Applications of the pyramidal clustering method to biological objects.

In conventional hierarchical clustering methods, any object can belong to only one class or cluster. We present here an application of the pyramidal classification method to biological objects, which illustrates the intuitively appealing idea that some objects may belong simultaneously to two classes. In a first step, we performed an all-by-all comparison of all the open reading frames in the genomes from S. cerevisiae, M. jannaschii, E. coli, H. influenzae and Synechocystis. In a second step, a series of connex classes was built, each connex class containing all those sequences that were linked by a Z-value (obtained after 100 sequence shufflings) greater than a given threshold. Finally, each connex class was submitted to a pyramidal classification. Three examples of such classifications are given, concerning two sets of multi-domains protein sequences and a family of aminoacyl-tRNA synthetases. They make it clear that the linear order among the classified objects that results from the pyramidal classification is useful in deciphering the multiple relationships that can exist between the objects under study. A program for calculating and displaying a pyramidal classification from a dissimilarity matrix is available from http:/(/)genome.genetique.uvsq.fr/Pyramids. The pyramidal classifications of the connex classes from the five organisms (intra- and inter-genomic comparisons) are available from http:/(/)www.gene-it.com under the family item.     

Conceptual distinctiveness supports detailed visual long-term memory for real-world objects.

Humans have a massive capacity to store detailed information in visual long-term memory. The present studies explored the fidelity of these visual long-term memory representations and examined how conceptual and perceptual features of object categories support this capacity. Observers viewed 2,800 object images with a different number of exemplars presented from each category. At test, observers indicated which of 2 exemplars they had previously studied. Memory performance was high and remained quite high (82% accuracy) with 16 exemplars from a category in memory, demonstrating a large memory capacity for object exemplars. However, memory performance decreased as more exemplars were held in memory, implying systematic categorical interference. Object categories with conceptually distinctive exemplars showed less interference in memory as the number of exemplars increased. Interference in memory was not predicted by the perceptual distinctiveness of exemplars from an object category, though these perceptual measures predicted visual search rates for an object target among exemplars. These data provide evidence that observers' capacity to remember visual information in long-term memory depends more on conceptual structure than perceptual distinctiveness. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Effect of hydrothermal ripening on the photoluminescence properties of pure and doped cerium oxide nanoparticles

We synthesized and characterized a set of undoped and doped cerium oxide nanoparticles with the following chemical formula: Ce_1−xM_xO_2−(x/2) (M: Y or Gd and x = 0 or 0.15) by different coprecipitation protocols at room temperature. Room temperature photoluminescence spectra were similar whatever the protocols and doping. After hydrothermal ripening at neutral pH, a moderate but significant particle growth was observed for doped particles whereas undoped ones remained the same. Simultaneously, the photoluminescence band at 400 nm was significantly red-shifted and practically vanished for doped particles whereas it was only slightly weaker and shifted for pure ceria. All other bands in the same region were much less affected: the bands at 363 and 378 nm became more intense, the shoulder at 420 nm remained roughly unchanged. These phenomena were observed systematically whatever the coprecipitation protocol. As a consequence, the band at 400 nm can be specifically attributed to surface defects that disappear during growth under hydrothermal conditions.     

A 69-mW 10-bit 80-MSample/s Pipelined CMOS ADC

A 10-bit 80-MS/s analog-to-digital converter (ADC) with an area- and power-efficient architecture is described. By sharing an amplifier between two successive pipeline stages, a 10-bit pipeline is realized using just four amplifiers with a separate sample-and-hold block. The proposed feedback signal polarity inverting (FSPI) technique addresses the drawback of the conventional amplifier sharing technique. A wide-swing wide-bandwidth telescopic amplifier and an early comparison technique with a constant delay circuit have been developed to further reduce power consumption. The ADC is implemented in a 0.18-/spl mu/m dual-gate-oxidation CMOS process technology, achieves 72.8-dBc spurious free dynamic range, 57.92-dBc signal-to-noise ratio, 9.29 effective number of bits (ENOB) for a 99-MHz input at full sampling rate, and consumes 69 mW from a 3-V supply. The ADC occupies 1.85 mm/sup 2/.     

On the generation of a variety of grasps

In everyday life, people use a large diversity of hand configurations while reaching out to grasp an object. They tend to vary their hands position/orientation around the object and their fingers placement on its surface according to the object properties such as its weight, shape, friction coefficient and the task they need to accomplish. Taking into account these properties, we propose a method for generating such a variety of good grasps that can be used for the accomplishment of many different tasks. Grasp synthesis is formulated as a single constrained optimization problem, generating grasps that are feasible for the hand’s kinematics by minimizing the norm of the joint torque vector of the hand ensuring grasp stability. Given an object and a kinematic hand model, this method can easily be used to build a library of the corresponding object possible grasps. We show that the approach is adapted to different representations of the object surface and different hand kinematic models.     

Seasonal and diel distributions of denitrifying and bacterial communities in a hypersaline microbial mat (Camargue, France)

Changes in spatio-temporal distribution of bacterial and denitrifying communities were qualitatively studied in a microbial mat from Camargue (France). During a diel and a seasonal cycle, patterns of 16S rRNA and nitrite reductase genes (nirS and nirK) were compared by denaturing gradient gel electrophoresis (DGGE). Statistical analysis of DGGE profiles showed a significant seasonal shift in the community structure of the nirS-containing bacteria with a winter superficial population that extended in summer, whereas the nirK-containing bacteria seemed more affected by vertical gradients rather than by month-to month-changes. Denitrifying activities remained stable during these sampling times. The bacterial community at the surface of the mat also changed according to season, but appeared stable over a day. Finally, during a diel cycle nirK populations were localized in zones with large fluctuations of environmental parameters (oxygen, pH, and sulfur levels) while nirS populations seemed more restricted to the permanent anoxic layer of the microbial mat.     

Solid‐state lasers for projection

Abstract— The unique advantage of projection displays is the ability to produce large images from small devices. The use of lasers as the projection light source will mean a further step in terms of compactness as well as efficiency for projection systems. However, the advent of laser projection is currently still limited by the availability of low‐cost green lasers. Blue‐diode‐pumped solid‐state lasers are one promising way to realize green as well as red lasers that are specifically suited for projection applications. An efficient solid‐state laser that is based on Pr³⁺:YLF as the laser material, pumped by a blue‐laser diode and emitting at 523 nm, is presented here. The laser reaches power‐conversion efficiencies of more than 7% and output powers of up to 378 mW at green wavelengths. By making only minor modifications to the laser resonator, a red laser emitting at 640 nm can be realized within the same setup. An output power of 166 mW at a power‐conversion efficiency of 6.9% is demonstrated in the red. By combining a red‐ and a green‐emitting blue‐diode‐pumped solid‐state laser with another blue diode, an integrated RGB projection light source can be realized that is based on a single‐diode technology.     

Estimating the non-linear dynamics of free-flying objects

This paper develops a model-free method to estimate the dynamics of free-flying objects. We take a realistic perspective to the problem and investigate tracking accurately and very rapidly the trajectory and orientation of an object so as to catch it in flight. We consider the dynamics of complex objects where the grasping point is not located at the center of mass.To achieve this, a density estimate of the translational and rotational velocity is built based on the trajectories of various examples. We contrast the performance of six non-linear regression methods (Support Vector Regression (SVR) with Radial Basis Function (RBF) kernel, SVR with polynomial kernel, Gaussian Mixture Regression (GMR), Echo State Network (ESN), Genetic Programming (GP) and Locally Weighted Projection Regression (LWPR)) in terms of precision of recall, computational cost and sensitivity to choice of hyper-parameters. We validate the approach for real-time motion tracking of 5 daily life objects with complex dynamics (a ball, a fully-filled bottle, a half-filled bottle, a hammer and a pingpong racket). To enable real-time tracking, the estimated model of the object’s dynamics is coupled with an Extended Kalman Filter for robustness against noisy sensing.     

An incremental algorithm for Z-value computations

The Z-value (Comput. Chem. 23 (1999) 333) is an extension of the Z-score that is classically used to compare sets of biological sequences. The Z-value has been successfully used to handle complete genome studies as well as analyze large sets of proteins. The Z-value computation is based on a Monte Carlo approach to estimate the statistical significance of a Smith & Waterman alignment score. Comet et al. (Comput. Chem. 23 (1999) 333) have shown that, in contrast to the alignment score, the Z-value largely reduces the bias due to the lengths and compositions of the sequences. They also described an estimator of the deviation of Z-values, that we extend in this paper in order to optimize Z-values computation. The incremental algorithm described here provides two characteristics which are usually incompatible: (i) it improves the accuracy of Z-values calculation; (ii) it reduces the time complexity (this algorithm has been named incremental because it iteratively adds random sequences to the Monte-Carlo process when needed). Results are presented, originating from the all-by-all comparison of the proteins from Saccharomyces cerevisiae and Escherichia coli.