SMART Protocols: seMAntic represenTation for experimental protocols

Two important characteristics of science are the ?reproducibility? and ?clarity?. By rigorous practices, scientists explore aspects of the world that they can reproduce under carefully controlled experimental conditions. The clarity, complementing reproducibility, provides unambiguous descriptions of results in a mechanical or mathematical form. Both pillars depend on well-structured and accurate descriptions of scientific practices, which are normally recorded in experimental protocols, scientific workflows, etc. Here we present SMART Protocols (SP), our ontology-based approach for representing experimental protocols and our contribution to clarity and reproducibility. SP delivers an unambiguous description of processes by means of which data is produced; by doing so, we argue, it facilitates reproducibility. Moreover, SP is thought to be part of e-science infrastructures. SP results from the analysis of 175 protocols; from this dataset, we extracted common elements. From our analysis, we identified document, workflow and domain-specific aspects in the representation of experimental protocols. The ontology is available at http://purl.org/net/SMARTprotocol

PCCMuTe v2.2: una herramienta para medir el consumo de energía en sistemas empotrados

Este Proyecto Fin de Grado (PFG) recoge el trabajo de depuración realizado sobre el prototipo PCCMuTe v2.2, un sistema empotrado que dispone de la instrumentación necesaria para medir el consumo de potencia/energía en cada uno de sus dominios de tensión, y posteriormente digitalizar y enviar los resultados al procesador que se encuentra en su interior. Su uso permite la obtención de información en tiempo real sobre el consumo del hardware de la placa, en especial del procesador, pudiendo relacionar la potencia consumida con el software ejecutado. El proyecto está orientado a medir el consumo de energía derivado de la decodificación de vídeo. El software utilizado para controlar el hardware se basa en Linux. En este proyecto se distinguen principalmente dos actividades, depuración hardware y depuración software. Los resultados muestran avances en la depuración hardware hasta obtener un prototipo en completo funcionamiento. Los avances en el apartado del software habilitan las comunicaciones SPI, necesarias para la transmisión de los resultados de consumo al procesador. En la fase final de este PFG se hace uso de una aplicación previamente desarrollada por miembros del GDEM con la que se obtienen los primeros datos de consumo, pero por falta de tiempo estos resultados no pueden ser verificados. Por la misma razón no ha sido posible diseñar y codificar una nueva aplicación que mejore la forma en la que se obtienen esos datos. ABSTRACT. This bachelor final project includes the debugging work done on the prototype PCCMuTe v2.2, an embedded system with the necessary instrumentation to measure the power/ energy consumption in each of its voltage domains, scan and send the results to its processor. The purpose of this device is to obtain real-time information about the hardware power consumption, especially from the processor, being able to relate the power consumed with the software executed. The project aims to measure the energy consumption of video decoding. The software used to control the hardware is based on Linux. In this project there are two main activities: hardware and software debugging. The results show advances in hardware debugging, and finally a fully functioning prototype is obtained. Advances in software debugging enable SPI communications, used to transmit the consumption data to the processor. In the last part of this final bachelor project an application previously coded by other members of the GDEM is used to obtain the first data. The results can not finally be verified because of the lack of time. For the same reason it is not possible to design and code a new application that improves the way the data is obtained.

Syndapin I, a Synaptic Dynamin-binding Protein that Associates with the Neural Wiskott-Aldrich Syndrome Protein

The GTPase dynamin has been clearly implicated in clathrin-mediated endocytosis of synaptic vesicle membranes at the presynaptic nerve terminal. Here we describe a novel 52-kDa protein in rat brain that binds the proline-rich C terminus of dynamin. Syndapin I (synaptic, dynamin-associated protein I) is highly enriched in brain where it exists in a high molecular weight complex. Syndapin I can be involved in multiple protein–protein interactions via a src homology 3 (SH3) domain at the C terminus and two predicted coiled-coil stretches. Coprecipitation studies and blot overlay analyses revealed that syndapin I binds the brain-specific proteins dynamin I, synaptojanin, and synapsin I via an SH3 domain-specific interaction. Coimmunoprecipitation of dynamin I with antibodies recognizing syndapin I and colocalization of syndapin I with dynamin I at vesicular structures in primary neurons indicate that syndapin I associates with dynamin I in vivo and may play a role in synaptic vesicle endocytosis. Furthermore, syndapin I associates with the neural Wiskott-Aldrich syndrome protein, an actin-depolymerizing protein that regulates cytoskeletal rearrangement. These characteristics of syndapin I suggest a molecular link between cytoskeletal dynamics and synaptic vesicle recycling in the nerve terminal.

A Novel Tetanus Neurotoxin-insensitive Vesicle-associated Membrane Protein in SNARE Complexes of the Apical Plasma Membrane of Epithelial Cells

The importance of soluble N-ethyl maleimide (NEM)-sensitive fusion protein (NSF) attachment protein (SNAP) receptors (SNAREs) in synaptic vesicle exocytosis is well established because it has been demonstrated that clostridial neurotoxins (NTs) proteolyze the vesicle SNAREs (v-SNAREs) vesicle-associated membrane protein (VAMP)/brevins and their partners, the target SNAREs (t-SNAREs) syntaxin 1 and SNAP25. Yet, several exocytotic events, including apical exocytosis in epithelial cells, are insensitive to numerous clostridial NTs, suggesting the presence of SNARE-independent mechanisms of exocytosis. In this study we found that syntaxin 3, SNAP23, and a newly identified VAMP/brevin, tetanus neurotoxin (TeNT)-insensitive VAMP (TI-VAMP), are insensitive to clostridial NTs. In epithelial cells, TI-VAMP–containing vesicles were concentrated in the apical domain, and the protein was detected at the apical plasma membrane by immunogold labeling on ultrathin cryosections. Syntaxin 3 and SNAP23 were codistributed at the apical plasma membrane where they formed NEM-dependent SNARE complexes with TI-VAMP and cellubrevin. We suggest that TI-VAMP, SNAP23, and syntaxin 3 can participate in exocytotic processes at the apical plasma membrane of epithelial cells and, more generally, domain-specific exocytosis in clostridial NT-resistant pathways.

Apical sorting of a voltage- and Ca2+-activated K+ channel α-subunit in Madin-Darby canine kidney cells is independent of N-glycosylation

The voltage- and Ca2+-activated K+ (KV,Ca) channel is expressed in a variety of polarized epithelial cells seemingly displaying a tissue-dependent apical-to-basolateral regionalization, as revealed by electrophysiology. Using domain-specific biotinylation and immunofluorescence we show that the human channel KV,Ca α-subunit (human Slowpoke channel, hSlo) is predominantly found in the apical plasma membrane domain of permanently transfected Madin-Darby canine kidney cells. Both the wild-type and a mutant hSlo protein lacking its only potential N-glycosylation site were efficiently transported to the cell surface and concentrated in the apical domain even when they were overexpressed to levels 200- to 300-fold higher than the density of intrinsic Slo channels. Furthermore, tunicamycin treatment did not prevent apical segregation of hSlo, indicating that endogenous glycosylated proteins (e.g., KV,Ca β-subunits) were not required. hSlo seems to display properties for lipid-raft targeting, as judged by its buoyant distribution in sucrose gradients after extraction with either detergent or sodium carbonate. The evidence indicates that the hSlo protein possesses intrinsic information for transport to the apical cell surface through a mechanism that may involve association with lipid rafts and that is independent of glycosylation of the channel itself or an associated protein. Thus, this particular polytopic model protein shows that glycosylation-independent apical pathways exist for endogenous membrane proteins in Madin-Darby canine kidney cells.

The Wheat Peptidyl Prolyl cis-trans-Isomerase FKBP77 Is Heat Induced and Developmentally Regulated1

We isolated a cDNA encoding a 568-amino acid, heat-stress-induced peptidyl prolyl isomerase belonging to the FK506-binding-protein (FKBP) family. The open reading frame encodes for a peptidyl prolyl isomerase that possesses three FKBP-12-like domains, a putative tetratricopeptide motif, and a calmodulin-binding domain. Specific antibodies showed that the open reading frame encodes a heat-induced 77-kD protein, the wheat FKBP77 (wFKBP77), which exhibits 84% identity with the wFKBP73 and 42% identity with the human FKBP59. Because of the high similarity in sequence to wFKBP73, wFKBP77 was designated as the heat-induced isoform. The wFKBP77 mRNA steady-state level was 14-fold higher at 37°C than at 25°C. The wFKBP77 transcript abundance was the highest in mature embryos that had imbibed and 2-d-old green shoots exposed to 37°C, and decreased to 6% in 6-d-old green shoots. The transcript level returned to the level detected at 25°C after recovery of the embryos for 90 min at 25°C. We compared wFKBP73 and wFKBP77 with the heat-shock proteins having cognate and heat-stress-induced counterparts.

Differential synaptic localization of two major gamma-aminobutyric acid type A receptor alpha subunits on hippocampal pyramidal cells.

Hippocampal pyramidal cells, receiving domain specific GABAergic inputs, express up to 10 different subunits of the gamma-aminobutyric acid type A (GABAA) receptor, but only 3 different subunits are needed to form a functional pentameric channel. We have tested the hypothesis that some subunits are selectively located at subsets of GABAergic synapses. The alpha 1 subunit has been found in most GABAergic synapses on all postsynaptic domains of pyramidal cells. In contrast, the alpha 2 subunit was located only in a subset of synapses on the somata and dendrites, but in most synapses on axon initial segments innervated by axo-axonic cells. The results demonstrate that molecular specialization in the composition of postsynaptic GABAA receptor subunits parallels GABAergic cell specialization in targeting synapses to a specific domain of postsynaptic cortical neurons.

Habilidades de processamento fonológico e de escrita em crianças com distúrbio específico de linguagem: um estudo comparativo com a normalidade

Introdução: Crianças com distúrbio específico de linguagem (DEL) são propensas a apresentar dificuldade no processo de alfabetização devido às múltiplas alterações de linguagem que possuem. Este estudo comparou e caracterizou o desempenho de crianças com DEL e em desenvolvimento típico de linguagem em atividades de aliteração, rima, memória de curto prazo fonológica, ditado de palavras e de pseudopalavras. A principal hipótese do estudo era de que o grupo DEL apresentaria desempenho inferior do que o grupo em desenvolvimento típico em todas as habilidades estudadas. Método: Participaram do estudo 12 crianças com DEL (GP) e 48 em desenvolvimento típico (GC) com idade entre 7 anos e 9 anos e 11 meses. Todos os sujeitos cursavam o 2º ou 3º ano do ensino fundamental I e apresentavam audição e rendimento intelectual não-verbal preservados. Para a seleção dos grupos foram utilizadas medidas de vocabulário receptivo, fonologia e nível socioeconômico. Já as medidas experimentais avaliadas foram testes padronizados de aliteração, rima, memória de curto prazo fonológica e a aplicação de um ditado de palavras e de pseudopalavras elaborados para esta pesquisa. Resultados: ambos os grupos apresentaram pior desempenho em tarefas de rima do que de aliteração e o GP apresentou desempenho inferior em ambas as tarefas quando comparado ao GC. A análise dos distratores nas atividades de aliteração e rima apontou que em tarefas de aliteração, o GP cometeu mais erros de tipologia semântico enquanto na prova de rima foram mais erros de tipologia fonológico. O GP obteve desempenho inferior ao GC nas avaliações da memória de curto prazo fonológica, ditado de palavras e de pseudopalavras. O GP evidenciou maior dificuldade no ditado de pseudopalavras no que no de palavras e o GC não apresentou diferença significativa no desempenho dos ditados. No ditado de palavras, o GP cometeu mais erros na palavra toda enquanto no ditado de pseudopalavras ocorreram mais erros na palavra toda e na sílaba final. Na comparação do desempenho dos grupos de acordo com a escolaridade, notou-se que os sujeitos do GC do 2º e 3º ano não evidenciaram diferença significativa em seu desempenho nas tarefas, enquanto os sujeitos do GP do 3º ano apresentaram melhor desempenho do que os do 2º ano em todas as medidas experimentais, com exceção da memória de curto prazo fonológica. Conclusões: o GP apresentou dificuldade em tarefas de processamento fonológico e de escrita que foram realizadas com relativa facilidade pelo GC. Os sujeitos com DEL evidenciaram uma análise mais global dos estímulos apresentados nas tarefas de consciência fonológica, o que os fez desprezar aspectos segmentais importantes. A dificuldade em abordar as informações de modo analítico, somado a alterações linguísticas e do processamento fonológico, levou o GP a apresentar maior taxa de erros nas tarefas de ditado. Apesar das alterações apontadas, os sujeitos do GP do 3º ano obtiveram melhor desempenho do que os do 2º ano em todas as habilidades com exceção da memória de curto prazo fonológica, que é sua marca clínica. Estes dados reforçam a necessidade do diagnóstico e intervenção precoces para esta população, onde as habilidades abordadas neste estudo devem ser incluídas no processo terapêutico

Transfer of Pattern Recall Skills May Contribute to the Development of Sport Expertise

Superior recall of domain-specific patterns is well established as a defining attribute of expert performers. Recent studies on the developmental histories of expert team ball sport players (e.g. Baker, Côté, & Abernethy, 2003a) also suggest that experts characteristically receive exposure to a wide range of sports in their developing years and that this related sports experience may reduce the amount of sport-specific training needed to become an expert. This study examined whether the facilitation of expertise associated with other sport experience might arise from positive transfer of pattern recall skills from one sport to another. Expert netball, basketball and field hockey players and experienced non-experts performed a recall task for patterns of play derived from each of these sports. Experts from sports different to those shown in the presented pattern consistently outperformed non-experts in their recall of defensive player positions, suggesting some selective transfer of pattern recall skills may indeed be possible

Évaluation des connaissances morphologiques dérivationnelles d’apprentis-lecteurs présentant une dysphasie

La dysphasie consiste en une atteinte sévère et persistante de l’acquisition et du développement du langage oral. Les élèves qui en sont atteints peinent à devenir des lecteurs habiles et sont à haut risque d’échec scolaire. Si ce trouble très complexe est étudié dans différents domaines (la santé et l’éducation, entre autres), peu d’études se sont spécifiquement intéressées à vérifier si les élèves dysphasiques possèdent des connaissances morphologiques dérivationnelles. Or, depuis un certain nombre d’années, de nombreux chercheurs soutiennent que ces connaissances, qui concernent la forme des mots et leurs règles de formation, peuvent constituer une stratégie supplémentaire aidante pour les élèves aux prises avec un déficit phonologique, comme les élèves dysphasiques. C’est dans ce cadre que se situe la présente étude, dont l’objectif général est d’évaluer les connaissances morphologiques dérivationnelles d’apprentis-lecteurs dysphasiques francophones du primaire. Pour y parvenir, trois tâches morphologiques, soit une tâche de jugement de relation, une tâche de dérivation et une tâche de plausibilité, ont été soumises à trois groupes de participants dont un groupe d’élèves dysphasiques (D=30) et deux groupes contrôles, c’est-à-dire des élèves du même âge chronologique (CA, n=30) et des élèves plus jeunes, mais du même niveau de lecture (CL, n=30). Nos résultats montrent que l’ensemble des trois groupes de participants a tiré profit des unités morphologiques contenues dans les items pour réussir les tâches proposées, les dysphasiques obtenant des résultats inférieurs aux CA mais comparables aux CL. Toutefois, ces résultats ne s’apparentent pas tout à fait au continuum de développement des connaissances morphologiques dérivationnelles établi par Tyler et Nagy (1989). De plus, aucun effet du type d’affixation (items préfixés vs suffixés) n’a été observé. Les résultats obtenus nous permettent de proposer des pistes d’interventions orthodidactiques visant l’enseignement de la morphologie dérivationnelle auprès des élèves aux prises avec des difficultés de lecture, à l’instar des participants dysphasiques qui ont participé à cette étude.

The Moldable Inspector

Object inspectors are an essential category of tools that allow developers to comprehend the run-time of object-oriented systems. Traditional object inspectors favor a generic view that focuses on the low-level details of the state of single objects. Based on 16 interviews with software developers and a follow-up survey with 62 respondents we identified a need for object inspectors that support different high-level ways to visualize and explore objects, depending on both the object and the current developer need. We propose the Moldable Inspector, a novel inspector model that enables developers to adapt the inspection workflow to suit their immediate needs by making the inspection context explicit, providing multiple interchangeable domain-specific views for each object, and supporting a workflow that groups together multiple levels of connected objects. We show that the Moldable Inspector can address multiple kinds of development needs involving a wide range of objects.

Towards moldable development tools

Developers commonly ask detailed and domain-specific questions about the software systems they are developing and maintaining. Integrated development environments (IDEs) form an essential category of tools for developing software that should support software engineering decision making. Unfortunately, rigid and generic IDEs that focus on low-level programming tasks, that promote code rather than data, and that suppress customization, offer limited support for informed decision making during software development. We propose to improve decision making within IDEs by moving from generic to context-aware IDEs through moldable tools. In this paper, we promote the idea of moldable tools, illustrate it with concrete examples, and discuss future research directions.

Évaluation des connaissances morphologiques dérivationnelles d’apprentis-lecteurs présentant une dysphasie

La dysphasie consiste en une atteinte sévère et persistante de l’acquisition et du développement du langage oral. Les élèves qui en sont atteints peinent à devenir des lecteurs habiles et sont à haut risque d’échec scolaire. Si ce trouble très complexe est étudié dans différents domaines (la santé et l’éducation, entre autres), peu d’études se sont spécifiquement intéressées à vérifier si les élèves dysphasiques possèdent des connaissances morphologiques dérivationnelles. Or, depuis un certain nombre d’années, de nombreux chercheurs soutiennent que ces connaissances, qui concernent la forme des mots et leurs règles de formation, peuvent constituer une stratégie supplémentaire aidante pour les élèves aux prises avec un déficit phonologique, comme les élèves dysphasiques. C’est dans ce cadre que se situe la présente étude, dont l’objectif général est d’évaluer les connaissances morphologiques dérivationnelles d’apprentis-lecteurs dysphasiques francophones du primaire. Pour y parvenir, trois tâches morphologiques, soit une tâche de jugement de relation, une tâche de dérivation et une tâche de plausibilité, ont été soumises à trois groupes de participants dont un groupe d’élèves dysphasiques (D=30) et deux groupes contrôles, c’est-à-dire des élèves du même âge chronologique (CA, n=30) et des élèves plus jeunes, mais du même niveau de lecture (CL, n=30). Nos résultats montrent que l’ensemble des trois groupes de participants a tiré profit des unités morphologiques contenues dans les items pour réussir les tâches proposées, les dysphasiques obtenant des résultats inférieurs aux CA mais comparables aux CL. Toutefois, ces résultats ne s’apparentent pas tout à fait au continuum de développement des connaissances morphologiques dérivationnelles établi par Tyler et Nagy (1989). De plus, aucun effet du type d’affixation (items préfixés vs suffixés) n’a été observé. Les résultats obtenus nous permettent de proposer des pistes d’interventions orthodidactiques visant l’enseignement de la morphologie dérivationnelle auprès des élèves aux prises avec des difficultés de lecture, à l’instar des participants dysphasiques qui ont participé à cette étude.

Hodgkin's lymphoma cell lines express a fusion protein encoded by intergenically spliced mRNA for the multilectin receptor DEC-205 (CD205) and a novel C-type lectin receptor DCL-1

Classic Hodgkin's lymphoma (HL) tissue contains a small population of morphologically distinct malignant cells called Hodgkin and Reed-Sternberg (HRS) cells, associated with the development of HL. Using 3'-rapid amplification of cDNA ends ( RACE) we identified an alternative mRNA for the DEC-205 multilectin receptor in the HRS cell line L428. Sequence analysis revealed that the mRNA encodes a fusion protein between DEC-205 and a novel C-type lectin DCL-1. Although the 7.5-kb DEC-205 and 4.2-kb DCL-1 mRNA were expressed independently in myeloid and B lymphoid cell lines, the DEC-205/DCL-1 fusion mRNA (9.5 kb) predominated in the HRS cell lines ( L428, KM-H2, and HDLM-2). The DEC-205 and DCL-1 genes comprising 35 and 6 exons, respectively, are juxtaposed on chromosome band 2q24 and separated by only 5.4 kb. We determined the DCL-1 transcription initiation site within the intervening sequence by 5'-RACE, confirming that DCL-1 is an independent gene. Two DEC-205/DCL-1 fusion mRNA variants may result from cotranscription of DEC-205 and DCL-1, followed by splicing DEC-205 exon 35 or 34-35 along with DCL-1 exon 1. The resulting reading frames encode the DEC-205 ectodomain plus the DCL-1 ectodomain, the transmembrane, and the cytoplasmic domain. Using DCL-1 cytoplasmic domain-specific polyclonal and DEC-205 monoclonal antibodies for immunoprecipitation/Western blot analysis, we showed that the fusion mRNA is translated into a DEC-205/DCL-1 fusion protein, expressed in the HRS cell lines. These results imply an unusual transcriptional control mechanism in HRS cells, which cotranscribe an mRNA containing DEC-205 and DCL-1 prior to generating the intergenically spliced mRNA to produce a DEC-205/DCL-1 fusion protein.

The application of cognitive orientation to daily occupational performance (CO-OP) with children 5-7 years with developmental coordination disorder

There has been an increase in the use of cognitive frameworks in occupational therapy with children with developmental coordination disorder (DCD). Investigations into the utility of one such cognitive approach, namely Cognitive Orientation to (daily) Occupational Performance (CO-OP), with children with DCD have shown the intervention to be effective with children over 7 years. However, there has been limited research into its utility with younger children. This paper presents two case studies to demonstrate the use of CO-OP with children aged 5-7 years. Two boys with DCD engaged in 10 sessions of CO-OP. These younger children were found to be able to use the global framework (Goal, Plan, Do, Check) to improve their task performance, to develop plans using domain-specific strategies and to engage in checking strategies. Issues relating to attention, motivation and goal setting are discussed in the context of the two case studies.