Cooperative Metaheuristics for Exploring Proteomic Data

Most combinatorial optimization problems cannotbe solved exactly. A class of methods, calledmetaheuristics, has proved its efficiency togive good approximated solutions in areasonable time. Cooperative metaheuristics area sub-set of metaheuristics, which implies aparallel exploration of the search space byseveral entities with information exchangebetween them. The importance of informationexchange in the optimization process is relatedto the building block hypothesis ofevolutionary algorithms, which is based onthese two questions: what is the pertinentinformation of a given potential solution andhow this information can be shared? Aclassification of cooperative metaheuristicsmethods depending on the nature of cooperationinvolved is presented and the specificproperties of each class, as well as a way tocombine them, is discussed. Severalimprovements in the field of metaheuristics arealso given. In particular, a method to regulatethe use of classical genetic operators and todefine new more pertinent ones is proposed,taking advantage of a building block structuredrepresentation of the explored space. Ahierarchical approach resting on multiplelevels of cooperative metaheuristics is finallypresented, leading to the definition of acomplete concerted cooperation strategy. Someapplications of these concepts to difficultproteomics problems, including automaticprotein identification, biological motifinference and multiple sequence alignment arepresented. For each application, an innovativemethod based on the cooperation concept isgiven and compared with classical approaches.In the protein identification problem, a firstlevel of cooperation using swarm intelligenceis applied to the comparison of massspectrometric data with biological sequencedatabase, followed by a genetic programmingmethod to discover an optimal scoring function.The multiple sequence alignment problem isdecomposed in three steps involving severalevolutionary processes to infer different kindof biological motifs and a concertedcooperation strategy to build the sequencealignment according to their motif conten

A solid state light-matter interface at the single photon level

Coherent and reversible mapping of quantum information between light and matter is an important experimental challenge in quantum information science. In particular, it is a decisive milestone for the implementation of quantum networks and quantum repeaters. So far, quantum interfaces between light and atoms have been demonstrated with atomic gases, and with single trapped atoms in cavities. Here we demonstrate the coherent and reversible mapping of a light field with less than one photon per pulse onto an ensemble of 10 millions atoms naturally trapped in a solid. This is achieved by coherently absorbing the light field in a suitably prepared solid state atomic medium. The state of the light is mapped onto collective atomic excitations on an optical transition and stored for a pre-programmed time up of to 1 mu s before being released in a well defined spatio-temporal mode as a result of a collective interference. The coherence of the process is verified by performing an interference experiment with two stored weak pulses with a variable phase relation. Visibilities of more than 95% are obtained, which demonstrates the high coherence of the mapping process at the single photon level. In addition, we show experimentally that our interface allows one to store and retrieve light fields in multiple temporal modes. Our results represent the first observation of collective enhancement at the single photon level in a solid and open the way to multimode solid state quantum memories as a promising alternative to atomic gases.Comment: 5 pages, 5 figures, version submitted on June 27 200

Utilidad de la electrocardiografía en la clínica veterinaria de animales de compañía

The electrocardiography is a diagnostic tool for the veterinary clinic of companion animals. In patients with cardiologic signs is the best non invasive means to evaluate the electric activity of the heart. It allows us to evaluate the present of arrhythmias, the pre-surgical state, assess the anaesthetic risk and check the pharmacologic treatments in cardiac patients amongst other. The objective of the present work was to illustrate the advantage of the electrocardiographic assess in canine and felíne patients, and its limitations and contraindications as well.La electrocardiografía es una herramienta diagnóstica de utilidad básica en la clínica veterinaria de animales de compañía. En pacientes con signos clínicos cardiológicos constituye la mejor alternativa diagnóstica para evaluar la actividad eléctrica del corazón de forma no invasiva El electrocardiograma permite demostrar la presencia de arritmias, colabora en la evaluación prequirúrgica y en la valoración del riesgo anestésico, ayuda a monitorear los tratamientos farmacológicos de pacientes cardiópatas, sugiere la presencia de sobrecargas camerales atriales y ventriculares cardíacas y complementa el diagnóstico en patologías de origen metabólico y endócrino. El objetivo del presenta trabajo es mostrar las distintas ventajas que presenta la evaluación electrocardiográfica en pacientes caninos y felinos, así como las límitaciones y contraindicaciones que presenta su estudio

A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics

<p>Abstract</p> <p>Background</p> <p>In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user.</p> <p>Results</p> <p>We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects.</p> <p>Conclusion</p> <p>Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.</p

New treatments for chronic hepatitis C

Treatments for chronic hepatitis C has evolved significantly in the past 15 years. The standard of care (SOC) is peginterferon alfa-2a/-2b with ribavirin for 48 weeks or 24 weeks in patients infected with HCV genotype 1 or 2/3, respectively. The treatment duration can be individualized based on the baseline viral load and the speed of the virologic response during treatment. However, current therapies are associated with side effects, complications, and poor patient tolerability. Therefore, there is an urgent need to identify better strategies for treating this disease. An improved sustained virologic response (SVR) can be achieved with new HCV-specific inhibitors against NS3/4A and NS5B polymerases. Recent trials have found SVR rates in patients with HCV genotype 1 infection of 61~68% and 67~75% for combining the SOC with the protease inhibitors telaprevir and boceprevir, respectively. Several new HCV-specific inhibitors such as protease inhibitors and nucleoside and non-nucleoside polymerase inhibitors as well as non-HCV-specific compounds with anti-HCV activity are currently in clinical evaluation. In this review we discuss these new treatments for chronic hepatitis C

Novel event classification based on spectral analysis of scintillation waveforms in Double Chooz

Liquid scintillators are a common choice for neutrino physics experiments, but their capabilities to perform background rejection by scintillation pulse shape discrimination is generally limited in large detectors. This paper describes a novel approach for a pulse shape based event classification developed in the context of the Double Chooz reactor antineutrino experiment. Unlike previous implementations, this method uses the Fourier power spectra of the scintillation pulse shapes to obtain event-wise information. A classification variable built from spectral information was able to achieve an unprecedented performance, despite the lack of optimization at the detector design level. Several examples of event classification are provided, ranging from differentiation between the detector volumes and an efficient rejection of instrumental light noise, to some sensitivity to the particle type, such as stopping muons, ortho-positronium formation, alpha particles as well as electrons and positrons. In combination with other techniques the method is expected to allow for a versatile and more efficient background rejection in the future, especially if detector optimization is taken into account at the design level

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

To identify novel genes associated with ALS, we undertook two lines of investigation. We carried out a genome-wide association study comparing 20,806 ALS cases and 59,804 controls. Independently, we performed a rare variant burden analysis comparing 1,138 index familial ALS cases and 19,494 controls. Through both approaches, we identified kinesin family member 5A (KIF5A) as a novel gene associated with ALS. Interestingly, mutations predominantly in the N-terminal motor domain of KIF5A are causative for two neurodegenerative diseases: hereditary spastic paraplegia (SPG10) and Charcot-Marie-Tooth type 2 (CMT2). In contrast, ALS-associated mutations are primarily located at the C-terminal cargo-binding tail domain and patients harboring loss-of-function mutations displayed an extended survival relative to typical ALS cases. Taken together, these results broaden the phenotype spectrum resulting from mutations in KIF5A and strengthen the role of cytoskeletal defects in the pathogenesis of ALS.Peer reviewe