Circular Map Research Articles

Polar Zernike moments and rotational invariance

Zernike moments (ZM) have potentials in pattern recognition, image analysis/processing, and in computer vision. Their invariance and orthogonality are attractive in many applications. Unfortunately, direct computation of factorials in them is time consuming and discouraging. Also, people have shown poor invariance for Cartesian ZM in the discrete case. Need of a faster computing algorithm with better rotational invariance is already felt in various research communities. To find a solution, we have examined a completely new approach which comprises a unique mapping of a gray-level image on a discrete circular disk to compute Cartesian as well as polar ZM through a new recursive relation. Such a map does not require any special sampling. The proposed new recursion is based on the computational structure of the radial polynomial embedded in the ZM. Fast computation of ZM, in our case, uses the developed new recursion and the properties of discrete circles, e.g., symmetry, uniqueness, and hole-free generation of discrete disk. This discrete circular map helps not only the fast computation of ZM but also lends its support to provide better rotational invariance for polar ZM over that of Cartesian ZM. The invariance is useful in recognition.

In vivo conformation and replication intermediates of circular mitochondrial plasmids in Neurospora and Cryphonectria parasitica

The in vivo conformation and replication intermediates of fungal circular mitochondrial plasmids and plasmid-like mitochondrial element (plMEs) were analyzed by two-dimensional gel electrophoresis and electron microscopy. Plasmids with circular restriction maps exist predominantly as circular molecules and were found to replicate by rolling circle mechanisms. However, the reverse transcriptase-encoding Mauriceville plasmid of Neurospora crassa was observed to replicate by two possible mechanisms: one that is consistent with a reverse transcriptase-mediated process and a second one might involve rolling circle DNA replication. Like the mtDNA-derived plasmid-like elements of N. crassa (Hausner et al. 2006a, b), a plasmid-like element of Cryphonectria parasitica (plME-C9), which consists predominantly of a 1.4 kb nucleotide sequence different from mitochondrial DNA, also was found to replicate by a rolling circle mechanism. Although the techniques used in this study were not suited for the establishment of the in vivo conformation and mode of replication of the mtDNAs of Neurospora or Cryphonectria, we surmise that the rolling circle mechanism might be the predominant mode of DNA replication in fungal mitochondria.

Circular polariscopic analysis of a ZnO wafer for highly sensitive and speedy evaluation of residual strains: Its relation with X‐ray diffraction pattern and topography

AbstractWe have explored the effectiveness of applying the circular polariscopic measurement to the mapping of the strains in a ZnO wafer. Initially, monochromatic X‐ray topography, which is regarded as a fundamental evaluation technique for wafers, is applied. The measured monochromatic X‐ray topograph shows that the image contrast is remarkably inhomogeneous; namely, the bark patterns exist in various regions. In order to clarify the origin of the above‐mentioned dark patterns, we apply the circular polariscopic measurement, which is sensitive to strains through the photoelastic effect. The brightness of the circular polariscopic wafer map reveals that the dark pattern in the monochromatic X‐ray topograph results from the strain. Thus, we conclude that the circular polariscopic analysis has the ability to compliment the information obtained by the monochromatic X‐ray topographic measurement. The presence of the relatively large strains is confirmed from the fact that the forbidden reflection lines are observed in the θ ‐2θ X‐ray diffraction pattern. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Circular Slits Map of Bounded Multiply Connected Regions

We present a boundary integral equation method for the numerical conformal mapping of bounded multiply connected region onto a circular slit region. The method is based on some uniquely solvable boundary integral equations with adjoint classical, adjoint generalized, and modified Neumann kernels. These boundary integral equations are constructed from a boundary relationship satisfied by a function analytic on a multiply connected region. Some numerical examples are presented to illustrate the efficiency of the presented method.

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

BackgroundThe complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need.ResultsWe have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities.ConclusionsCPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.

Enhancement of exciton photoluminescence intensity caused by the distortion of the crystal plane originating from the internal strain in a ZnO wafer

We have investigated the relation between the exciton photoluminescence intensity and distortion of the crystal plane in a ZnO wafer. The present investigation utilizes the following two characterization methods that complement the result of the photoluminescence measurement: a circular polariscopic measurement and a θ-2θ x-ray diffraction measurement. The circular polariscopic map clarifies the distribution of the strain exists in the ZnO wafer. The strain found in the circular polariscopic analysis indicates the existence of the crystal-plane distortion, which is confirmed from the appearance of the forbidden reflection line in the x-ray diffraction pattern. The photoluminescence measurements at different positions sensitive to the crystal-plane distortion were performed on the basis of the above-mentioned complementary information. It is found that the crystal-plane distortion causes the enhancement of the exciton photoluminescence intensity. The responsible factor is attributed to the suppression of the exciton diffusion caused by the crystal-plane distortion. This is in contrast to the usual interpretation that the lowering of the crystalline quality leads to the reduction of the exciton photoluminescence intensity; namely, the aid of complementary information is essential to precisely interpret the photoluminescence intensity.

AKARIOBSERVATION OF THE FLUCTUATION OF THE NEAR-INFRARED BACKGROUND

We report a search for fluctuations of the sky brightness toward the north ecliptic pole (NEP) with the Japanese infrared astronomical satellite AKARI,at 2.4, 3.2, and 4.1 \mum. We obtained circular maps with 100 diameter field of view which clearly show a spatial structure on scale of a few hundred arcsec. A power spectrum analysis shows that there is a significant excess fluctuation at angular scales larger than 10000 that can't be explained by zodiacal light, diffuse Galactic light, shot noise of faint galaxies or clustering of low redshift galaxies. These results are consistent with observations at 3.6 and 4.5 \mum by NASA's Spitzer Space Telescope. The fluctuating component observed at large angular scales has a blue stellar spectrum which is similar to that of the spectrum of the excess isotropic emission observed with IRTS. A significant spatial correlation between wavelength bands was found, and the slopes of the linear correlations is consistent with the spectrum of the excess fluctuation. These findings indicate that the detected fluctuation could be attributed to the first stars of the universe, i.e. pop. III stars. The observed fluctuation provides an important constraints on the era of the first stars.

Circular polariscopic measurement of a semi‐insulating SiC wafer for evaluating strains and its relation with Raman spectra: Superiority to monochromatic Lang X‐ray topography

AbstractWe have explored the effectiveness of applying the circular polariscopic measurement to the mapping of the strains in a semi‐insulating 6H‐SiC wafer. Initially, monochromatic Lang X‐ray topography, which is regarded as a fundamental evaluation technique for wafers, is applied. In the monochromatic Lang X‐ray topograph, the disappearance of the images is found in various areas, which suggests that the monochromatic Lang X‐ray topographic measurement is not almighty. Next, we apply the circular polariscopic measurement, which is sensitive to strains through the photoelastic effect. The brightness of the circular polariscopic wafer map reveals that the inhomogeneous distribution of the strains. The observed phenomenon indicates that the magnitude of the crystal‐plane distortion is too strong to apply monochromatic Lang X‐ray topography. The presence of the relatively large strains is confirmed from the fact that the forbidden reflection lines are observed in the θ ‐2θ X‐ray diffraction pattern. We also measure the Raman spectra of the several region of the wafer to evaluate the stress from the phonon frequency shift. The maximum stress is estimated to be ∼490 MPa. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

A freshwater cyanophage whose genome indicates close relationships to photosynthetic marine cyanomyophages.

Bacteriophage S-CRM01 has been isolated from a freshwater strain of Synechococcus and shown to be present in the upper Klamath River valley in northern California and Oregon. The genome of this lytic T4-like phage has a 178,563 bp circular genetic map with 297 predicted protein-coding genes and 33 tRNA genes that represent all 20-amino-acid specificities. Analyses based on gene sequence and gene content indicate a close phylogenetic relationship to the 'photosynthetic' marine cyanomyophages infecting Synechococcus and Prochlorococcus. Such relatedness suggests that freshwater and marine phages can draw on a common gene pool. The genome can be considered as being comprised of three regions. Region 1 is populated predominantly with structural genes, recognized as such by homology to other T4-like phages and by identification in a proteomic analysis of purified virions. Region 2 contains most of the genes with roles in replication, recombination, nucleotide metabolism and regulation of gene expression, as well as 5 of the 6 signature genes of the photosynthetic cyanomyophages (hli03, hsp20, mazG, phoH and psbA; cobS is present in Region 3). Much of Regions 1 and 2 are syntenic with marine cyanomyophage genomes, except that a segment encompassing Region 2 is inverted. Region 3 contains a high proportion (85%) of genes that are unique to S-CRM01, as well as most of the tRNA genes. Regions 1 and 2 contain many predicted late promoters, with a combination of CTAAATA and ATAAATA core sequences. Two predicted genes that are unusual in phage genomes are homologues of cellular spoT and nusG.

Circular polariscopic analysis of strains in a semi-insulating SiC wafer: Its high potential to complement the information obtained from monochromatic x-ray topography

We demonstrate that circular polariscopy is highly sensitive to strains in SiC wafers. In the monochromatic x-ray topographic analysis, which is regarded as a fundamental characterization method, the image information is disappeared in various areas: x-ray topography is not always suitable to evaluate wafer-size regions. Using circular polarizer plates, we apply the polariscopic analysis, which reveals the inhomogeneous strain distributed in the whole wafer region; namely, the circular polariscopic map has the high potential to complement the conventional monochromatic x-ray topograph. From the phonon-frequency shift observed in the Raman scattering spectra, the maximum stress is estimated to be ∼490 MPa. The crystal-plane distortion causing the strains is confirmed from the appearance of the forbidden reflections in the θ-2θ x-ray diffraction pattern.

Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins

Linear chromosomes and linear plasmids of Streptomyces possess covalently bound terminal proteins (TPs) at the 5′ ends of their telomeres. These TPs are proposed to act as primers for DNA synthesis that patches the single-stranded gaps at the 3′ ends during replication. Most (‘archetypal’) Streptomyces TPs (designated Tpg) are highly conserved in size and sequence. In addition, there are a number of atypical TPs with heterologous sequences and sizes, one of which is Tpc that caps SCP1 plasmid of Streptomyces coelicolor. Interactions between the TPs on the linear Streptomyces replicons have been suggested by electrophoretic behaviors of TP-capped DNA and circular genetic maps of Streptomyces chromosomes. Using chemical cross-linking, we demonstrated intramolecular and intermolecular interactions in vivo between Tpgs, between Tpcs and between Tpg and Tpc. Interactions between the chromosomal and plasmid telomeres were also detected in vivo. The intramolecular telomere interactions produced negative superhelicity in the linear DNA, which was relaxed by topoisomerase I. Such intramolecular association between the TPs poses a post-replicational complication in the formation of a pseudo-dimeric structure that requires resolution by exchanging TPs or DNA.

Strand Invasion Structures in the Inverted Repeat of Candida albicans Mitochondrial DNA Reveal a Role for Homologous Recombination in Replication

Molecular recombination and transcription are proposed mechanisms to initiate mitochondrial DNA (mtDNA) replication in yeast. We conducted a comprehensive analysis of mtDNA from the yeast Candida albicans. Two-dimensional agarose gel electrophoresis of mtDNA intermediates reveals no bubble structures diagnostic of specific replication origins, but rather supports recombination-driven replication initiation of mtDNA in yeast. Specific species of Y structures together with DNA copy number analyses of a C. albicans mutant strain provide evidence that a region in a mainly noncoding inverted repeat is predominantly involved in replication initiation via homologous recombination. Our further findings show that the C. albicans mtDNA forms a complex branched network that does not contain detectable amounts of circular molecules. We provide topological evidence for recombination-driven mtDNA replication initiation and introduce C. albicans as a suitable model organism to study wild-type mtDNA maintenance in yeast.

Full Positional Accuracy Analysis of Spatial Data by Means of Circular Statistics

AbstractThe positional error in spatial data is defined as a vector by comparing the coordinates between the true position and the measured position. The standard tests to assess the positional accuracy use only the magnitude of the vector and omit the azimuth. This article suggests that the use of both values allows a much more complete analysis of the positional error. A set of tests is proposed that are relevant for this purpose and demonstrate that some important features are not identified by the common procedures. The test samples come from two datasets. The first is obtained from the comparison of 100 homologous points in two conventional maps, and the second one comes from the geometric calibration of a photogrammetric scanner. The results are analyzed and discussed, showing that important issues such as error anisotropy are detected only by means of the circular statistics tests and density maps of distribution. Therefore, tests that assess the goodness of fit for uniform distribution in azimuths, such as Rayleigh and Rao tests, give low probabilities (P = 0 and P > 0.01). Moreover, density maps working with both magnitude and angle can locate the outlier candidate and offer more information about the spatial distribution of error.

Current trends in chloroplast genome research

Chloroplast is an important cellular organelle of autotrophs which has an independent, circular, doublestranded DNA molecule termed as chloroplast genome. The chloroplast DNA (cpDNA) contains essential genes for its maintenance and operation. Several components of the photosystems and proteins involved in biosynthetic pathways are also encoded by the chloroplast genome. Exploring the genetic repository of this organelle is vital due to its conserved nature, small size, persistent gene organization and promising ability for transgenic expression. Therefore, cpDNA sequence information has been instrumental in phylogenetic studies and molecular taxonomy of plants. Chloroplast genome sequencing efforts have being initiated with conventional cloning and chain-termination sequencing technologies. Dedicated databases such as CGDB and GOBASE among others have been established as more and more complete cpDNA sequences are being reported. Presently, elegant molecular biology techniques including shotgun sequencing, rolling circle amplification (RCA), Amplification, Sequencing and Annotation of Plasteome (ASAP) and Next generation sequencing are being used to accelerate data output. Owing to many fold increase in submission of cpDNA sequences in nucleotide databases, challenges of in-depth data analysis stimulated the emergence of devoted annotation, assembling and phylogenetic software. Recently, reported bioinformatics software for chloroplast genome studies comprise of DOGMA for annotation, SCAN-SE, ARAGON and PREP suit for RNA analyses and CG viewer for circular map construction/comparative analysis. Faster algorithms for gene-order based phylogenetic reconstruction and bootstrap analysis have attracted the attention of research community. Current trends in sequencing strategies and bioinformatics with reference to chloroplast genomes hold great potential to illuminate more hidden corners of this ancient cell organelle.

3D Genome Tuner: Compare Multiple Circular Genomes in a 3D Context

Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not offer feature-based comparison. For remedying these shortcomings, we developed 3D Genome Tuner, a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D space offers great benefits to the study of comparative genomics. The program is freely available (under an LGPL licence) at http://sourceforge.net/projects/dgenometuner.

The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus

* We have determined the complete mitochondrial genome sequence of an isolate of Glomus intraradices, a widespread and well-studied species of arbuscular mycorrhizal fungus. * The total genomic DNA of 24 spores from an in vitro root organ culture of the Swiss isolate G. intraradices 494 was amplified by multiple displacement and sequenced using the Roche 454 FLX platform. Contigs were joined by PCR and Sanger sequencing. * The circular genome map of 70 606 bp has a G + C content of 37.2%. All the standard fungal mitochondrial genes are present and encoded on the same strand. There are 26 introns and five complete LAGLIDADG homing endonuclease genes. There is no evidence of substantial sequence variation. * A well-supported phylogeny based on 14 mitochondrially encoded proteins indicates that the Glomeromycota are not the sister group of the Dikarya.

Visual Field Map Clusters in Macaque Extrastriate Visual Cortex

The macaque visual cortex contains >30 different functional visual areas, yet surprisingly little is known about the underlying organizational principles that structure its components into a complete "visual" unit. A recent model of visual cortical organization in humans suggests that visual field maps are organized as clusters. Clusters minimize axonal connections between individual field maps that represent common visual percepts, with different clusters thought to carry out different functions. Experimental support for this hypothesis, however, is lacking in macaques, leaving open the question of whether it is unique to humans or a more general model for primate vision. Here we show, using high-resolution blood oxygen level-dependent functional magnetic resonance imaging data in the awake monkey at 7 T, that the middle temporal area (area MT/V5) and its neighbors are organized as a cluster with a common foveal representation and a circular eccentricity map. This novel view on the functional topography of area MT/V5 and satellites indicates that field map clusters are evolutionarily preserved and may be a fundamental organizational principle of the Old World primate visual cortex.

Circular map for supercavitating flow in a multiply connected domain

A nonlinear free boundary-value problem of supercavitating flow past n + 1 hydrofoils is analyzed. To describe the cavities' closure mechanism, the Tulin-Terent'ev single-spiral-vortex model is employed. The flow domain is considered as the image of an (n + 1)-connected circular domain. The conformal map is constructed in terms of the solutions to two Riemann-Hilbert problems of the theory of symmetric automorphic functions. One of the problems is homogeneous and its coefficients are continuous functions while the second problem is inhomogeneous and has discontinuous coefficients. The exact solutions to the problems are found by using quasiautomorphic and quasimultiplicative analogs of the Cauchy kernel. The case of a single plate is considered in detail and the numerical results are reported.

Genome Projector: zoomable genome map with multiple views

BackgroundMolecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional nature of biological information, software interfaces for database browsing should provide an intuitive interface that allows for rapid migration across different views and scales. The Zoomable User Interface (ZUI) and tabbed browsing have proven successful for this purpose in other areas, especially to navigate the vast information in the World Wide Web.ResultsThis paper presents Genome Projector, a Web-based gateway for genomics information with a zoomable user interface using Google Maps API, equipped with four seamlessly accessible and searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. The Web application for 320 bacterial genomes is available at . All data and software including the source code, documentations, and development API are freely available under the GNU General Public License. Zoomable maps can be easily created from any image file using the development API, and an online data mapping service for Genome Projector is also available at our Web site.ConclusionGenome Projector is an intuitive Web application for browsing genomics information, implemented with a zoomable user interface and tabbed browsing utilising Google Maps API and Asynchronous JavaScript and XML (AJAX) technology.

WeGAS: A Web-Based Microbial Genome Annotation System

We have developed WeGAS, a Web based microbial Genome Annotation System, which provides features that include gene prediction, homology search, promoter/motif analysis, genome browsing, gene ontology analysis based on the COGs and GO, and metabolic pathway analysis with web-based interfaces. Most raw data and intermediate data from genome projects can be managed with the WeGAS database system, and analysis results, including information on each gene and final genome maps, are provided by its visualization modules. Especially, a pie-view browser displaying circular maps of contigs and a COG-GO combination browser are very helpful for an overview of projects. Major public microbial genome databases can be imported, searched, and browsed through the WeGAS modules. WeGAS is freely accessible via web site http://ns.smallsoft.co.kr:8051.