Lossless filter for multiple repeats with bounded edit distance

Background: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Finding such fragments while allowing for a certain number of insertions, deletions, and substitutions, is however known to be a computationally expensive task, and consequently exact methods can usually not be applied in practice. Results: The filter TUIUIU that we introduce in this paper provides a possible solution to this problem. It can be used as a preprocessing step to any multiple alignment or repeats inference method, eliminating a possibly large fraction of the input that is guaranteed not to contain any approximate repeat. It consists in the verification of several strong necessary conditions that can be checked in a fast way. We implemented three versions of the filter. The first is simply a straightforward extension to the case of multiple sequences of an application of conditions already existing in the literature. The second uses a stronger condition which, as our results show, enable to filter sensibly more with negligible (if any) additional time. The third version uses an additional condition and pushes the sensibility of the filter even further with a non negligible additional time in many circumstances; our experiments show that it is particularly useful with large error rates. The latter version was applied as a preprocessing of a multiple alignment tool, obtaining an overall time (filter plus alignment) on average 63 and at best 530 times smaller than before (direct alignment), with in most cases a better quality alignment. Conclusion: To the best of our knowledge, TUIUIU is the first filter designed for multiple repeats and for dealing with error rates greater than 10% of the repeats length.

Diffraction gratings fabricated in DLC thin films

This work presents the fabrication of two-dimensional diffraction gratings in diamond-like carbon (DLC) thin films, with applications in computer-generated holography and micro optics. In order to achieve high diffraction efficiency and to have a very simple manufacturing process, the device is designed to modulate only the phase of an incoming coherent monochromatic laser beam (632.8 nm, HeNe laser). This modulation is obtained by implementing a binary microrelief in the DLC film, responsible for generating a localized optical path difference of half a wavelength. This microrelief is obtained by anisotropic reactive ion etching of the DLC surface in an oxygen based plasma. The DLC layer was grown by reactive magnetron sputtering, using a methane-based plasma chemistry. AFM measurements show a low-level surface roughness of less than 1% of the operation wavelength, and optical characterization shows a good quality of the reconstructed diffraction patterns. (C) 2010 Elsevier B.V. All rights reserved.

Ultrasound-assisted synthesis of symmetrical biaryls by palladium-catalyzed detelluration of 1,2-diaryiditellanes

An ultrasound-assisted synthesis of functionalized symmetrical biaryls with electron-withdrawing or electron-donating substituents is described and illustrated by the palladium-catalyzed detelluration of 1,2-diarylditellanes. This procedure offers easy access to symmetrical biaryls in short reaction time and the products are achieved in good to excellent yields. (c) 2009 Published by Elsevier Ltd.

Ultrasound-Assisted Synthesis of Symmetrical Biaryls by Palladium-Catalyzed Homocoupling of Aryl n-Butyl Tellurides

An ultrasound-assisted synthesis of symmetrical biaryls with electron-withdrawing or -donating substituents is described and illustrated by palladium-catalyzed homocoupling reaction of aryl tellurides. This procedure offers easy access to biaryls in short reaction time, and the products are achieved in good to excellent yields.

Copper salt-catalyzed homo-coupling reaction of potassium alkynyltrifluoroborates: a simple and efficient synthesis of symmetrical 1,3-diynes

The copper-catalyzed dimerization of alkynyltrifluoroborates proceeds readily with good yields. The homo-coupling reaction can be effected in DMSO, in the open air, using Cu(OAc)(2) as catalyst in the absence of any other additives. A variety of functional groups are tolerated. (C) 2008 Elsevier Ltd. All rights reserved.

Synthesis of symmetrical 1,3-diynes via homocoupling reaction of n-butyl alkynyltellurides

An ultrasound-assisted synthesis of symmetrical 1,3-diyne compounds with electron-withdrawing or donating substituents is described and illustrated by the palladium-catalyzed homocoupling reaction of n-butyl alkynyltellurides. This procedure offers easy access to 1,3-diynes in very short reaction times, and the products are achieved in good to excellent yields. (C) 2009 Elsevier Ltd. All rights reserved.

Synthesis of (Z)-1-Organylthiobut-1-en-3-ynes: Hydrothiolation of Symmetrical and Unsymmetrical Buta-1,3-diynes

Hydrothiolation of 1-organylbuta-1,3-diynes and 1,4-diorganylbuta-1,3-diynes with the sodium organylthiolate anions, which were generated in situ by reacting diphenyl and dibutyl disulfide with NaBH(4) in ethanol, results in the regio-, stereo-, and chemoselective formation of (Z)-1-organylthio-4-organylbut-1-en-3-ynes and (Z)-1-organylthio-1,4-diorganylbut-1-en-3-ynes, respectively.

Aging and stationary properties of non-equilibrium symmetrical three-state models

We consider a non-equilibrium three-state model whose dynamics is Markovian and displays the same symmetry as the three-state Potts model, i.e. the transition rates are invariant under the cyclic permutation of the states. Unlike the Potts model, detailed balance is, in general, not satisfied. The aging and the stationary properties of the model defined on a square lattice are obtained by means of large-scale Monte Carlo simulations. We show that the phase diagram presents a critical line, belonging to the three-state Potts universality class, that ends at a point whose universality class is that of the Voter model. Aging is considered on the critical line, at the Voter point and in the ferromagnetic phase.

Laser microstructuring of azopolymers via surface relief gratings: controlling hydrophobicity

In this paper the large-scale mass transport mechanism is used to microstructure azopolymeric films, aiming at controllable hydrophobic surfaces. Using an Ar(+) laser with intensity of 70 mW/cm(2), we produced egg-crate-like surfaces with periods from 1.0 to 3.5 mu m that present distinct wetting properties. The static contact angle of water was measured on the microstructured surfaces, and the results revealed an increase of approximately 9 degrees for a surface pattern period of 2 mu m. Our results indicate the use of the microstructuring method described here for the fabrication of devices with controllable hydrophobicity.

Palladium-catalyzed oxidative homocoupling of potassium alkenyltrifluoroborates: synthesis of symmetrical 1,3-dienes

Herein, we describe a convenient method for the synthesis of symmetrical 1,3-dienes employing an oxidative palladium-catalyzed homocoupling of potassium alkenyltrifluoroborates providing products in good yields relative to existing methodologies. This is the first report of a cross-dimerization of potassium alkenyltrifluoroborates. (C) 2009 Elsevier Ltd. All rights reserved.

Construção de um espectrógrafo de projeção e sua utilização em demonstrações de espectroscopia óptica

This article describes a projection spectrograph for use in optical spectroscopy classrooms demonstrations. The apparatus is based on an overhead projector and permits the visualization of several phenomena such as, light dispersion by diffraction gratings, diffraction order, optical fluorescence, continuous and discrete optical emission spectra, and light absorption by liquids and solids. A historical survey about the optical spectroscopy development is also presented.

Psychophysical measurements of luminance and chromatic spatial and temporal contrast sensitivity in Duchenne muscular dystrophy

In children with Duchenne muscular dystrophy, color vision losses have been related to dystrophin deletions downstream of exon 30, which affect a dystrophin isoform, Dp260, present in the retina. To further evaluate visual function in DMD children, we measured spatial, temporal, and chromatic red-green and blue-yellow contrast sensitivity in two groups of DMD children with gene deletion downstream and upstream of exon 30. Psychophysical spatial contrast sensitivity was measured for low, middle, and high spatial frequencies with achromatic gratings and for low and middle frequencies with red-green and blue-yellow chromatic gratings. Temporal contrast sensitivity was also measured with achromatic stimuli. A reduction in sensitivity at all spatial luminance contrasts was found for the DMD patients with deletion downstream of exon 30. Similar results were found for temporal luminance contrast sensitivity. Red-green chromatic contrast sensitivity was reduced in DMD children with deletion downstream of exon 30, whereas blue-yellow chromatic contrast sensitivity showed no significant differences. We conclude that visual function is impaired in DMD children. Furthermore, we report a genotype-phenotype relationship because the visual impairment occurred in children with deletion downstream but not upstream of exon 30, affecting the retinal isoform of dystrophin Dp260.

Visual contrast sensitivity in tonic-clonic epileptic patients

We measured the effects of epilepsy on visual contrast sensitivity to linear and vertical sine-wave gratings. Sixteen female adults, aged 21 to 50 years, comprised the sample in this study, including eight adults with generalized tonic-clonic seizure-type epilepsy and eight age-matched controls without epilepsy. Contrast threshold was measured using a temporal two-alternative forced-choice binocular psychophysical method at a distance of 150 cm from the stimuli, with a mean luminance of 40.1 cd/m². A one-way analysis of variance (ANOVA) applied to the linear contrast threshold showed significant differences between groups (F[3,188] = 14.829; p < .05). Adults with epilepsy had higher contrast thresholds (1.45, 1.04, and 1.18 times for frequencies of 0.25, 2.0, and 8.0 cycles per degree of visual angle, respectively). The Tukey Honestly Significant Difference post hoc test showed significant differences (p < .05) for all of the tested spatial frequencies. The largest difference between groups was in the lowest spatial frequency. Therefore, epilepsy may cause more damage to the neural pathways that process low spatial frequencies. However, epilepsy probably alters both the magnocellular visual pathway, which processes low spatial frequencies, and the parvocellular visual pathway, which processes high spatial frequencies. The experimental group had lower visual contrast sensitivity to all tested spatial frequencies.

Registration of Alfven resonances in TCABR tokamak by the scanning reflectometer at sideband frequencies

A frequency scanning O-mode reflectometer was used for studies of plasma density oscillations during local Alfven wave (LAW) excitation in the Tokamak Chauffage Alfven Bresilien (TCABR) at the frequency f(A) = 5 MHz. It was found that the spectrum of the reflectometer output signal, which consists mainly of the ""beat"" frequency f(B), is modified by the LAW excitation, and two additional frequency peaks appear, which are symmetrical in relation to the LAW excitation frequency f = f(A) +/- f(B). This result opens the possibility to improve the efficiency of studying the LAW induced density oscillations. The symmetry of these frequency peaks yields the possibility of finding the microwave frequency at which the reflectometer cutoff layer coincides with radial position of the LAW resonance zone in the TCABR tokamak. (C) 2011 American Institute of Physics. [doi:10.1063/1.3541756]

Femtosecond laser waveguide micromachining of PMMA films with azoaromatic chromophores

We report on the femtosecond-laser micromachining of poly(methyl methacrylate) (PMMA) films doped with nonlinear azoaromatic chromophores: Disperse Red 1, Disperse Red 13 and Disperse Orange 3. We study the conditions for controlling chromophore degradation during the micromachining of PMMA doped with each chromophore. Furthermore, we successfully used fs-micromachining to fabricate optical waveguides within a bulk sample of PMMA doped with these azochromophores. (c) 2008 Optical Society of America.