Statistical method for predicting protein coding regions in nucleic acid sequences

Protein coding regions of a genome fragment can be mathematically predicted by studying variations in the statistical properties or by searching the signals characteristic of the junctions between the coding and non-coding regions. We propose here a new statistical method using correspondence analysis. This method does not use any reference codon set but takes into account the codon usage homogeneity along the studied genome fragment. Comparison with previously published methods especially the 'codon usage method' of Staden has been made, and two examples are presented here. Applications to analysis of prokaryotic operon and eukaryotic split genes are also discussed. Use of the method has also shown two structures not previously described: i) in the human prt gene, a strong triplet structure exists in a non-coding region; ii) in the human tp-a codon usage is not uniform between the different exons.     

Mode transformation in very oversized circular waveguides

Very oversized waveguides used in FIR lasers have an unexpected electromagnetic behavior. For high frequencies, situated between IR and FIR, the classical equations are no longer valid.     

Space and time efficiency of the forest-of-quadtrees representation

A forest of quadtrees is a refinement of a quadtree data structure that is used to represent planar regions. A forest of quadtrees provides space savings over regular quadtrees by concentrating vital information. The paper presents some of the properties of a forest of quadtrees and studies the storage requirements for the case in which a single 2^m × 2^m region is equally likely to occur in any position within a 2ⁿ × 2ⁿ image. Space and time efficiency are investigated for the forest-of-quadtrees representation as compared with the quadtree representation for various cases.     

Effect of the light on MESFETs application to optically controlled devices

Light has some influence on static and dynamic characteristics of MESFETs illuminated by an optical fiber connected at the output of a laser diode (λ=845nm). They are first described from a theoretical point of view with a new unidimensional model for the component. An equivalent scheme extraction software gives the elements of the transistor scheme, using the results of the network analyzer measurements. A good agreement between the theoretical and experimental results exists. It is thus possible to design optically controlled devices such as amplifiers or oscillators. Good results have been obtained with both.     

Micromechanical analysis of the finite element calculation of a diffusional transformation

A micromechanical model of a diffusional transformation has been developed, which describes the progress of the transformation within a three-dimensional “unit cell” submitted to an external stress state. The example chosen is that of an isothermal pearlitic transformation of a steel. The transformation plastic strain is due to interactions occurring between the local stresses and the transformation process, resulting in an oriented plastic flow in or in the vicinity of the material layers swept by the transformation front. The analysis of the local mechanical states of the simulation provides a good interpretation of the evolution of transformation plastic strain, when considering the effect of applied stress level and the way mechanical properties are imposed on the newly formed phase. In particular, the normality law for transformation plasticity is related to the shape of the local plastic zones. The discrepancy observed between simulation and experience is then discussed, following two main points: the influence of the behaviour law of the phases and the way interactions between neighbouring cells are prescribed. The difficulty and importance of obtaining realistic mechanical properties of the forming pearlite is pointed out. This revised version was published online in November 2006 with corrections to the Cover Date.     

Microemboli in cerebral circulation and alteration of cognitive abilities in patients with mechanical prosthetic heart valves

BACKGROUND AND PURPOSE: It has been shown previously that cerebral microemboli may occur frequently in patients with a normal mechanical heart valve (MHV) without prior history of stroke. Some arguments strongly suggest that these microemboli have a gaseous origin. In other circumstances such as extracorporeal circulation or decompression in divers, it has been demonstrated that cerebral microbubbles could lead to some deterioration in cognitive functions. Therefore, we have studied attention and memory, which are among the most impaired cognitive functions as demonstrated in previous studies, in patients with an MHV. METHODS: Three groups of 12 volunteers each were composed of patients with an MHV and embolic signals in the cerebral circulation (group 1), patients with biological prostheses (group 2), and healthy subjects (group 3). Groups were carefully matched for age and verbal intellectual abilities. For each group, a transcranial Doppler examination was performed and a set of cognitive tests assessing sustained and selective attention and episodic and working memory was administered. RESULTS: The mean embolic rate was 29 per hour in patients with an MHV. No embolus was detected in the other 2 groups. Episodic memory was significantly modified in both groups 1 and 2 compared with the control group for tasks that required high-processing resources. Working memory performance was significantly decreased in MHV patients. No between-groups differences were observed for the other parameters. CONCLUSIONS: Alteration of episodic memory can be attributed to a long-term effect of the surgical procedure. Deterioration of working memory can be related to the presence of cerebral microemboli in MHV patients.     

Influence of Oxygen Vacancies on the Electronic Structure of Yttrium Oxide

The influence of oxygen vacancies on the electronic structure of yttrium oxide was investigated both experimentally and theoretically. By means of X-ray absorption spectroscopy, at the yttrium K and L ₁₁ edges and at the oxygen K edge, information on the local densities of states of various orbital symmetries, around each type of atom, was obained. The total density of states in the valence band was studied using X-ray photoelectron spectroscopy. Experimental results were compared with those obtained on stoichiometric yttria. The evolution of the densities of states is well reproduced by self-consistent, semiempirical tight-binding calculations applied to clusters of increasing size, in which oxygen vacancies are introduced. The charge transfer between oxygen and yttrium is modified, as experimentally observed from the study of the O KLL Auger line shape. The decrease of the local atomic charge on oxygen is theoretically confirmed by the tight-binding calculations, showing a tendency toward a more covalent bond in nonstoichiometric yttria.     

A poly(cyclopentadithiophene) matrix suitable for electrochemically controlled DNA delivery

A conducting polymer is tested for DNA delivery trials. The conducting matrix used is successful for electrochemical delivery of DNA accumulated by covalent immobilization. The electrochemical process consists of the reduction of arylsulfonamide moieties, which occur as linker groups. The specific design of the polymer allows the electronic properties to be promoted, making available the cleavage potential in physiological media. The amount of DNA released from a modified platinum electrode is investigated by quartz crystal microbalance. The released species used to prove the system performance are long sequences of DNA strands, which are amplified by PCR after liberation and identified by electrophoresis migration.     

Plasma-deposited fluoropolymer film mask for local porous silicon formation

ABSTRACT: The study of an innovative fluoropolymer masking layer for silicon anodization is proposed. Due to its high chemical resistance to hydrofluoric acid even under anodic bias, this thin film deposited by plasma has allowed the formation of deep porous silicon regions patterned on the silicon wafer. Unlike most of other masks, fluoropolymer removal after electrochemical etching is rapid and does not alter the porous layer. Local porous regions were thus fabricated both in p+-type and low-doped n-type silicon substrates.     

Validation of a liquid chromatography-tandem mass spectrometry screening method to monitor 58 antibiotics in milk: a qualitative approach

A multi-residue method was developed for monitoring antibiotic residues in milk using liquid chromatography coupled to a tandem quadrupole mass spectrometer (LC/MS-MS). Two very short extractions followed by two LC/MS-MS acquisitions allowed the screening of 58 antibiotics belonging to eight different families (penicillins, cephalosporins, sulfonamides, macrolides, lincosamides, aminoglycosides, tetracyclines, and quinolones). This method is currently implemented in the laboratory in a qualitative way, i.e. monitoring the presence or absence of residue in a sample and identification of the analyte before the confirmation step. In order to assess the performance of this method, a validation strategy described in an internal guideline for the validation of screening methods was applied. The aim of the validation was to prove sufficient sensitivity of the method to detect all the targeted antibiotics at the level of interest (maximum residue limit, MRL) at least. According to European Commission Decision 2002/657/EC, the suitable sensitivity of a screening method can be demonstrated when the CCβ is below or equal to the MRL and so the false-compliant rate below or equal to 5% at the MRL level. The validation scheme was established in order to take into account various variability factors: the apparatus response, the interday repeatability, the matrix effect, etc. The results of the validation clearly demonstrate the suitability of this method for the detection and identification of more than 50 antibiotics and they are in agreement with the results obtained in routine analysis.