EasyInterface: a toolkit for the rapid development of GUIs for research prototype tools

During the lifetime of a research project, different partners develop several research prototype tools that share many common aspects. This is equally true for researchers as individuals and as groups: during a period of time they often develop several related tools to pursue a specific research line. Making research prototype tools easily accessible to the community is of utmost importance to promote the corresponding research, get feedback, and increase the tools’ lifetime beyond the duration of a specific project. One way to achieve this is to build graphical user interfaces (GUIs) that facilitate trying tools; in particular, with web-interfaces one avoids the overhead of downloading and installing the tools. Building GUIs from scratch is a tedious task, in particular for web-interfaces, and thus it typically gets low priority when developing a research prototype. Often we opt for copying the GUI of one tool and modifying it to fit the needs of a new related tool. Apart from code duplication, these tools will “live” separately, even though we might benefit from having them all in a common environment since they are related. This work aims at simplifying the process of building GUIs for research prototypes tools. In particular, we present EasyInterface, a toolkit that is based on novel methodology that provides an easy way to make research prototype tools available via common different environments such as a web-interface, within Eclipse, etc. It includes a novel text-based output language that allows to present results graphically without requiring any knowledge in GUI/Web programming. For example, an output of a tool could be (a structured version of) “highlight line number 10 of file ex.c” and “when the user clicks on line 10, open a dialog box with the text ...”. The environment will interpret this output and converts it to corresponding visual e_ects. The advantage of using this approach is that it will be interpreted equally by all environments of EasyInterface, e.g., the web-interface, the Eclipse plugin, etc. EasyInterface has been developed in the context of the Envisage [5] project, and has been evaluated on tools developed in this project, which include static analyzers, test-case generators, compilers, simulators, etc. EasyInterface is open source and available at GitHub2.

Experiencia de la Escuela de Bibliotecología, Documentación e Información en el Desarrollo de Bases de Datos con el Programa Computacional Microisis Versión 3.0

En el campo bibliotecológico para desarrollar instrumentos de trabajo que nos permitan comunicarnos con las demás unidades y clientes de información, debemos pensar en normalizar nuestros procesos.Normalizar, en el sentido más amplio, significa seguir reglas que hagan un registro uniforme en cualquier lugar del mundo. Esto se logra mediante la aplicación de códigos y normas que han sido aceptadas internacionalmente por los organismos creados para este fin.El valor de la normalización estriba en evitar la duplicación de los esfuerzos de la catalogación en las diferentes unidades de información documental y facilitar el intercambio de datos bibliográficos tan pronto como sea posible. También, cosiste en darle al cliente la posibilidad de localizar la información en un a forma homogénea que obvie las barreras idiomáticas.

Identyfikacja i wielkoskalowa analiza retrogenów w genomach zwierzęcych

Wydział Biologii

Algorithmes de construction et correction d'arbres de gènes par la réconciliation

Les gènes, qui servent à encoder les fonctions biologiques des êtres vivants, forment l'unité moléculaire de base de l'hérédité. Afin d'expliquer la diversité des espèces que l'on peut observer aujourd'hui, il est essentiel de comprendre comment les gènes évoluent. Pour ce faire, on doit recréer le passé en inférant leur phylogénie, c'est-à-dire un arbre de gènes qui représente les liens de parenté des régions codantes des vivants. Les méthodes classiques d'inférence phylogénétique ont été élaborées principalement pour construire des arbres d'espèces et ne se basent que sur les séquences d'ADN. Les gènes sont toutefois riches en information, et on commence à peine à voir apparaître des méthodes de reconstruction qui utilisent leurs propriétés spécifiques. Notamment, l'histoire d'une famille de gènes en terme de duplications et de pertes, obtenue par la réconciliation d'un arbre de gènes avec un arbre d'espèces, peut nous permettre de détecter des faiblesses au sein d'un arbre et de l'améliorer. Dans cette thèse, la réconciliation est appliquée à la construction et la correction d'arbres de gènes sous trois angles différents: 1) Nous abordons la problématique de résoudre un arbre de gènes non-binaire. En particulier, nous présentons un algorithme en temps linéaire qui résout une polytomie en se basant sur la réconciliation. 2) Nous proposons une nouvelle approche de correction d'arbres de gènes par les relations d'orthologie et paralogie. Des algorithmes en temps polynomial sont présentés pour les problèmes suivants: corriger un arbre de gènes afin qu'il contienne un ensemble d'orthologues donné, et valider un ensemble de relations partielles d'orthologie et paralogie. 3) Nous montrons comment la réconciliation peut servir à "combiner'' plusieurs arbres de gènes. Plus précisément, nous étudions le problème de choisir un superarbre de gènes selon son coût de réconciliation.

EXPLICIT WRITTEN CORRECTIVE FEEDBACK AND LANGUAGE APTITUDE IN SLA: IMPLICATIONS FOR IMPROVEMENT OF LINGUISTIC ACCURACY

Most second language researchers agree that there is a role for corrective feedback in second language writing classes. However, many unanswered questions remain concerning which linguistic features to target and the type and amount of feedback to offer. This study examined two new pieces of writing by 151 learners of English as a Second Language (ESL), in order to investigate the effect of direct and metalinguistic written feedback on errors with the simple past tense, the present perfect tense, dropped pronouns, and pronominal duplication. This inquiry also considered the extent to which learner differences in language-analytic ability (LAA), as measured by the LLAMA F, mediated the effects of these two types of explicit written corrective feedback. Learners in the feedback groups were provided with corrective feedback on two essays, after which learners in all three groups completed two additional writing tasks to determine whether or not the provision of corrective feedback led to greater gains in accuracy compared to no feedback. Both treatment groups, direct and metalinguistic, performed better than the comparison group on new pieces of writing immediately following the treatment sessions, yet direct feedback was more durable than metalinguistic feedback for one structure, the simple past tense. Participants with greater LAA proved more likely to achieve gains in the direct feedback group than in the metalinguistic group, whereas learners with lower LAA benefited more from metalinguistic feedback. Overall, the findings of the present study confirm the results of prior studies that have found a positive role for written corrective feedback in instructed second language acquisition.

La imagen en el discurso multimodal cortazariano, una poética en movimiento

The selection and proposed cortazarian image in multimodal speech, a poetic moving as a doctoral thesis title, is the result of a process that forms several progressive stages. more than satisfy our curiosity and literary artistic concerns, the questions multiply increases our desire to bring more creative Cortazarian the colossus, that not only ruins a way of making literature , but in its revolutionary labyrinth gives a turn of the screw to the already tangled world of artistic writing , breaking in 1967 with the first of four hybrids books, La vuelta al día en ochenta mundos through which converts the traditional plastic unitextual and unimodal space in a palempsesto inexhaustible generator senses and meanings. Far from appeasing the wrath of conservative critics, caused by his narrative masterpiece, Hopscotch (1963), sparked the debate to denounce the regression of the classic molds of writing, proposing the imagination as the setting for creative freedom, it is not as arbitrary and nonsense, but as a process of higher state of consciousness in which it operates an underlying logic. Hence, our objective is to crawl into the underworld and plastics other multisígnicas border spaces, fleeting and ephemeral alliances that relate not just as complementary and similar texts which may be the same speech and can transmit the same, but quite the contrary, the oft-repeated notion of analogy is the first victim, fortunately, this kind of creative-artistic operations that raise the creative act to a sublime state capable of converting the inexhaustible multitextuales constellations in different ways: opposition, confrontation, invasion, dialogue, shadow, duplication, theft, etc. However this multiple transgression pushed to the limit by Julio Cortazar and his friend Julio Silva through four books proposed for analysis often does not translate into jobs and research in literature departments of the universities of the world, nor the critics are echoes the striking abundance and clarity of expression multimodal phenomenon as is the case with other works of Cortazar unimodal type, which makes it impassable fences mysterious worlds...

Aa necessidades de informação conducentes ao desenvolvimento da contabilidade de gestão na GNR

O presente trabalho de investigação aplicado perspetiva os contributos do desenvolvimento da contabilidade de gestão na Guarda subordina-se ao tema: “As necessidades de informação conducentes ao desenvolvimento da contabilidade de gestão na Guarda Nacional Republicana”. Para a prossecução da investigação, adotou-se o modelo hipotético-dedutivo. Assim sendo, o estudo prima por verificar as hipóteses, responder às perguntas derivadas e tem o propósito último de dar resposta à questão de partida. A metodologia empregue na realização deste trabalho de investigação, foi delineada por Quivy & Campenhoudt (2008) e Sarmento (2013), na qual a análise documental e a pesquisa bibliográfica, as entrevistas, os inquéritos por questionário e as observações diretas foram os procedimentos de recolha de dados empregues. Este trabalho de investigação é constituído por cinco capítulos, esquematizados em três partes, designadamente a Parte I – Enquadramento teórico, a Parte II – Parte prática e as conclusões e recomendações. Na parte I, são apresentados conceitos teóricos, nomeadamente a definição de informação e os conceitos relacionados com os sistemas de informação. Em seguida, é efetuada a abordagem teórica aos conceitos, finalidade e contributos da contabilidade de gestão. A parte II expõe os métodos e procedimentos utilizados, a análise e discussão dos resultados obtidos e são expostas as principais necessidades de informação de gestão das chefias. As conclusões e recomendações futuras são redigidas no último capítulo. Conclui-se que o contributo da contabilidade de gestão, poderá ser preponderante para suprir as necessidades de informação das chefias da Guarda Nacional Republicana, uma vez que estas disporão de informação de gestão que por sua vez permite: a) avaliação dos serviços mais criteriosa; b) determinação de necessidades; c) concretização da economia, eficiência e eficácia; d) efetuar comparações, análises e o controlo dos gastos; e, e) identificar a duplicação de gastos e tarefas. Em suma, contribui para a melhoria do desempenho organizacional.

Integração entre frameworks de suporte à gestão e governação das tecnologias de informação : modelação da Norma ISO 9001

A ISO 9001 e Arquiteturas Empresariais (AE), diferentes ferramentas de Governação com diferentes perspetivas, são dominantes entre os seus praticantes. Uma representação de uma ISO 9001 em ArchiMate pode potenciar ainda mais alinhamentos com outras frameworks representadas por AE e pode ajudar na obtenção de melhores resultados na implementação da Qualidade numa organização, obviando os custos e a duplicação de esforços. Esta tese propõe uma abordagem de integração entre a ISO 9001 e AE na perspetiva das AE ao propor um mapeamento de conceitos de ISO 9001 em EA pela definição de uma Arquitetura de Referência da ISO 9001 utilizando a linguagem de modelação do ArchiMate Dois objetivos são endereçados: a demonstração da capacidade de representar todos os requisitos da ISO 9001 em componentes de AE através do desenvolvimento da Arquitetura de Referência e reciprocamente a capacidade de desenvolver uma AE de um Sistema de Gestão da Qualidade (SGQ) teórico baseado na ISO 9001 com as componentes dessa Arquitetura de Referência. Adicionalmente, ao identificar e avaliar a existência das componentes da Arquitetura de Referência numa organização concreta, se estes não estão completamente mapeados, pode-se concluir a existência de um desvio relativamente ao referencial ISO 9001. Por ultimo, uma Arquitetura de Referência ArchiMate da ISO 9001 permite a partilha de conhecimento, a comunicação entre partes interessadas e contribui para a discussão e validação da ISO 9001 entre os utilizadores de Arquiteturas Empresariais.

Identification, characterisation and expression analysis of natural killer receptor genes in chlamydia pecorum infected koalas (phascolarctos cinereus)

BACKGROUND: Koalas (Phascolarctos cinereus), an iconic Australian marsupial, are being heavily impacted by the spread of Chlamydia pecorum, an obligate intracellular bacterial pathogen. Koalas vary in their response to this pathogen, with some showing no symptoms, while others suffer severe symptoms leading to infertility, blindness or death. Little is known about the pathology of this disease and the immune response against it in this host. Studies have demonstrated that natural killer (NK) cells, key components of the innate immune system, are involved in the immune response to chlamydial infections in humans. These cells can directly lyse cells infected by intracellular pathogens and their ability to recognise these infected cells is mediated through NK receptors on their surface. These are encoded in two regions of the genome, the leukocyte receptor complex (LRC) and the natural killer complex (NKC). These two families evolve rapidly and different repertoires of genes, which have evolved by gene duplication, are seen in different species. METHODS: In this study we aimed to characterise genes belonging to the NK receptor clusters in the koala by searching available koala transcriptomes using a combination of search methods. We developed a qPCR assay to quantify relative expression of four genes, two encoded within the NK receptor cluster (CLEC1B, CLEC4E) and two known to play a role in NK response to Chalmydia in humans (NCR3, PRF1). RESULTS: We found that the NK receptor repertoire of the koala closely resembles that of the Tasmanian devil, with minimal genes in the NKC, but with lineage specific expansions in the LRC. Additional genes important for NK cell activity, NCR3 and PRF1, were also identified and characterised. In a preliminary study to investigate whether these genes are involved in the koala immune response to infection by its chlamydial pathogen, C. pecorum, we investigated the expression of four genes in koalas with active chlamydia infection, those with past infection and those without infection using qPCR. This analysis revealed that one of these four, CLEC4E, may be upregulated in response to chlamydia infection. CONCLUSION: We have characterised genes of the NKC and LRC in koalas and have discovered evidence that one of these genes may be upregulated in koalas with chlamydia, suggesting that these receptors may play a role in the immune response of koalas to chlamydia infection.

Discovery of stable and variable differences in the Mycobacterium avium subsp. paratuberculosis type I, II, and III genomes by pan-genome microarray analysis

Mycobacterium avium subsp. paratuberculosis is an important animal pathogen widely disseminated in the environment that has also been associated with Crohn's disease in humans. Three M. avium subsp. paratuberculosis genomotypes are recognized, but genomic differences have not been fully described. To further investigate these potential differences, a 60-mer oligonucleotide microarray (designated the MAPAC array), based on the combined genomes of M. avium subsp. paratuberculosis (strain K-10) and Mycobacterium avium subsp. hominissuis (strain 104), was designed and validated. By use of a test panel of defined M. avium subsp. paratuberculosis strains, the MAPAC array was able to identify a set of large sequence polymorphisms (LSPs) diagnostic for each of the three major M. avium subsp. paratuberculosis types. M. avium subsp. paratuberculosis type II strains contained a smaller genomic complement than M. avium subsp. paratuberculosis type I and M. avium subsp. paratuberculosis type III genomotypes, which included a set of genomic regions also found in M. avium subsp. hominissuis 104. Specific PCRs for genes within LSPs that differentiated M. avium subsp. paratuberculosis types were devised and shown to accurately screen a panel (n = 78) of M. avium subsp. paratuberculosis strains. Analysis of insertion/deletion region INDEL12 showed deletion events causing a reduction in the complement of mycobacterial cell entry genes in M. avium subsp. paratuberculosis type II strains and significantly altering the coding of a major immunologic protein (MPT64) associated with persistence and granuloma formation. Analysis of MAPAC data also identified signal variations in several genomic regions, termed variable genomic islands (vGIs), suggestive of transient duplication/deletion events. vGIs contained significantly low GC% and were immediately flanked by insertion sequences, integrases, or short inverted repeat sequences. Quantitative PCR demonstrated that variation in vGI signals could be associated with colony growth rate and morphology.

Stepwise evolution of the centriole-assembly pathway

The centriole and basal body (CBB) structure nucleates cilia and flagella, and is an essential component of the centrosome, underlying eukaryotic microtubule-based motility, cell division and polarity. In recent years, components of the CBB-assembly machinery have been identified, but little is known about their regulation and evolution. Given the diversity of cellular contexts encountered in eukaryotes, but the remarkable conservation of CBB morphology, we asked whether general mechanistic principles could explain CBB assembly. We analysed the distribution of each component of the human CBB-assembly machinery across eukaryotes as a strategy to generate testable hypotheses. We found an evolutionarily cohesive and ancestral module, which we term UNIMOD and is defined by three components (SAS6, SAS4/CPAP and BLD10/CEP135), that correlates with the occurrence of CBBs. Unexpectedly, other players (SAK/PLK4, SPD2/CEP192 and CP110) emerged in a taxon-specific manner. We report that gene duplication plays an important role in the evolution of CBB components and show that, in the case of BLD10/CEP135, this is a source of tissue specificity in CBB and flagella biogenesis. Moreover, we observe extreme protein divergence amongst CBB components and show experimentally that there is loss of cross-species complementation among SAK/PLK4 family members, suggesting species-specific adaptations in CBB assembly. We propose that the UNIMOD theory explains the conservation of CBB architecture and that taxon- and tissue-specific molecular innovations, gained through emergence, duplication and divergence, play important roles in coordinating CBB biogenesis and function in different cellular contexts.

Transportation Coordination in Iowa (2016)

Iowa Code section 324A.4, subsection 2, states the Iowa Department of Transportation (DOT) “shall biennially prepare a report to be submitted to the general assembly and the governor prior to December 15 of even-numbered years. The report shall recommend methods to increase transportation coordination and improve the efficiency of federal, state, and local government programs used to finance public transit services and may address other topics as appropriate.” Iowa has long been a leader in transportation coordination, from designated public transit agencies covering all 99 counties with little duplication, to requiring any agency receiving public dollars for the provision of transportation to first coordinate with the local public transit agency before providing the transportation on their own, to the creation of the Iowa Transportation Coordination Council. Coordination allows Iowa to provide much needed transportation services to the citizens of Iowa with the most efficient use of public funds. Coordination has been an important topic in Iowa for many years, but during these times of economic constraint and restraint and Iowa’s changing demographics, coordination of transportation services becomes even more critical.

Registro de pacientes con distrofinopatías en Colombia

INTRODUCCIÓN. La distrofia muscular de Duchenne es una enfermedad neuromuscular con una herencia recesiva ligada al X que afecta a 1 de cada 3500 niños nacidos vivos. Se produce por mutaciones en el gen DMD que codifica para la distrofina. Se caracteriza por manifestaciones clínicas variables típicas de una distrofia muscular proximal progresiva. OBJETIVO. Realizar el primer registro en Colombia de los pacientes identificados con distrofinopatías, teniendo en cuenta características clínicas y paraclínicas, así como las mutaciones causales de esta patología. METODOLOGÍA Es un estudio descriptivo, transversal, de la revisión de historias clínicas de los pacientes con diagnóstico de DMD atendidos en la consulta de Genética de la Universidad del Rosario durante los años 2006 a 2015. RESULTADOS Se identificaron 99 pacientes, de los cuales 56 (56,56%) corresponden al fenotipo Duchenne y 12 (12,12%) al Becker. No fue posible clasificar a 31 pacientes (31,3%) por falta de datos clínicos. La edad de inicio de los síntomas fue en promedio de 4,41 años. Las mutaciones más frecuentes fueron las deleciones (69%), seguidas por las mutaciones puntuales(14%), las duplicaciones (11%) y por otras mutaciones (4%). CONCLUSIONES Este registro de distrofinopatías es el primero reportado en Colombia y el punto de partida para conocer la incidencia de la enfermedad, caracterización clínica y molecular de los pacientes, garantizando así el acceso oportuno a los nuevos tratamientos de medicina de precisión que permitan mejorar la calidad de vida de los pacientes y sus familias.

Double trouble: French colonialism in Morocco and the early history of the Pasteur institutes of Tangier and Casablanca (1895-1932)

Morocco was the last North African country in which a Pasteur institute was created, nearly two decades later than in Tunisia and Algeria. In fact, two institutes were opened, the first in Tangier in 1913 and the second in Casablanca in 1932. This duplication, far from being a measure of success, was the material expression of the troubles Pastorians had experienced in getting a solid foothold in the country since the late 19th century. These problems partly derived from the pre-existence of a modest Spanish-Moroccan bacteriological tradition, developed since the late 1880s within the framework of the Sanitary Council and Hygiene Commission of Tangier, and partly from the uncoordinated nature of the initiatives launched from Paris and Algiers. Although a Pasteur Institute was finally established, with Paul Remlinger as director, the failure of France to impose its colonial rule over the whole country, symbolized by the establishment of an international regime in Tangier, resulted in the creation of a second centre in Casablanca. While elucidating many hitherto unclear facts about the entangled origins of both institutes, the author points to the solidity of the previously independent Moroccan state as a major factor behind the troubled translation of Pastorianism to Morocco. Systematically dismissed or downplayed by colonial and postcolonial historiography, this solidity disrupted the French takeover of the country and therefore Pastorian expectations.

Toxicity of the herbicide clomazone on duckweed Lemna valdiviana.

The duckweed Lemna valdiviana is commonly founded colonizing small shallow waters (lakes on the lowland in south Brazil. This organism may have been affected by herbicide input into lakes from aerial application and/or drainage office paddy fields. Clomazone (2- (2-chlorophenyl) methyl-4.4-dimethyl-3-isoxazolidinone) is one of the herbicides more fiequentely used as post-emergence in rice paddies. For this work assays were carried as EC50(96h) semi-statics with aseptic culture. The sterile fronds were abtained from material harvest on the paddy fields, and the concentration of Clomazone ranged from 14.0 to 229.0 mg/l. two procedures were considered: diluted in water and sprayed applicated Clomazone. The observed phytotoxic effects were evaluated by growth rate (kt), duplication time (Td), frond yield, plant yield, mortality, chlorophyll a and b and protochlorophyll concentration. The EC50 values obtained to sprayed Clomazone (Kt=31.7; Td=31.9) were significantly small than to diluted Clomazone (Kt=46.4; td=47.3). These dadta suggest that aerial route is more hazardous than diluted procedure. Presence of chlorotic, necrotic, abnormal and died frond were common at the 114.0 and 229.0 mg/l treatment. Recuperation test corroborated the evidence that the sprayed procedure were more deleterious and L. valdiviana doesn't recovery his reproductive ability at the 114.0 and 229.0 mg/l treatment.