Circular Sequence Research Articles

Complete Genome Sequence of Methanothermobacter marburgensis , a Methanoarchaeon Model Organism

The circular genome sequence of the chemolithoautotrophic euryarchaeon Methanothermobacter marburgensis, with 1,639,135 bp, was determined and compared with that of Methanothermobacter thermautotrophicus. The genomes of the two model methanogens differ substantially in protein coding sequences, in insertion sequence (IS)-like elements, and in clustered regularly interspaced short palindromic repeats (CRISPR) loci.

Effective one body description of tidal effects in inspiralling compact binaries

The late part of the gravitational wave signal of binary neutron star inspirals can in principle yield crucial information on the nuclear equation of state via its dependence on relativistic tidal parameters. In the hope of analytically describing the gravitational wave phasing during the late inspiral (essentially up to contact) we propose an extension of the effective one body (EOB) formalism which includes tidal effects. We compare the prediction of this tidal-EOB formalism to recently computed nonconformally flat quasi-equilibrium circular sequences of binary neutron star systems. Our analysis suggests the importance of higher-order (post-Newtonian) corrections to tidal effects, even beyond the first post-Newtonian order, and their tendency to {\it significantly} increase the ``effective tidal polarizability'' of neutron stars. We compare the EOB predictions to some recently advocated, nonresummed, post-Newtonian based (``Taylor-T4'') description of the phasing of inspiralling systems. This comparison shows the strong sensitivity of the late-inspiral phasing to the choice of the analytical model, but raises the hope that a sufficiently accurate numerical--relativity--``calibrated'' EOB model might give us a reliable handle on the nuclear equation of state

On the conditional and unconditional distributions of the number of success runs on a circle with applications

In this paper, we study the distributions of the number of success runs of length k and the number of success runs of length k given the number of successes in a sequence of independent and identically distributed (i.i.d.) binary trials arranged on a circle (circular sequence) based on three different enumeration schemes. The double generating functions, the probability functions and a formula for the evaluation of the higher order moments are given. Furthermore, we show that the results established in the case of an i.i.d. circular sequence can be extended to study the distribution of the number of success runs in a circular sequence of binary exchangeable trials. We offer tools for addressing the run-related problems arising from the circular exchangeable sequence. Some applications to practical problems such as reliability theory and Pólya urn models are given in order to show our theoretical results, which illustrate the potential use of run statistics. Finally, we address the parametric estimation in the distributions of the number of success runs.

Magnetic beads based rolling circle amplification–electrochemiluminescence assay for highly sensitive detection of point mutation

The identification of point mutations is particularly essential in the fields of medical diagnosis and prognosis of many pathogenic and genetic diseases. In this study, an rolling circle amplification (RCA) based electrochemiluminescence (ECL) assay for highly sensitive point mutation detection was developed. In the assay, an allele-discriminating padlock probe was designed for targeting the sequence in the p53 oncogene locus. A circular template generated by enzymatic ligation upon the recognition of a point mutation (CGT to CAT) on the oncogene could be amplified isothermally by Phi29 DNA polymerase. The elongated products, containing hundreds of copies of the circular DNA template sequence, were hybridized with Ru(bpy)32+ (TBR)-tagged probes and then captured onto streptavidin-coated paramagnetic beads. The resulting products were analyzed by magnetic bead based ECL platform. As low as 2amol of mutated strands was detected by this assay, which could be attributed to the high amplification efficiency of Phi29 DNA polymerase and current magnetic bead based ECL detection platform. In addition, the positive mutation detection was achieved with a wild-type to mutant ratio of 10000:1, due to the high fidelity of DNA ligase in differentiating mismatched bases at the ligation site. It is demonstrated that this proposed method provides a highly sensitive and specific approach for point mutation detection.

CSA: An efficient algorithm to improve circular DNA multiple alignment

BackgroundThe comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools.ResultsIn this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes.To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView.ConclusionThe results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment algorithms when used in the alignment of circular DNA sequences. The resulting alignments lead to more realistic phylogenetic comparisons between species.

Microsphere-based rolling circle amplification microarray for the detection of DNA and proteins in a single assay.

We describe a high-density microarray for simultaneous detection of proteins and DNA in a single test. In this system, Rolling Circle Amplification (RCA) was used as a signal amplification method for both protein and nucleic acid detection. The microsphere sensors were tested with synthetic DNA and purified recombinant protein analytes. The target DNA sequence was designed from a highly conserved gene that encodes the outer membrane protein P6 (OMP-P6) of both typeable and nontypeable strains of Haemophilus influenzae. The proinflammatory mediators IL-6 and IL-8 were selected as target proteins. Capture antibodies were first immobilized on fluorescently encoded microspheres. The microspheres were then loaded into the etched microwells of an imaging optical fiber bundle. A sandwich assay was performed for target proteins IL-6 and IL-8 using biotin-labeled secondary antibodies. Biotinylated capture DNA probes were then attached to the detection antibodies via an avidin bridge. A padlock probe, complementary to the target sequence, was subsequently hybridized to the capture probe. In the presence of the target sequence, the padlock probe was ligated, and this circular sequence was used for RCA. Following RCA, multiple fluorescently labeled signal probes were hybridized to each amplified sequence, and the microarray was imaged using an epi-fluorescence microscope. With this assay, detection limits down to 10 fM and 1 pM were achieved for proteins and target DNA, respectively. In addition to this new approach for detecting both protein and DNA in a single test using RCA, the limit of detection for IL-8 and IL-6 was improved by 3 orders of magnitude compared to similar microsphere-based assays.

SigWinR; the SigWin-detector updated and ported to R

BackgroundOur SigWin-detector discovers significantly enriched windows of (genomic) elements in any sequence of values (genes or other genomic elements in a DNA sequence) in a fast and reproducible way. However, since it is grid based, only (life) scientists with access to the grid can use this tool. Therefore and on request, we have developed the SigWinR package which makes the SigWin-detector available to a much wider audience. At the same time, we have introduced several improvements to its algorithm as well as its functionality, based on the feedback of SigWin-detector end users.FindingsTo allow usage of the SigWin-detector on a desktop computer, we have rewritten it as a package for R: SigWinR. R is a free and widely used multi platform software environment for statistical computing and graphics. The package can be installed and used on all platforms for which R is available. The improvements involve: a visualization of the input-sequence values supporting the interpretation of Ridgeograms; a visualization allowing for an easy interpretation of enriched or depleted regions in the sequence using windows of pre-defined size; an option that allows the analysis of circular sequences, which results in rectangular Ridgeograms; an application to identify regions of co-altered gene expression (ROCAGEs) with a real-life biological use-case; adaptation of the algorithm to allow analysis of non-regularly sampled data using a constant window size in physical space without resampling the data. To achieve this, support for analysis of windows with an even number of elements was added.ConclusionBy porting the SigWin-detector as an R package, SigWinR, improving its algorithm and functionality combined with adequate performance, we have made SigWin-detector more useful as well as more easily accessible to scientists without a grid infrastructure.

1D Camera Geometry and Its Application to the Self-Calibration of Circular Motion Sequences

This paper proposes a novel method for robustly recovering the camera geometry of an uncalibrated image sequence taken under circular motion. Under circular motion, all the camera centers lie on a circle and the mapping from the plane containing this circle to the horizon line observed in the image can be modelled as a 1D projection. A 2 x 2 homography is introduced in this paper to relate the projections of the camera centers in two 1D views. It is shown that the two imaged circular points of the motion plane and the rotation angle between the two views can be derived directly from such a homography. This way of recovering the imaged circular points and rotation angles is intrinsically a multiple view approach, as all the sequence geometry embedded in the epipoles is exploited in the estimation of the homography for each view pair. This results in a more robust method compared to those computing the rotation angles using adjacent views only. The proposed method has been applied to self-calibrate turntable sequences using either point features or silhouettes, and highly accurate results have been achieved.

Biocorrosion of stainless steel grade 304L (SS304L) in sugar cane juice

The main objective of this research study is to assess the behaviour of stainless steel AISI 304L in contact with sugar cane juice. Stainless steel grade 304L is largely used in the sugar cane industry but the acidic nature of sugar cane juice pose a serious challenge in maintaining the life span of vital components. Sugar cane juice is acid having a pH value of around 5.6 at extraction. This acidic property is accounted for by the presence of a variety of acids namely: aconitic, citric, malic, oxalic, glycolic, mesaonic, tartic, succinic, fumaric and syringic in sugar cane juice. In addition to these acids there are approximately 50 different kinds of microorganisms present in the green cane and which are very active. These microorganisms will act as a contributor to a rather quick drop in pH (pH∼3.1) of the sugar cane juice once extracted. The more so, several minerals like water, salt, sulphate and silica are also present throughout the process line and are other contributor in the surface degradation wear mechanism. Faced with all these adverse elements, it is therefore fundamental to investigate thoroughly in the wear corrosion mechanism and biocorrosion on stainless steel grade 304L. To evaluate the mass loss, several corrosion experimentations were carried with the help of a potentiostat both in a sterilized juice and none sterilized juice. From these experimentations, it has been noted that corrosion was present on the surface of the disc (SS304L) in contact with none sterilized juice in the form of pitting while no corrosion wear was observed in the case of sterilized juice. The presence of biofilm was also observed on the sample disc surface. Biofilm formed on the surface of the sample disc was transferred to a potato dextrose agar (PDA) plate by stamping the disc in a circular sequence on the plate in sterilized condition in view to measure the density and resistance of the film. It was noted through this stamping protocol that the biofilm was very resistant due to the fact that after 12 stamping time we still observe the trace of the biofilm on the PDA plate. Microorganisms present in the biofilm have growth on the PDA plate and isolation of each colony was carried out in view of their identification.

Absolute-Type Shaft Encoding Using LFSR Sequences With a Prescribed Length

Maximal-length binary sequences have existed for a long time. They have many interesting properties, and one of them is that, when taken in blocks of n consecutive positions, they form 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> - 1 different codes in a closed circular sequence. This property can be used to measure absolute angular positions as the circle can be divided into as many parts as different codes can be retrieved. This paper describes how a closed binary sequence with an arbitrary length can be effectively designed with the minimal possible block length using linear feedback shift registers. Such sequences can be used to measure a specified exact number of angular positions using the minimal possible number of sensors that linear methods allow.

A democratic story: collaboration in the use of public budget

PurposeThe purpose of this paper is to illustrate how the notion of “storying collaboration” can benefit democratic participation, collaboration among different social actors, and local development.Design/methodology/approachThe methodology relies initially on a hermeneutical epistemological view which also incorporates Aristotelian analysis of speech as a deconstructive tool. Initial findings suggest a further shift in approach towards the assumptions made by critical theory. The basic methodological tool is in‐depth interviews. The level of analysis is the individual who participates in collaborative processes.FindingsThe paper shows how collaboration is unlikely to be successful in situations where certain key conditions are absent. Ultimately, what may be seen as a conversion process reveals a circular sequence of ideals, acts and outcomes in which stories about the future become realities and realities become new stories.Practical implicationsThe findings suggest that the creation of appropriate environments is required in order for individuals to become aware of their wishes and demands and make conscious choices. If the actors involved are aware of the rhetorical components of speech, then they can utilise them to persuade others. The storyteller must take into consideration which kind of assumptions, intentions and orientations respect individual and social notions of legitimacy and, thus, are likely to succeed.Originality/valueThe originality of the paper lies in the use of a bricolage of methodologies in order to shed light on the role of stories in the collaborative process.

Stratified Self-Calibration and Metric Reconstruction for Zooming/Refocusing Circular Motion Sequences

Self-calibration for imaging sensors is essential to many computer vision applications. In this paper, a new stratified self-calibration and metric reconstruction method is proposed for zooming/refocusing cameras under circular motion. With the assumption of known rotation angles, the circular motion constraints are first formulated. By enforcing the constraints gradually, metric reconstruction is retrieved up to a two-parameter ambiguity. The closed form expression of the absolute conic w.r.t. the two parameters is deduced. The ambiguity is then resolved with the square pixel assumption of the camera. The advantages of this method are mainly as follows: It gives precise results by defining and enforcing the circular motion constraints; It is flexible that it allows both the focal lengths and the principal point to vary; It requires no scene constraint. Experimental results with both synthetic data and real images are presented, demonstrating the accuracy and robustness of the new method.

OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes

Mitochondria and plastids are DNA-containing cell organelles whose genomes occur at high copy numbers per cell. Organellar genomes vary greatly in size ranging from approximately 15 kb for some animal mitochondrial genomes to more than 2 Mb for some plant mitochondrial genomes. The vast majority of organellar genomes map as circular molecules that are difficult to illustrate by available commercial or free software tools. Thus, published genome maps are extremely heterogeneous in design, often tediously drawn semi-manually and lack any consensus in display. Here, we present a new web-based tool, OrganellarGenomeDRAW (OGDRAW), which produces high-resolution custom graphical maps of DNA sequences as stored in standard GenBank format entries. GenBank data can be provided as either file uploads or accession numbers. The program is specially optimized for the display of chloroplast and mitochondrial genomes but can also be used to depict other circular DNA sequences. The design of the program core as a Perl module with an object-oriented interface allows easy integration into custom scripts.

The expected convex hull trimmed regions of a sample

Given a data set in the multivariate Euclidean space, we study regions of central points built by averaging all their subsets with a fixed number of elements. The averaging of these sets is performed by appropriately scaling the Minkowski or elementwise summation of their convex hulls. The volume of such central regions is proposed as a multivariate scatter estimate and a circular sequence algorithm to compute the central regions of a bivariate data set is described.

A Circumplex Model of Interpersonal Attributes in Middle Childhood

This article presents evidence for the validity of the circumplex model to represent how parents and teachers organize interpersonal attributes in children. Study 1 showed that the ratings of adults using interpersonal adjectives to describe 4- to 10-year-old children conformed to a circumplex structure. Eight scales-labeled Interpersonal Adjective Scales for Children (IAS-C)-were developed to represent the circular sequence of children's interpersonal attributes, as ordered around the reference axes of Extraversion and Social Appropriateness. The continuum of interpersonal variables substantially corresponded to Schaefer's model for social and emotional behavior, as follows: Warm-Agreeable, Sociable-Cheerful, Exuberant-Dominant, Impulsive-Aggressive, Egocentric-Irritable, Fearful-Insecure, Shy-Silent, and Mild-Placid. Study 2 demonstrated cross-validity for the IAS-C and how they are related to Big Five measures. Study 3 used data from Studies 1 and 2 in a confirmatory approach to test the circumplex IAS-C structure. Findings are discussed in relation to the adult circumplex model and suggest that the child circumplex has distinctive features that must be kept in due consideration when attempting to assess interpersonal qualities in children validly.

Three themes in one, which wondrous scope affords : Ambiguous Speaker and Storytelling in Shakespeare's Sonnets

Three themes in one, which wondrous scope affords:Ambiguous Speaker and Storytelling in Shakespeare's Sonnets Danijela Kambasković-Sawers The nature of a sonnet sequence as a poetic art form is essentially twofold: it contains self-sufficient, prosodically complex poems, each seeking to develop an idea to its conclusion; but it also typically functions as a sequence, an integrated work in which poems have been ordered, and characters fashioned, to make sense when the work is read from beginning to end. It seems hardly necessary to point this out; yet, while the sonnets of the Petrarchan discourse receive what appears to be continuous critical attention, acknowledgment of their "sequentiality" is rare and at best tacit. There is a need to turn critical attention to mechanisms that sonneteers employ to foster a perception of cohesion, as well as to acknowledge that such preoccupations betray the presence of novelistic thinking. The sonnet sequence genre constructs a double sense of immediacy: drawing on the lyricism of its constituent sonnets, it also often generates a perception of a personal narrative when the sequence is read from beginning to end. Sonneteers use many speaker figures or voices in the sonnets that constitute a sequence; one of the more striking examples is certainly Petrarch's giving of the first-person-plural voice to "little animals" in his sonnet 8.1 Yet varied uses of voice in individual sonnets detract little, if at all, from the impression created in the mind of the reader that they are reading a love story told in the first person. The disjointed nature of the sonnet sequence "voice" is an important part of its effect. Thus, talking about the birth of the sonnet sequence vogue, Jacques Barzun writes: "[Petrarch] fashioned into a shapely quasi narrative work, a kind of allusive autobiography . . . Sonnet sequences like Petrarch's or Shakespeare's make possible a narrative-by-episode; the poet need not versify any connective matter as he must in an epic. Rather, he anticipates by five or six hundred years the technique of film [End Page 285] and television";2 and Roland Greene considers the history of Petrarchism from the fourteenth to the twentieth century representative of the staged development of the sequence's "fictional" mode.3 As such, it is a rare literary genre to offer first-person fictions to the medieval and early modern reader, and for a long time the only one to deal with erotic subject matter in the first person.4 The link between medieval first-person genres and Dante and Petrarch, originators of the genre, is clear: St. Augustine's Soliloquia and Confessions, and Boethius's Consolatio Philosophiae are considered to be standard sources for Dante's work as well as Petrarch's Secretum.5 The public letter, another one of Petrarch's favorite genres, also relies on the first-person voice and self-fictionalization, a unique, creative process of authored selfhood based on literary and cultural subtext, as well as the essentially documentary processes such as self-betrayal, self-representation, self-fashioning, and auto-ethnography.6 Petrarch's decision to remove the first-person prose surrounding the poems in Dante's La Vita Nuova, the resulting complexity of his Il Canzoniere, and the subsequent popularity of the Petrarchan (proseless) sonnet sequence model may all have had implications for the development of first-person narration. The context within which individual sonnets in a sequence are considered is a question of importance where sequences initially circulated in manuscript form (yet carefully numbered by their authors), such as Petrarch's Il Canzoniere and Sir Philip Sidney's Astrophil and Stella, are concerned. It is equally important for linear and circular sequences; seemingly disjointed or frequently revised sequences, such as Michael Drayton's Idea; as well as those sequences, such as Shakespeare's Sonnets, that have the best of both worlds: printed to be read in a linear manner yet, as James Schiffer has suggested, potentially brilliantly constructed to make the collection seem as if it originally had an exclusive primary audience.7 Whether read more or less linearly, the voices of the sonnet sequence speakers are constructed by their authors, and it is methods used to construct them in...

Small Anellovirus Infections in Korean Children

To the Editor: Recently, Jones et al. (1) identified circular DNA sequences, classified as Anellovirus genus, in plasma from patients with acute viral infection syndromes. These anelloviruses were then labeled as “small anellovirus (SAV)” because of their smaller genomes when compared with Torque Teno Virus (TTV) and Torque Teno Mini Virus (TTMV), which have small, circular, single-stranded DNA genomes. Although anelloviruses are not associated with any specific disease, TTV has been suggested to play a role in acute respiratory disease (ARD) and in asthma of children (2,3). Kawasaki disease and Henoch-Schonlein purpura are important vasculitis disorders in children, possibly triggered by unknown infectious agents. Recently, Gergely et al. (4) reported that molecular mimicry involving TTV and the generation of autoantibodies may have a role in the pathogenesis of systemic lupus erythematosus. The purpose of our study was to investigate the prevalence of SAV and its association with various clinical diseases in children. The study population comprised 81 serum samples from healthy children and 151 serum samples from children hospitalized with hepatitis (81 cases), ARD (40 cases), Kawasaki disease (12 cases), or Henoch-Schonlein purpura (18 cases) during the period January 2002–June 2006. Nasopharyngeal aspirates paired with serum samples were collected from 34 children with ARD, including upper respiratory tract infections, pneumonia, and acute bronchiolitis. Samples were collected after informed consent was obtained at admission from patients’ parents. PCRs for SAV were performed to amplify a 5′ noncoding region of SAV with specific primers, as described previously (5). PCR products were directly sequenced, and nucleotide sequences were registered in GenBank (accession nos. {type:entrez-nucleotide,attrs:{text:DQ978791,term_id:119656310,term_text:DQ978791}}DQ978791–DQ9788810). The χ2 test with Yates correction and Mann-Whitney U-test were used for statistical comparison by using MedCalc (MedCalc Software, Mariakerke, Belgium). A p value <0.05 was defined as statistically significant. In our study population, serum SAV DNA was detected in 28 (34.5%) of 81 children in the control group and in 66 (43.7%) of 151 children in the disease group. In the healthy control group, the SAV-positive rate was 7.4% (6/81) in children <12 months of age, 16.0% (13/81) in children 1–4 years of age, and 11.1% (9/81) in children 5–15 years of age. In the disease group, the SAV-positive rate was 35.8% (29/81) in patients with hepatitis, 67.5% (27/40) in ARD, 50% (6/12) in Kawasaki disease, and 22.2% (4/18) in Henoch-Schonlein purpura, respectively (Table). Among 34 nasopharyngeal aspirates collected from children with ARD, SAV DNA was detected in 19 (55.9%). Codetection of SAV and respiratory syncytial virus in nasopharyngeal aspirates was observed in 4 patients. Table Prevalence of SAV viremia in the study population, Republic of Korea, January 2002–June 2006* Percent similarity of nucleotide sequence of PCR products was 99% among SAV isolates. To our knowledge, this is the first report of SAV infections in children. The prevalence and role of SAV in clinical diseases have yet to be determined. Recently, Biagini et al. (5) reported that the prevalence of SAV infection was 20% (12/60) in French blood donors. In an Italian study (6), the positive rate of SAV DNA was 9.1% (5/55) in patients with hepatitis C compared with 8.6% (3/35) in healthy controls. Thus, the prevalence of SAV in Korean children is much higher than rates reported in adults from other countries (5,6). Further studies are needed to confirm this finding. In our study, the prevalence of SAV did not differ significantly between the hepatitis group and the healthy control group. Our results indicate that SAV presence does not appear to have a defining role in hepatitis, as do TTV or TTMV infection (7). In a previous study, several groups of viruses including TTV were ruled out as etiologic agents of Kawasaki disease (8), findings similar to those of our study. We found that the prevalence of SAV was significantly higher in ARD and that SAV-positive serum results were consistent with those of nasopharyngeal aspirates in 76% (26/34). These findings suggest that the respiratory tract may be a transmission route of SAV in children. In conclusion, we confirmed the presence of SAV in serum samples and nasopharyngeal aspirates from Korean children. A significantly higher detection of SAV DNA was observed in children with ARD compared with healthy children or children with other clinical diseases.

Silhouette Coherence for Camera Calibration under Circular Motion

We present a new approach to camera calibration as a part of a complete and practical system to recover digital copies of sculpture from uncalibrated image sequences taken under turntable motion. In this paper, we introduce the concept of the silhouette coherence of a set of silhouettes generated by a 3D object. We show how the maximization of the silhouette coherence can be exploited to recover the camera poses and focal length. Silhouette coherence can be considered as a generalization of the well-known epipolar tangency constraint for calculating motion from silhouettes or outlines alone. Further, silhouette coherence exploits all the geometric information encoded in the silhouette (not just at epipolar tangency points) and can be used in many practical situations where point correspondences or outer epipolar tangents are unavailable. We present an algorithm for exploiting silhouette coherence to efficiently and reliably estimate camera motion. We use this algorithm to reconstruct very high quality 3D models from uncalibrated circular motion sequences, even when epipolar tangency points are not available or the silhouettes are truncated. The algorithm has been integrated into a practical system and has been tested on more than 50 uncalibrated sequences to produce high quality photo-realistic models. Three illustrative examples are included in this paper. The algorithm is also evaluated quantitatively by comparing it to a state-of-the-art system that exploits only epipolar tangents.

Control of IS911 target selection: how OrfA may ensure IS dispersion

IS911 transposition involves a closed circular insertion sequence intermediate (IS-circle) and two IS-encoded proteins: the transposase OrfAB and OrfA which regulates IS911 insertion. OrfAB alone promotes insertion preferentially next to DNA sequences resembling IS911 ends while the addition of OrfA strongly stimulates insertion principally into DNA targets devoid of the IS911 end sequences. OrfAB shares its N-terminal region with OrfA. This includes a helix-turn-helix (HTH) motif and the first three of four heptads of a leucine zipper (LZ). OrfAB binds specifically to IS911 ends via its HTH whereas OrfA does not. We show here: that OrfA binds DNA non-specifically and that this requires the HTH; that OrfA LZ is required for its multimerization; and that both motifs are essential for OrfA activity. We propose that these OrfA properties are required to assemble a nucleoprotein complex committed to random IS911 insertion. This control of IS911 insertion activity by OrfA in this way would assure its dispersion.

Definitions of state variables and state space for brain-computer interface

Neocortical state variables are defined and evaluated at three levels: microscopic using multiple spike activity (MSA), mesoscopic using local field potentials (LFP) and electrocorticograms (ECoG), and macroscopic using electroencephalograms (EEG) and brain imaging. Transactions between levels occur in all areas of cortex, upwardly by integration (abstraction, generalization) and downwardly by differentiation (speciation). The levels are joined by circular causality: microscopic activity upwardly creates mesoscopic order parameters, which downwardly constrain the microscopic activity that creates them. Integration dominates in sensory cortices. Microscopic activity evoked by receptor input in sensation induces emergence of mesoscopic activity in perception, followed by integration of perceptual activity into macroscopic activity in concept formation. The reverse process dominates in motor cortices, where the macroscopic activity embodying the concepts supports predictions of future states as goals. These macroscopic states are conceived to order mesoscopic activity in patterns that constitute plans for actions to achieve the goals. These planning patterns are conceived to provide frames in which the microscopic activity evolves in trajectories that adapted to the immediate environmental conditions detected by new stimuli. This circular sequence forms the action-perception cycle. Its upward limb is understood through correlation of sensory cortical activity with behavior. Now brain-machine interfaces (BMI) offer a means to understand the downward sequence through correlation of behavior with motor cortical activity, beginning with macroscopic goal states and concluding with recording of microscopic MSA trajectories that operate neuroprostheses. Part 1 develops a hypothesis that describes qualitatively the neurodynamics that supports the action-perception cycle and derivative reflex arc. Part 2 describes episodic, "cinematographic" spatial pattern formation and predicts some properties of the macroscopic and mesoscopic frames by which the embedded trajectories of the microscopic activity of cortical sensorimotor neurons might be organized and controlled.