performed using the GPVE algorithm produces better registration consistency than the other two popular similarity measures, namely, mean squared difference (MSD) and normalized cross correlation (NCC), used for the registration of multitemporal remote sensing images.

Generalized periodically focused beams and multiple on-axis lens imaging

A class of periodically focused propagation-invariant monochromatic beams with sharp central peak is extended to the beams, of which the patterns of intensity at discrete transverse planes regularly spaced along the propagation axis may have an arbitrary, but the same, form. It is shown that the wave field of such beams in free space may be represented as a discrete set of nonuniform phase-distorted spherical wavelets converging to the vicinities of axial points at the indicated transverse planes and possessing the property of mutual similarity. High-order azimuth angular constituents of these wavelets are shown to have phase singularities appearing in the transverse planes as dark coaxial spots with bright rims. Hybrid refractive–diffractive systems are proposed, which are suited both for the direct high efficient production of the beams considered and for the multiple imaging of arbitrary plane objects. The results of numerical simulations are given for two cases of multiple reproduction of rings with large and small radii.

Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced.

We have isolated and characterized a novel giant retroelement, named Ogre, which is over 22 kb long and makes up at least 5% of the pea (Pisum sativum L.) genome. This element can be classified as a Ty3/gypsy-like LTR retrotransposon based on the presence of long terminal repeats (LTRs) and the order of the domains coding for typical retrotransposon proteins. In addition to its extreme length, it has several features which make it unique among the retroelements described so far: (1) the sequences coding for gag and prot proteins are separated from the rt/rh-int domains by several stop codons; (2) the region containing these stop codons is removed from the element transcripts by splicing which results in reconstitution of the complete gag-pol coding sequence; (3) only a part of the transcripts is spliced which probably determines the ratio of translated proteins; (4) the element contains an extra ORF located upstream the gag-pol coding sequences, potentially coding for a protein of 546-562 amino acids with unknown function. The transcriptional activity of the Ogre elements has been detected in all organs tested (leaves, roots, flowers) as well as in wounded leaves and protoplasts. Considering this retroelement's constitutive expression and observed high mutual similarity of the element genomic sequences, it is possible to speculate about its recent amplification in the genomes of pea and other legume plants.

A quick AND/OR search for multimedia signals based on histogram features

AbstractThe problem of finding the point in time at which a known audio or video source (reference signal) appears in a long audio or video source (input signal) is referred to as a time series search, in contrast to a text string search. In a time series search, a search can be performed quickly by combining the audio and video, and then identifying several search conditions using logical equations. Thus, in this paper the authors describe the application of the time series active search method, a method to search audio signals proposed in the authors' previous paper, to video searches. Next, the authors propose an efficient algorithm for AND searches and OR searches of reference signals. In addition, the authors propose a multimodal AND search which combines audio and video. The proposed algorithms are faster than combining the results of searches performed individually. For instance, in an OR search of a reference signal, when the mutual similarity in the reference signals is above 0.8, five reference signals can be searched in a search time that is 1.2 times faster than searching one reference signal. © 2003 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 86(12): 54–64, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjc.10142

Path-based clustering for grouping of smooth curves and texture segmentation

Perceptual grouping organizes image parts in clusters based on psychophysically plausible similarity measures. We propose a novel grouping method in this paper, which stresses connectedness of image elements via mediating elements rather than favoring high mutual similarity. This grouping principle yields superior clustering results when objects are distributed on low-dimensional extended manifolds in a feature space, and not as local point clouds. In addition to extracting connected structures, objects are singled out as outliers when they are too far away from any cluster structure. The objective function for this perceptual organization principle is optimized by a fast agglomerative algorithm. We report on perceptual organization experiments where small edge elements are grouped to smooth curves. The generality of the method is emphasized by results from grouping textured images with texture gradients in an unsupervised fashion.

Identification of anabolic steroids in serum, urine, sweat and hair: Comparison of metabolic patterns

Anabolic steroids usually undergo a complex metabolism which is mainly dependent on structural variation and application pathway. In contrast to doping analysis, where the presence of a prohibited substance constitutes a doping offence without regarding the origin or application, in forensic cases any information related to anabolic steroids may be required to evaluate the cause of death, liability of defendants, or self-consumption. 19-Norsteroids proved to be appropriate model compounds for the investigation, because of their prevalence in recent doping cases, analytical and biochemical similarity to endogenous steroids, well explored biochemistry, and the availability of numerous reference standards. Typical urinary metabolites are conjugates of terminal biotransformation products like norandrosterone–glucuronide, which are relatively unspecific and do not reveal details about administration time, pathway, dosages or structural details. Therefore, metabolic patterns in blood, hair and sweat were examined to study metabolism, distribution and incorporation behaviour of the steroids and hence the traceability in the respective matrices. Concentration profiles of the steroids in blood and the resulting bioavailability show distinct particularities after oral or transdermal application of steroids. Oral application of steroid precursors is followed by extensive first pass biotransformation of the steroid to inactive metabolites, while transdermal administration appears to be an efficient pathway, leading to effective and durable concentrations of active steroids in blood. Due to the mutual similarity of metabolic patterns in hair and sweat corresponding to the regional presence of sweat and sebum glands, steroid incorporation appears to proceed mainly via sweat absorption.