Visibility recovery on images acquired in attenuating media. Application to underwater, fog, and mammographic imaging

136 p.

Evaluation of bioactive sphingolipids in 4-HPR-resistant leukemia cells

Background -- N-(4-hydroxyphenyl)retinamide (4-HPR, fenretinide) is a synthetic retinoid with potent pro-apoptotic activity against several types of cancer, but little is known regarding mechanisms leading to chemoresistance. Ceramide and, more recently, other sphingolipid species (e.g., dihydroceramide and dihydrosphingosine) have been implicated in 4-HPR-mediated tumor cell death. Because sphingolipid metabolism has been reported to be altered in drug-resistant tumor cells, we studied the implication of sphingolipids in acquired resistance to 4-HPR based on an acute lymphoblastic leukemia model. Methods -- CCRF-CEM cell lines resistant to 4-HPR were obtained by gradual selection. Endogenous sphingolipid profiles and in situ enzymatic activities were determined by LC/MS, and resistance to 4-HPR or to alternative treatments was measured using the XTT viability assay and annexin V-FITC/propidium iodide labeling. Results -- No major crossresistance was observed against other antitumoral compounds (i.e. paclitaxel, cisplatin, doxorubicin hydrochloride) or agents (i.e. ultra violet C, hydrogen peroxide) also described as sphingolipid modulators. CCRF-CEM cell lines resistant to 4-HPR exhibited a distinctive endogenous sphingolipid profile that correlated with inhibition of dihydroceramide desaturase. Cells maintained acquired resistance to 4-HPR after the removal of 4-HPR though the sphingolipid profile returned to control levels. On the other hand, combined treatment with sphingosine kinase inhibitors (unnatural (dihydro)sphingosines ((dh)Sph)) and glucosylceramide synthase inhibitor (PPMP) in the presence or absence of 4-HPR increased cellular (dh)Sph (but not ceramide) levels and were highly toxic for both parental and resistant cells. Conclusions -- In the leukemia model, acquired resistance to 4-HPR is selective and persists in the absence of sphingolipid profile alteration. Therapeutically, the data demonstrate that alternative sphingolipid-modulating antitumoral strategies are suitable for both 4-HPR-resistant and sensitive leukemia cells. Thus, whereas sphingolipids may not be critical for maintaining resistance to 4-HPR, manipulation of cytotoxic sphingolipids should be considered a viable approach for overcoming resistance.

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.

Design,optimization and in vivo evaluation of non-viral vectors for gene therapy. Applications in ocular disorders

227 págs.

Online exercise for the design and simulation of PCR and PCR-RFLP experiments

[EN] Background: Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings: An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes,compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions: The exercise is freely available at http://insilico.ehu.es/edu.

Water quality assessment and characterisation of chlorophyll-a variability related to river discharges, within the southeastern Bay of Biscay : evaluation and development of chlorophyll-a algorithms for MODIS and MERIS imagery

222 p. : il.

Using the system dynamics paradigm in teaching and learning technological university subjets

2nd International Conference on Education and New Learning Technologies

Plataforma de investigación en el ámbito de la resucitación cardio-pulmonar basada en un maniquí de entrenamiento sensorizado

[ES]Hoy en día las muertes por parada cardiorrespiratoria superan en número a otras más mediáticas como aquellas que se producen por incendios o en accidentes de tráfico, y sin embargo su repercusión es mucho menor. Este hecho debe ser motivo de preocupación ya que, con una correcta formación de la población en materia de resucitación cardíaca, muchas de estas muertes podrían ser evitadas. Con el objetivo de reducir estas estadísticas han surgido multitud de estudios y proyectos de investigación consistentes en tratar de mejorar las herramientas disponibles tanto para personal sanitario como no sanitario. En este marco se encuadra el proyecto presentado en este documento, consistente en la sensorización de un maniquí de entrenamiento para episodios de parada cardiorrespiratoria, el cual ofrecerá la posibilidad de analizar con detalle el artifact o interferencia generada por el rescatador sobre el paciente en el momento de efectuar la maniobra de resucitación, así como la interferencia causada por el contacto electrodo-piel. Paralelamente podrá ser utilizado como mero instrumento de entrenamiento para posibles situaciones reales. El porqué de la utilización de este tipo de maniquíes reside principalmente en la imposibilidad de emplear personas debido a las posibles lesiones torácicas que pueden ocurrir por las compresiones realizadas. Finalmente debe citarse el hecho de que no es imprescindible tener conocimientos médicos para poder aplicar las técnicas básicas de resucitación cardíaca, acción que incrementa las posibilidades de supervivencia de un paciente de manera excepcional, ya que cada minuto que pasa desde la parada cardiorrespiratoria la probabilidad de supervivencia disminuye en un porcentaje significativamente elevado. Tomando como base lo descrito hasta ahora, en este documento se detalla la solución técnica de la sensorización de un maniquí genérico para la adquisición de las señales de fuerza de compresión, aceleración sufrida por el pecho en tres ejes ortogonales, profundidad de compresión, impedancia entre los dos electrodos colocados sobre el pecho del paciente y señal electrocardiográfica emitida por el corazón; además, se incluye la posibilidad de inyectar una señal electrocardiográfica previamente grabada. La base de registros obtenida de estos ensayos podrá ser utilizada posteriormente para su análisis, ya que su similitud con señales extraídas en un caso real es máxima.