Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

Background: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions.Results: We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts.Conclusions: These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.

A method for extracting semantic information from on-line art music discussion forums

In this paper a method for extracting semantic informationfrom online music discussion forums is proposed. The semantic relations are inferred from the co-occurrence of musical concepts in forum posts, using network analysis. The method starts by defining a dictionary of common music terms in an art music tradition. Then, it creates a complex network representation of the online forum by matchingsuch dictionary against the forum posts. Once the complex network is built we can study different network measures, including node relevance, node co-occurrence andterm relations via semantically connecting words. Moreover, we can detect communities of concepts inside the forum posts. The rationale is that some music terms are more related to each other than to other terms. All in all, this methodology allows us to obtain meaningful and relevantinformation from forum discussions.

Análisis, comparativa y visualización de redes sociales on-line representadas como grafos

El presente documento conduce a un análisis y comparativa de diferentes y variados conjuntos de redes sociales on-line. Para ello, primero se explica la base teórica de teoría de grafos para su interpretación y comprensión, así como de la base matemática que fundamenta el tipo específico de red estudiada y las diferentes métricas (estadísticas) extraídas de estas. Luego, se ofrece una detallada explicación del entorno de trabajo tanto para la aplicación informática desarrollada, como para posterior visualización y también una explicación y los algoritmos utilizados en las funciones implementadas con tales fines. Para finalizar el documento, se realiza una inmersión particular en cada red social on-line, puntualizando sus características y finalizando con una comparativa general entre todas ellas, siempre acompañadas con sus respectivas visualizaciones en el espacio 2D representadas en forma de grafo.

Integració del motor APIS de qüestionaris on-line en una plataforma d'eLearning basada en serveis

El projecte Integració del motor APIS de qüestionaris on-line en una plataformad'eLearning basada en serveis descriu el procés d'anàlisi i implementació del codi necessari per integrar dins de la plataforma d'eLearning SLeD tot el motor d'APIS de manera que SLeD pugui reproduir preguntes o items i exàmens complets o tests dins d'una UOL o unitat d'aprenentatge. Això permetrà dotar a APIS d'un control de sessió d'usuari i permetrà una utilitat que fins ara no tenia, la possibilitat de entrar al món online mitjançant SLeD. Tot aixòs’implementa gràcies a la connexió WebServices amb el mòdul CCSI de CopperCore i SLeD que s'encarrega de donar facilitats al programador de cara a ampliar el ventall d'eines que ofereix aquesta plataforma i fomentar encara més la idea del codi lliure (open source) i la utilitat globalitzadora d'e-Learning.

A New Model for Designing a Product Line Using TURF Analysis

This paper introduces the approach of using TURF analysis to design a product line through a binary linear programming model. This improves the efficiency of the search for the solution to the problem compared to the algorithms that have been used to date. Furthermore, the proposed technique enables the model to be improved in order to overcome the main drawbacks presented by TURF analysis in practice.

Gestión operaciones logísticas : planificación, gestión y control on-line de operaciones de descarga

Aplicación en entorno web para facilitar la planificación, control y gestión de operaciones logísticas de descarga en un almacén regulador que gestione diferentes clientes con varios orígenes y destinos. Permite el acceso concurrente de varios usuarios previamente autorizados con diferentes niveles de acceso a datos y actualizaciones. Su utilización y actualización de los datos permite mantener un control on-line de la actividad y dar visibilidad a los clientes. Los datos almacenados se convierten en una fuente única, compartida y exportable para posteriores usos en análisis de datos y procesos de mejora. Incorpora informes de actividad y de indicadores de calidad.

Desenvolupament d'una aplicació per a la creació de pressupostos on-line

En aquests moments, el mercat no es troba en una bona situació, per aquest motiu les empreses han de buscar noves maneres de créixer, expandir-se i noves formes d’interactuar amb els clients. La idea original d’aquest projecte sorgeix de la necessitat de disposar d’una manera diferent de promocionar-se i oferir nous serveis a través d’internet mitjançant una pàgina web. Degut a la situació actual, el preu és un aspecte molt important i influent a l’hora de realitzar una obra. Per aquest motiu es va pensar que seria molt interessant que el client pogués demanar de forma fàcil i ràpida un pressupost, i a l’instant tingués un preu orientatiu del que li pot costar la obra. D’aquesta manera l’interessat s’estalvia i agilitza molts passos previs abans de començar una obra. Després d’analitzar quina era la millor manera de portar a terme el projecte informàtic, s’ha determinat que la pàgina web es desenvoluparà utilitzant els llenguatges HTML i PHP combinant-lo amb el framework CodeIgniter. El disseny de la web es realitzarà mitjançant fulles d’estil CSS conjuntament amb el framework BootStrap. Per realitzar l’aplicació web que realitza els pressupostos s’utilitzarà AJAX i jQuery perquè d’aquesta manera el procés sigui dinàmic. L’entorn de desenvolupament escollit és el NetBeans i per provar el projecte s’utilitza el XAMPP. Un usuari només necessitarà un navegador i connexió a internet per fer servir totes les funcions de la web. Podrà realitzar pressupostos, concertar visites, contactar i per suposat veure tota la part informativa de la pàgina.

Disseny i elaboració d'un gimnàs on-line

L’evolució que ha experimentat la societat, les grans ciutats, la industrialització i molts altres factors han modificat l’estil de vida de les persones accentuant-ne, irremediablement, el sedentarisme i l’abstinència de realitzar exercici físic. La pràctica esportiva i/o d’exercici físic realitzada sota les condicions recomanades pels professionals, és beneficiosa per millorar el nivell de salut o mantenir-lo en tot el possible, ja que provoca modificacions beneficioses sobre el metabolisme, el sistema cardiovascular i l’aparell locomotor. Lamentablement, l’hàbit de realitzar exercici físic no és comú en totes les persones, ja sigui per l’estil de vida que genera incompatibilitats d’horaris amb la feina, fills i familiars o bé per mandra o desgana d’haver d’aprofitar aquelles estones de temps lliure per dedicar-los al culte del cos i de la salut. Els efectes negatius que suposa una modalitat de vida sedentària per a la salut són notablement elevats, amb la qual cosa, cal buscar sistemes per augmentar l’ interès de la població per la pràctica de l’esport i l’activitat física. La creació d’aquest projecte neix de la idea d’unir el fet d’enginyar un mètode per incrementar l’interès de les persones per l’exercici físic amb els avenços tecnològics que s’han realitzat aquesta última dècada relacionats amb el desenvolupament web i multimèdia. A grans trets, la idea general d’aquest projecte es basa en el cas d’un gimnàs real i en actiu, amb necessitat de crear un portal web que serveixi alhora de pàgina web informativa i d’eina de gestió acadèmica del centre proporcionant certes funcionalitats als clients tot presentant-los una nova modalitat de realitzar exercici físic dirigit: realitzar-lo des de casa. Per desenvolupar tot el sistema informàtic que ho durà a terme, després de realitzar una recerca, anàlisi i elecció de les eines mitjançant les quals poder-ho realitzar, s’ha optat per crear l’entorn web mitjançant els llenguatges HTML i PHP en combinació amb els fulls d’estil CSS. Pel que fa a l’entorn de desenvolupament, s’ha utilitzat Notepad++ i com a entorn de proves, WAMP Server. Per últim, pel que fa a la transmissió del contingut multimèdia (vídeos de les sessions d’activitats) s’ha utilitzat Flash Media Interactive Server en combinació de Flash Media Live Encoder per codificar-ne el contingut. L’usuari final, des de qualsevol punt del planeta, podrà realitzar (sempre i quan disposi del temps i el material necessari i una connexió a Internet) en temps real i en directe les classes dirigides que es realitzen al centre. Tanmateix, també s’ha desenvolupat una botiga virtual on qualsevol persona podrà comprar-hi, entre d’altres coses relacionades amb la pràctica de l’exercici físic, tot el material necessari per realitzar qualsevol de les activitats que s’imparteixen al gimnàs i ho rebrà còmodament a casa. Aprofitar unes circumstàncies econòmiques adverses per generar una nova manera de captar clients proporcionant-los una alternativa econòmica, diferent, nova i original d’anar al gimnàs. Temps de crisis, temps d’oportunitats. Aquesta és la moralitat que pretén donar aquest projecte.

Moesin interacts with the cytoplasmic region of intercellular adhesion molecule-3 and is redistributed to the uropod of T Lymphocytes during cell polarization

During activation, T lymphocytes become motile cells, switching from a spherical to a polarized shape. Chemokines and other chemotactic cytokines induce lymphocyte polarization with the formation of a uropod in the rear pole, where the adhesion receptors intercellular adhesion molecule-1 (ICAM-1), ICAM-3, and CD44 redistribute. We have investigated membrane-cytoskeleton interactions that play a key role in the redistribution of adhesion receptors to the uropod. Immunofluorescence analysis showed that the ERM proteins radixin and moesin localized to the uropod of human T lymphoblasts treated with the chemokine RANTES (regulated on activation, normal T cell expressed, and secreted), a polarization-inducing agent; radixin colocalized with arrays of myosin II at the neck of the uropods, whereas moesin decorated the most distal part of the uropod and colocalized with ICAM-1, ICAM-3, and CD44 molecules. Two other cytoskeletal proteins, ß-actin and ¿-tubulin, clustered at the cell leading edge and uropod, respectively, of polarized lymphocytes. Biochemical analysis showed that moesin coimmunoprecipitates with ICAM-3 in T lymphoblasts stimulated with either RANTES or the polarization- inducing anti-ICAM-3 HP2/19 mAb, as well as in the constitutively polarized T cell line HSB-2. In addition, moesin is associated with CD44, but not with ICAM-1, in polarized T lymphocytes. A correlation between the degree of moesin-ICAM-3 interaction and cell polarization was found as determined by immunofluorescence and immunoprecipitation analysis done in parallel. The moesin-ICAM-3 interaction was specifically mediated by the cytoplasmic domain of ICAM-3 as revealed by precipitation of moesin with a GST fusion protein containing the ICAM-3 cytoplasmic tail from metabolically labeled Jurkat T cell lysates. The interaction of moesin with ICAM-3 was greatly diminished when RANTES-stimulated T lymphoblasts were pretreated with the myosin-disrupting drug butanedione monoxime, which prevents lymphocyte polarization. Altogether, these data indicate that moesin interacts with ICAM-3 and CD44 adhesion molecules in uropods of polarized T cells; these data also suggest that these interactions participate in the formation of links between membrane receptors and the cytoskeleton, thereby regulating morphological changes during cell locomotion.

Micropatterning of single endothelial cell shape reveals a tight coupling between nuclear volume in G1 and proliferation

Shape-dependent local differentials in cell proliferation are considered to be a major driving mechanism of structuring processes in vivo, such as embryogenesis, wound healing, and angiogenesis. However, the specific biophysical signaling by which changes in cell shape contribute to cell cycle regulation remains poorly understood. Here, we describe our study of the roles of nuclear volume and cytoskeletal mechanics in mediating shape control of proliferation in single endothelial cells. Micropatterned adhesive islands were used to independently control cell spreading and elongation. We show that, irrespective of elongation, nuclear volume and apparent chromatin decondensation of cells in G1 systematically increased with cell spreading and highly correlated with DNA synthesis (percent of cells in the S phase). In contrast, cell elongation dramatically affected the organization of the actin cytoskeleton, markedly reduced both cytoskeletal stiffness (measured dorsally with atomic force microscopy) and contractility (measured ventrally with traction microscopy), and increased mechanical anisotropy, without affecting either DNA synthesis or nuclear volume. Our results reveal that the nuclear volume in G1 is predictive of the proliferative status of single endothelial cells within a population, whereas cell stiffness and contractility are not. These findings show that the effects of cell mechanics in shape control of proliferation are far more complex than a linear or straightforward relationship. Our data are consistent with a mechanism by which spreading of cells in G1 partially enhances proliferation by inducing nuclear swelling and decreasing chromatin condensation, thereby rendering DNA more accessible to the replication machinery.

On-line event detection by recursive dynamic principal component analysis and gas sensor arrays under drift conditions

Leakage detection is an important issue in many chemical sensing applications. Leakage detection hy thresholds suffers from important drawbacks when sensors have serious drifts or they are affected by cross-sensitivities. Here we present an adaptive method based in a Dynamic Principal Component Analysis that models the relationships between the sensors in the may. In normal conditions a certain variance distribution characterizes sensor signals. However, in the presence of a new source of variance the PCA decomposition changes drastically. In order to prevent the influence of sensor drifts the model is adaptive and it is calculated in a recursive manner with minimum computational effort. The behavior of this technique is studied with synthetic signals and with real signals arising by oil vapor leakages in an air compressor. Results clearly demonstrate the efficiency of the proposed method.

Entropy change of martensitic transformations in Cu-based shape-memory alloys

We have investigated the different contributions to the entropy change at the martensitic transition of different families of Cu-based shape-memory alloys. The total entropy change has been obtained through calorimetric measurements. By measuring the evolution of the magnetic susceptibility with temperature, the entropy change associated with conduction electrons has been evaluated. The contribution of the anharmonic vibrations of the lattice has also been estimated using various parameters associated with the anharmonic behavior of these alloys, collected from the literature. The results found in the present work have been compared to values published for the martensitic transition of group-IV metals. For Cu-based alloys, both electron and anharmonic contributions have been shown to be much smaller than the overall entropy change. This finding demonstrates that the harmonic vibrations of the lattice are the most relevant contribution to the stability of the bcc phase in Cu-based alloys.

Vibrational behaviour of bcc Cu-based shape memory alloys close to the martensitic transition

Experimental data from ultrasonic and inelastic neutron scattering measurements are analyzed for different families of Cu-based shape-memory alloys. It is shown that the transition occurs at a value, independent of composition and alloy family, of the ratio between the elastic constants associated with the two shears necessary to accomplish the lattice distortion from the bcc to the close-packed structure. The zone boundary frequency of the TA2[110] branch evaluated at the transition point (TM), weakly depends, for each family, on composition. A linear relationship between this frequency and the inverse of the elastic constant C', both quantities evaluated at TM, has been found, in agreement with the prediction of a Landau model proposed for martensitic transformations.

On the stability of the bcc phase in Cu-Al-Mn shape memory alloys

Measurements of the entropy change at the martensitic transition of two composition-related sets of Cu-Al-Mn shape-memory alloys are reported. It is found that most of the entropy change has a vibrational origin, and depends only on the particular close-packed structure of the low-temperature phase. Using data from the literature for other Cu-based alloys, this result is shown to be general. In addition, it is shown that the martensitic structure changes from 18R to 2H when the ratio of conduction electrons per atom reaches the same value as the eutectoid point in the equilibrium phase diagram. This finding indicates that the structure of the metastable low-temperature phase is reminiscent of the equilibrium structure.