Precursor ion scans for the targeted detection of stable-isotope-labeled peptides.

Stable isotope labels are routinely introduced into proteomes for quantification purposes. Full labeling of cells in varying biological states, followed by sample mixing, fractionation and intensive data acquisition, is used to obtain accurate large-scale quantification of total protein levels. However, biological processes often affect only a small group of proteins for a short time, resulting in changes that are difficult to detect against the total proteome background. An alternative approach could be the targeted analysis of the proteins synthesized in response to a given biological stimulus. Such proteins can be pulse-labeled with a stable isotope by metabolic incorporation of 'heavy' amino acids. In this study we investigated the specific detection and identification of labeled proteins using acquisition methods based on Precursor Ion Scans (PIS) on a triple-quadrupole ion trap mass spectrometer. PIS-based methods were set to detect unique immonium ions originating from labeled peptides. Different labels and methods were tested in standard mixtures to optimize performance. We showed that, in comparison with an untargeted analysis on the same instrument, the approach allowed a several-fold increase in the specificity of detection of labeled proteins over unlabeled ones. The technique was applied to the identification of proteins secreted by human cells into growth media containing bovine serum proteins, allowing the preferential detection of labeled cellular proteins over unlabeled bovine ones. However, compared with untargeted acquisitions on two different instruments, the PIS-based strategy showed some limitations in sensitivity. We discuss possible perspectives of the technique.

Efficient in vivo induction of CTL by cell-associated covalent H-2Kd-peptide complexes.

A novel procedure is presented describing the induction of antigen-specific cytolytic T lymphocytes (CTL) in vivo, that uses as immunogen syngeneic Concanavalin A stimulated spleen cells expressing H-2Kd (Kd) molecules photocrosslinked with a photoreactive peptide derivative. The Kd restricted Plasmodium berghei circumsporozoite (PbCS) peptide 253-260 (YIPSAEKI) was conjugated with photoreactive iodo-4-azidosalicylic acid (IASA) at the NH2-terminus and with 4-azidobenzoic acid (ABA) at the TCR contact residue Lys259 to make IASA-YIPSAEK(ABA)I. Selective photoactivation of the IASA group allowed specific photoaffinity labeling of cell-associated Kd molecules. Optimal peptide derivative binding to Kd molecules of concanavalin A stimulated spleen cells was obtained upon 4-6 h incubation at 26 degrees C in the presence of human beta 2 microglobulin. Photocrosslinking prevented the rapid dissociation of cell-associated Kd-peptide derivative complexes at 37 degrees C. The photoaffinity labeled cells were injected i.p. into syngeneic recipients. After 10 days, the peritoneal exudate lymphocytes were harvested and in vitro stimulated with peptide derivative pulsed P815 mastocytoma cells. The resulting bulk cultures displayed high cytolytic activity that was specific for IASA-YIPSAEK(ABA)I and YIPSAEK(ABA)I. In contrast, peritoneal exudate lymphocytes from mice inoculated with concanavalin A blasts that were pulsed, but not photocrosslinked, with IASA-YIPSAEK(ABA)I expressed only marginal levels of IASA-YIPSAEK(ABA)I-specific cytolytic activity. This immunization strategy, using neither adjuvants nor potentially hazardous transfected/transformed cells, is safe and should be universally applicable.

Diseñador de Formularios Web Wform

El presente proyecto tiene como finalidad facilitar al desarrollador y usuario en general el diseño de formularios en forma visual, haciendo uso de los componentes frecuentemente utilizados como cajas de texto, etiquetas, áreas de texto, calendarios, casillas de selección, listas desplegables, entre otros para generar código xhtml con JavaServerFaces.Para este fin me he basado en el diseñador de formularios de Joget Workflow, el cual posee una licencia GPLv2, permitiendo modificar su código, está desarrollado bajo Java, dicho diseñador de formulario tiene un entorno web, los cuales son utilizados e interpretados únicamente por su suite, utiliza en la vista páginas JSP y dentro de ellas JSON (JavaScript Object Notation), para el negocio utiliza el framework Spring y para la persistencia Hibernate. Joget persiste en la Base de Datos MySQL y se sugiere alojarse en un servidor Apache Tomcat, pero podría alojarse en cualquiera servidor de aplicaciones web para Java como Jboss Server Applicaction, Glassfish, entre otros.El diseñador de formularios permite la gestión de los formularios como crear, editar y/o eliminar formularios, y generar archivos código XHTML para JSF (Java Server Faces)ayudándolo en gran medida a un desarrollador especialmente de JAVA a visualizar comoquedará su formulario, menor tiempo en la construcción y personalizar su formulario a través de la modificación del código generado.

Distintiu de garantia de qualitat ambiental per a equipaments culturals: aplicació pilot en biblioteques

El DGQA per a Equipaments Culturals és un distintiu per a la certificació ambiental de biblioteques i museus. L’objectiu del projecte és avaluar el distintiu mitjançant una aplicació pilot en 26 biblioteques de la província de Barcelona, i proposar millores tant per al distintiu com per a les biblioteques. També es pretén fer recerca sobre l’ecoetiquetatge de serveis, ja que és un àmbit poc desenvolupat, i sobre el sistema d’estudi, les biblioteques. Una anàlisi de les ecoetiquetes a nivell mundial, considerant 4 macroregions, ha permès caracteritzar les ecoetiquetes i determinar la situació actual dels serveis en l’ecoetiquetatge. Hi han variacions en el nombre de categories entre ecoetiquetes, i el percentatge de categories de serveis és, en general, reduït (8% de mitjana). Els subsectors serveis dominants són els d’Hosteleria, serveis de neteja i comerç. No hi ha cap experiència de certificació ambiental de serveis culturals, per tant, l’ecoetiquetatge de serveis culturals és un àmbit nou. El sistema d’estudi són 26 biblioteques de la província de Barcelona. L’aplicació del distintiu a aquestes s’ha dut a terme realitzant treball de camp a cadascuna per tal de determinar el seu estat ambiental. Posteriorment, s’han analitzat les dades per establir el grau de compliment de cadascuna. La majoria de les biblioteques (85%) compleixen més de la meitat dels criteris bàsics, i un 60% superen la puntuació mínima de compliment dels criteris opcionals. Els resultats obtinguts han permès avaluar la viabilitat de la implantació del distintiu, a través de l’anàlisi de cadascun dels seus criteris. Per tal de millorar les possibilitats d’èxit en la implantació del distintiu, s’han aportat un seguit de propostes a nivell individual i col·lectiu. S’ha realitzat una fitxa per a cadascuna de les 26 biblioteques, per tal d’orientar els gestors de les biblioteques en l’adopció de mesures per a l’acompliment dels criteris. També s’han inclòs propostes a l’avaluació dels criteris, dirigides als gestors del distintiu.

Asymmetric tunnels in P2MP LSPs as a label space reduction method

The objective of traffic engineering is to optimize network resource utilization. Although several works have been published about minimizing network resource utilization, few works have focused on LSR (label switched router) label space. This paper proposes an algorithm that takes advantage of the MPLS label stack features in order to reduce the number of labels used in LSPs. Some tunnelling methods and their MPLS implementation drawbacks are also discussed. The described algorithm sets up NHLFE (next hop label forwarding entry) tables in each LSR, creating asymmetric tunnels when possible. Experimental results show that the described algorithm achieves a great reduction factor in the label space. The presented works apply for both types of connections: P2MP (point-to-multipoint) and P2P (point-to-point)

A Label space reduction algorithm for P2MP LSPs using asymmetric tunnels

The aim of traffic engineering is to optimise network resource utilization. Although several works on minimizing network resource utilization have been published, few works have focused on LSR label space. This paper proposes an algorithm that uses MPLS label stack features in order to reduce the number of labels used in LSPs forwarding. Some tunnelling methods and their MPLS implementation drawbacks are also discussed. The algorithm described sets up the NHLFE tables in each LSR, creating asymmetric tunnels when possible. Experimental results show that the algorithm achieves a large reduction factor in the label space. The work presented here applies for both types of connections: P2MP and P2P

Mapping sub-flows to p2mp LSPs

In previous work we proposed a multi-objective traffic engineering scheme (MHDB-S model) using different distribution trees to multicast several flows. In this paper, we propose a heuristic algorithm to create multiple point-to-multipoint (p2mp) LSPs based on the optimum sub-flow values obtained with our MHDB-S model. Moreover, a general problem for supporting multicasting in MPLS networks is the lack of labels. To reduce the number of labels used, a label space reduction algorithm solution is also considered

SuperSense tagger for Italian

In this paper we present the procedure we followed to develop the Italian Super Sense Tagger. In particular, we adapted the English SuperSense Tagger to the Italian Language by exploiting a parallel sense labeled corpus for training. As for English, the Italian tagger uses a fixed set of 26 semantic labels, called supersenses, achieving a slightly lower accuracy due to the lower quality of the Italian training data. Both taggers accomplish the same task of identifying entities and concepts belonging to a common set of ontological types. This parallelism allows us to define effective methodologies for a broad range of cross-language knowledge acquisition tasks.

Hierarchical categorisation of tags for delicious

In the scenario of social bookmarking, a user browsing the Web bookmarks web pages and assigns free-text labels (i.e., tags) to them according to their personal preferences. In this technical report, we approach one of the practical aspects when it comes to represent users' interests from their tagging activity, namely the categorization of tags into high-level categories of interest. The reason is that the representation of user profiles on the basis of the myriad of tags available on the Web is certainly unfeasible from various practical perspectives; mainly concerning the unavailability of data to reliably, accurately measure interests across such fine-grained categorisation, and, should the data be available, its overwhelming computational intractability. Motivated by this, our study presents the results of a categorization process whereby a collection of tags posted at Delicious #http://delicious.com# are classified into 200 subcategories of interest.

Medium-sized neurofilament protein related to maturation of a subset of cortical neurons.

Neurofilaments are typical structures of the neuronal cytoskeleton and participate in the formation and stabilization of the axonal and dendritic architecture. In this study, we have characterized a murine monoclonal antibody, FNP7, that is directed against the medium-sized neurofilament subunit NF-M. This antibody identifies a subset of neurons in the cerebral cortex of various species including human and in organotypic cultures of rat cortex. In the neocortex of all species examined, the antibody labels pyramidal cells in layers III, V, and VI, with a distinctive laminar distribution between architectonic boundaries. In comparison with other antibodies directed against NF-M, the FNP7 antibody identifies on blots two forms of NF-M that appear relatively late during development, at the time when dynamic growth of processes changes to the stabilization of the formed processes. Dephosphorylation with alkaline phosphatase unmasks the site, making it detectable for the FNP7 antibody. The late appearance suggests that the site is present during early development in phosphorylated form and with increasing maturation becomes dephosphorylated, mainly in dendrites. This event may relate to changes in cytoskeleton stability in a late phase of dendritic maturation. Furthermore, mainly corticofugal projections and only few callosal axons are stained, suggesting a differential phosphorylation in a subset of axons. The antibody provides a useful marker to study subsets of pyramidal cells in vivo, in vitro, and under experimental conditions.

Eduard Toldrà : sis sonets per a violí i piano

Eduard Toldrà i Soler fou una persona important i significativa per a la societat catalana de principis del segle XX. La seva vida musical és increïblement ampla, ja que abasta facetes de violinista, compositor, director i pedagog. A més, Toldrà va estar sempre immers en la cultura catalana, en l'art en general, i en particular en la poesia. És per aquest motiu que trobem tanta poesia en la seva música. En el següent treball aprofundeixo en l'estudi d'una de les seves obres, Sis Sonets per a violí i piano. A través de l'anàlisi d'aquestes sis peces, coneixerem també al personatge d'Eduard Toldrà i el seu context cultural. Veurem que la seva música se situa fora dels trets estilístics “hispànics” de l'època i que, sota els tòpics de música española, les etiquetes no hi fan cap mena de justícia.

The Swiss regulatory framework for pædiatric health research

Medical research on minors entails both risks and benefits. Under Swiss law, clinical trials on children, including nontherapeutic drug trials, are permissible. However, ethics committees must systematically verify that all clinical studies have a favorable risk-benefit profile. Additional safeguards are designed to ensure that children are not unnecessarily involved in research and that proper consent is always obtained. Federal Swiss law is undergoing revision to extend these protections beyond clinical trials to a broad array of health research. The Swiss drug agency also seeks to improve the incentives for pharmaceutical firms to develop new paediatric drugs and relevant paediatric drug labels.

Art painting Data Collection

The classification of Art painting images is a computer vision applications that isgrowing considerably. The goal of this technology, is to classify an art paintingimage automatically, in terms of artistic style, technique used, or its author. For thispurpose, the image is analyzed extracting some visual features. Many articlesrelated with these problems have been issued, but in general the proposed solutionsare focused in a very specific field. In particular, algorithms are tested using imagesat different resolutions, acquired under different illumination conditions. Thatmakes complicate the performance comparison of the different methods. In thiscontext, it will be very interesting to construct a public art image database, in orderto compare all the existing algorithms under the same conditions. This paperpresents a large art image database, with their corresponding labels according to thefollowing characteristics: title, author, style and technique. Furthermore, a tool thatmanages this database have been developed, and it can be used to extract differentvisual features for any selected image. This data can be exported to a file in CSVformat, allowing researchers to analyze the data with other tools. During the datacollection, the tool stores the elapsed time in the calculation. Thus, this tool alsoallows to compare the efficiency, in computation time, of different mathematicalprocedures for extracting image data.

Covalent assembly of a soluble T cell receptor-peptide-major histocompatibility class I complex.

We used stepwise photochemical cross-linking for specifically assembling soluble and covalent complexes made of a T-cell antigen receptor (TCR) and a class I molecule of the major histocompatibility complex (MHC) bound to an antigenic peptide. For that purpose, we have produced in myeloma cells a single-chain Fv construct of a TCR specific for a photoreactive H-2Kd-peptide complex. Photochemical cross-linking of this TCR single-chain Fv with a soluble form of the photoreactive H-2Kd-peptide ligand resulted in the formation of a ternary covalent complex. We have characterized the soluble ternary complex and showed that it reacted with antibodies specific for epitopes located either on the native TCR or on the Kd molecules. By preventing the fast dissociation kinetics observed with most T cell receptors, this approach provides a means of preparing soluble TCR-peptide-MHC complexes on large-scale levels.

Interaction of antigenic peptides with MHC class I molecules on living cells studied by photoaffinity labeling.

Using a direct binding assay based on photoaffinity labeling, we have studied the interaction of antigenic peptides with murine MHC class I molecules on living cells. Photoreactive derivatives were prepared by N-terminal amidation with iodo, 4-azido salicylic acid of the Kd restricted Plasmodium berghei circumsporozoite (P.b. CS) peptide 253-260 (YIPSAEKI) and the Db-restricted Adenovirus 5 early region 1A (Ad5 E1A) peptide 234-243 (SGPSNTPPEI). As assessed in functional competition experiments, both peptide derivatives retained the specific binding activity of the parental peptides for Kd or Dd, respectively. The P.b. CS photoprobe specifically labeled Kd molecules on P815 (H-2d) cells, but failed to label RMA (H-2b) cells. Conversely, the Ad5 E1A photoprobe specifically labeled Db molecules on RMA cells, but failed to label P815 cells. When the two photoprobes were tested on a panel of Con A-activated spleen cells expressing 10 different H-2 haplotypes, significant photoaffinity labeling was observed only on H-2d cells with the P.b. CS photoprobe and on H-2b cells with the Ad5 E1A photoprobe. Labeling of cell-associated Kd or Db molecules with the photoprobes was specifically inhibited by antigenic peptides known to be presented by the same class I molecule. Photoaffinity labeling of Kd with the P.b. CS photoprobe was used to study the dynamics of peptide binding on living P815 cells. Binding increased steadily with the incubation period (up to 8 h) at 37 degrees C and at ambient temperature, but was greatly reduced (greater than 95%) at 0 to 4 degrees C or in the presence of ATP synthesis inhibitors. The magnitude of the labeling was twofold higher at room temperature than at 37 degrees C. In contrast, binding to isolated Kd molecules in solution rapidly reached maximal binding, particularly at 37 degrees C. Dissociation of the photoprobe from either cell-associated or soluble Kd molecules was similar, with a half time of approximately 1 h at 37 degrees C, whereas the complexes were long-lived at 4 degrees C in both instances.