PAnalyzer: A software tool for protein inference in shotgun proteomics

Background Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data. Results In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server. Conclusions We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.

Creación Colectiva. Teorías sobre la noción de autoría, modelos colaborativos de creación e implicaciones para la práctica y la educación del arte contemporáneo

Es una tesis muy extensa a propósito para probar la presencia e importancia del arte colaborativo a lo largo de la historia reciente y la necesidad de darle cabida en el terreno de la educación. No podemos seguir ignorando su potencial amparándonos en un concepto trasnochado y romántico de artista genial que trabaja en solitario. El arte está para muchas más cosas que la mera exposición y en un futuro cercano veremos trabajar en colaboración a artistas con expertos de muy distintas áreas de conocimiento.

Fine mapping and functional analysis of the multiple sclerosis risk gene CD6

CD6 has recently been identified and validated as risk gene for multiple sclerosis (MS), based on the association of a single nucleotide polymorphism (SNP), rs17824933, located in intron 1. CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation. In this study, we performed a haptag SNP screen of the CD6 gene locus using a total of thirteen tagging SNPs, of which three were non-synonymous SNPs, and replicated the recently reported GWAS SNP rs650258 in a Spanish-Basque collection of 814 controls and 823 cases. Validation of the six most strongly associated SNPs was performed in an independent collection of 2265 MS patients and 2600 healthy controls. We identified association of haplotypes composed of two non-synonymous SNPs [rs11230563 (R225W) and rs2074225 (A257V)] in the 2nd SRCR domain with susceptibility to MS (Pmax(T) permutation=161024). The effect of these haplotypes on CD6 surface expression and cytokine secretion was also tested. The analysis showed significantly different CD6 expression patterns in the distinct cell subsets, i.e. – CD4+ naı¨ve cells, P = 0.0001; CD8+ naı¨ve cells, P,0.0001; CD4+ and CD8+ central memory cells, P = 0.01 and 0.05, respectively; and natural killer T (NKT) cells, P = 0.02; with the protective haplotype (RA) showing higher expression of CD6. However, no significant changes were observed in natural killer (NK) cells, effector memory and terminally differentiated effector memory T cells. Our findings reveal that this new MS-associated CD6 risk haplotype significantly modifies expression of CD6 on CD4+ and CD8+ T cells.

Creatividad en la búsqueda de ideas de negocio innovadoras, viables y exitosas

Duración (en horas): Más de 50 horas. Destinatario: Estudiante y Docente

Euskarara bikoizten diren ikus-entzunezko telebista-produktuak: ikerketa esparru landu gabea

Raquel Merino Álvarez, José Miguel Santamaría, Eterio Pajares (eds.)

Innovación en la Escuela Universitaria de Estudios Empresariales de San Sebastián

El objeto del presente artículo consiste en realizar una breve exposición de los aspectos innovadores puestos en marcha en la Escuela Universitaria de Estudios Empresariales de San Sebastián recientemente, en relación tanto a aspectos docentes como de gestión.

Prognostic Role of Host Cyclooxygenase and Cytokine Genotypes in a Caucasian Cohort of Patients with Gastric Adenocarcinoma

11 p.

Kazetaritza infografiaren garapena espainiako prentsan. "El Correo Español-El Pueblo Vasco"-ren kasua

383 p. : il.; gráf.

Cartas enviadas por Ramón María de Aldasoro a Justo Garate en 1940

8 cartas (mecanografiadas) ; 225x285 mmm. Ubicación: Caja 1 - Carpeta 20

Carta enviada por Jesús Arpal Poblador a Justo Garate en 1978

1 carta (mecanografiada) ; 207x295mm. Ubicación: Caja 1 - Carpeta 54

Rhythm Analysis during Cardiopulmonary Resuscitation: Past, Present, and Future

Survival from out-of-hospital cardiac arrest depends largely on two factors: early cardiopulmonary resuscitation (CPR) and early defibrillation. CPR must be interrupted for a reliable automated rhythm analysis because chest compressions induce artifacts in the ECG. Unfortunately, interrupting CPR adversely affects survival. In the last twenty years, research has been focused on designing methods for analysis of ECG during chest compressions. Most approaches are based either on adaptive filters to remove the CPR artifact or on robust algorithms which directly diagnose the corrupted ECG. In general, all the methods report low specificity values when tested on short ECG segments, but how to evaluate the real impact on CPR delivery of continuous rhythm analysis during CPR is still unknown. Recently, researchers have proposed a new methodology to measure this impact. Moreover, new strategies for fast rhythm analysis during ventilation pauses or high-specificity algorithms have been reported. Our objective is to present a thorough review of the field as the starting point for these late developments and to underline the open questions and future lines of research to be explored in the following years.

Carta enviada por José María de Azcárraga a Justo Garate en 1964

1 carta (manuscrita) : 275x214mm. Ubicación: Caja 1 - Carpeta 81

Cartas enviadas por José María Azcona a Justo Garate entre 1930 y 1936

7 cartas (mecanografiadas y manuscritas) ; entre 180x130mm y 214x139mm. Ubicación: Caja 1 - Carpeta 82

Ekonomian lizentziaturako matematika II. Azterketak

Ekonomian Lizentziaturako Matematika II irakasgaia gainditu behar duten ikasleentzat, eta baita ere, gai batzuetan, gradu berriko Matematika I eta Matematika II irakasgaiko ikasleentzat. Ekonomian Lizentziaturako Matematika II irakasgaiko azken hamar urteetan jarri diren azterketak eta haien erantzunak aurkituko dituzue. Lehenengo zatian, egin gabeko azterketak daude, ordena kronologikoan, zaharrenetik berrienera, eta bigarren zatian, erantzunak daude, ordena kronologikoan ere baina gaika ere. Horrela, programaren gai bakoitzaren ariketa guztiak elkarrekin aurkituko dituzue, gaiz gai ikasi nahi izanez gero

Ekonomian lizentziaturako matematika III. Azterketak

irakasgaia gainditu behar duten ikasleentzat, eta baita ere, gai batzuetan, gradu berriko Matematika I eta Matematika II irakasgaiko ikasleentzat.Ekonomian Lizentziaturako Matematika III irakasgaiko azken hamar urteetan jarri diren azterketak eta haien erantzunak aurkituko dituzue. Lehenengo zatian, egin gabeko azterketak daude, ordena kronologikoan, zaharrenetik berrienera, eta bigarren zatian, erantzunak daude, ordena kronologikoan ere baina gaika ere. Horrela, programaren gai bakoitzaren ariketa guztiak elkarrekin aurkituko dituzue, gaiz gai ikasi nahi izanez gero.