UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and computational linguists

As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs (Single Nucleotide Polymorphisms) and diseases from the literature.

A first challenge that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research groups from different and unrelated expert fields. Often, biologists (even computer-savvy ones) are hard pressed to use and adapt sophisticated Natural Language Processing systems, and computational linguists are challenged by the intricacies of biology in applying their processing pipelines to elicit knowledge from texts. The flow of knowledge (needed to develop a usable, practical tool) to and from the parties involved in the development of such systems is not always easy or straightforward.

The modular and versatile architecture of UIMA (Unstructed Information Management Architecture) provides a framework to address these challenges. UIMA is a component architecture and software framework implementation (including a UIMA SDK) to develop applications that analyse large volumes of unstructured information, and has been increasingly adopted by a significant part of the BioNLP community that needs industrial-grade and robust applications to exploit the whole bibliome. The use of UIMA to develop Text Mining applications useful for curation purposes allows the combination of diverse expertises which is beyond the individual know-how of biologists, computer scientists or linguists in isolation. A good synergy and circulation of knowledge between these experts is fundamental to the development of a successful curation tool

Eigenstate versus Zeeman-based approaches to the solid-effect

The solid effect is one of the simplest and most effective mechanisms for Dynamic Nuclear Polarization. It involves the exchange of polarization between one electron and one nuclear spin coupled via the hyperfine interaction. Even for such a small spin system, the theoretical understanding is complicated by the contact with the lattice and the microwave irradiation. Both being weak, they can be treated within perturbation theory. In this work, we analyze the two most popular perturbation schemes: the Zeeman and the eigenstate-based approaches which differ in the way the hyperfine interaction is treated. For both schemes, we derive from first principles an effective Liouville equation which describes the density matrix of the spin system; we then study numerically the behavior of the nuclear polarization for several values of the hyperfine coupling. In general, we obtain that the Zeeman-based approach underestimates the value of the nuclear polarization. By performing a projection onto the diagonal part of the spin-system density matrix, we are able to understand the origin of the discrepancy, which is due to the presence of parasite leakage transitions appearing whenever the Zeeman basis is employed.Comment: 9 pages, 4 figures, 7 pages of supplementary materia

Inhibition of an extracellular polygalacturonase from Geotrichum candidum by a proteinaceous inhibitor isolated from lemon fruits

An extracellular polygalacturonase [EC 3.2.1.15], named PG-543, was purified from the culture of Geotrichum candidum IEV 543, a phytopathogenic fungi isolated from infected lemon. The molecular mass of the enzyme was estimated to be 26 kDa by SDS-PAGE. The pH optimum determined was 5.5; the enzyme showed high stability in the pH range between 4.0 and 6.0. The temperature optimum was 37 ºC. Furthermore, a proteinaceous inhibitor of the polygalacturonase (PG) named PGIP was isolated from lemon albedo. This protein was able to maintain the inhibitory activity in a wide range of pH and temperature. The maximal interaction between PG-PGIP was reached after 20 min of contact. PGIP did not show toxic effect on Artemia salina in the concentration range that was active on PG enzyme. Also, the proteinaceous inhibitor did not show mutagenic nor phytotoxic effects.Our results suggest that, the PGIP isolated from lemon could be used as a natural product to decrease the propagation of pathogenic fungi responsible for postharvest diseases in citrus by the inhibition of hydrolytic enzymes secreted by pathogens.Fil: Rodriguez, Ivana Fabiola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Química del Noroeste. Universidad Nacional de Tucumán. Facultad de Bioquímica, Química y Farmacia. Instituto de Química del Noroeste; ArgentinaFil: Torres, Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Química del Noroeste. Universidad Nacional de Tucumán. Facultad de Bioquímica, Química y Farmacia. Instituto de Química del Noroeste; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Sayago, Jorge Esteban. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Zampini, Iris Catiana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Química del Noroeste. Universidad Nacional de Tucumán. Facultad de Bioquímica, Química y Farmacia. Instituto de Química del Noroeste; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Isla, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Química del Noroeste. Universidad Nacional de Tucumán. Facultad de Bioquímica, Química y Farmacia. Instituto de Química del Noroeste; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Ordóñez, Roxana Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Química del Noroeste. Universidad Nacional de Tucumán. Facultad de Bioquímica, Química y Farmacia. Instituto de Química del Noroeste; Argentina. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; Argentin

Efectos subletales de la lambda-cialotrina sobre eisenia fetida (Annelida, Oligochaeta, Lumbricidae)

El uso intensivo de agroquímicos provoca efectos indeseables sobre la fauna no blanco. Dentro de la misma, los oligoquetos contribuyen a mantener la estructura y fertilidad del suelo. La lambda-cialotrina es uno de los insecticidas piretroides más utilizados en Argentina, pero son escasos los datos existentes acerca de su toxicidad sobre oligoquetos. Los objetivos de este trabajo fueron evaluar mediante bioensayos de toxicidad crónica los efectos de lambda-cialotrina (producto comercial al 5%) en Eisenia fetida sobre los 2 parámetros de comportamiento, sobrevivencia, biomasa, reproducción y bioacumulación, así como la persistencia en suelo OECD de dicho tóxico. Los resultados muestran un comportamiento de huída intenso a partir de la concentración más baja, con un EC50 de 1,36 mg.kg-1 (95% C.L. 0,24 - 2,80). No se observaron efectos en sobrevivencia y alimentación. La reproducción fue afectada significativamente (F= 11,94, P<0,05). La producción y fertilidad de ootecas disminuyó a la vez que se prolongó el tiempo de incubación de las mismas respecto al control. El BAF osciló entre 0,005 y 0,08 en las distintas concentraciones y el tiempo de degradación total del tóxico en suelo fue de 86 días.Fil: Ricardo, Tamara. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias; ArgentinaFil: Maitre, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química (i); Argentina. Universidad Nacional del Litoral; ArgentinaFil: Rodriguez, Alba Rut. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química (i); Argentin

Evaluación de la Abundancia y Diversidad de Lombrices de tierra en relación con el Uso del Suelo en el Cinturón Hortícola de Santa Fe (Argentina)

Las lombrices de tierra constituyen un componente importante en la fauna del suelo contribuyendo activa y beneficiosamente en su estructura y fertilidad. Estos organismos son sensibles ante distintos manejos y grados de perturbación del suelo respondiendo como bioindicadores de la «salud» del mismo. El Cinturón Hortícola Santafesino (Santa Fe, Argentina) exhibe diferencias no sólo en tipos de cultivos sino también en sistemas de producción y condiciones de trabajo. El objetivo del estudio fue determinar la abundancia y diversidad de la oligoquetofauna en los suelos con distintos tipos de manejo en las localidades de Ángel Gallardo y Monte Vera (Dpto. La Capital, Santa Fe - Argentina). Se seleccionaron tres agroecosistemas: labranza convencional (LC), siembra directa orgánica (SDO) y siembra directa (SD). En cada campo se realizaron dos muestreos, correspondiendo uno a la estación verano y el otro a otoño de 2008. Se analizaron algunas propiedades físicas y químicas de los suelos como también residuos de plaguicidas. La densidad de oligoquetos presentó diferencias por estación y sistemas de producción (p = 0,001) destacándose el sitio de SDO con el mayor número de individuos en las dos estaciones muestreadas. La taxocenosis constó de dos familias: Lumbricidae y Megascolecidae, y tres especies: Aporrectodea rosea, Aporrectodea trapezoides y Amynthas morrisi. La diversidad fue baja (H’= 0,33), siendo A. rosea la especie más común en los sitios muestreados y A. trapezoides la más abundante, incorporándose esta última a la lista de oligoquetos para la zona hortícola ya que en estudios anteriores no se hallaba registrada. La composición y estructura de la taxocenosis de lombrices de tierra se ve afectada no sólo por las condiciones ambientales y labores de producción, sino también por los parámetros físicos y químicos del suelo, que en conjunto condicionan la sensibilidad de la oligoquetofauna.Earthworms are an important component of soil fauna, contributing actively to improve soil structure and fertility. These organisms are highly sensitive to different soil managements and degrees of soil disturbance and were therefore adopted as biomarkers of the soil «health». The Cinturón Hortícola Santafesino (Santa Fe, Argentina) exhibits a large variability in crop species, production systems and working conditions. The aim of this study was to determine the abundance and diversity of earthworms in soils under different types of managements near the villages of Ángel Gallardo and Monte Vera (Dept. La Capital, Santa Fe, Argentina). The three agroecosystems selected were: conventional tillage (LC), notillage with added organic amendments (SDO) and no-tillage (SD). Two samplings were conducted in each field: one in summer and the other in fall of 2008. In addition, some physical and chemical properties of soils were analyzed, as well as the presence of pesticide residues. The density of oligochaetes showed significant differences between seasons and production systems (= 0.001). The SDO site had the greatest number of individuals in the two sampled seasons. The taxocenosis consisted of two families: Lumbricidae and Megacolescidae, and three species: Aporrectodea rosea, Aporrectodea trapezoides and Amynthas morrisi. The diversity was low (H’= 0.33), resulting A. rosea the most common and A. trapezoides the most abundant species, respectively. A. trapezoides was incorporated to the earthworm records of the area because it had never been reported in previous studies. The composition and structure of the earthworm’s taxonomy is not only affected by the different agricultural practices and the edaphic and environmental conditions, but also by the soil´s physical and chemical properties that influence the oligoquetofauna sensitivity.Fil: Masin, Carolina Elisabet. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias; ArgentinaFil: Rodriguez, Alba Rut. Universidad Nacional del Litoral. Facultad de Humanidades y Ciencias; ArgentinaFil: Maitre, Maria Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química (i); Argentin

De la historia a la literatura: Diferentes interpretaciones sobre Sofonisba en la tragedia italiana

Sofonisba, fue una joven cartaginesa que vivió durante la segunda guerra púnica y cuyas vicisitudes fueron narradas por los historiadores Tito Livio, Apiano y Polibio. Su singular vivencia, su patriotismo, fortaleza y la digna y valiente aceptación de su temprana y trágica muerte la convirtieron en protagonista de numerosas tragedias desde el Renacimiento. En el presente artículo se analizan las tragedias italianas centradas en este personaje y el diferente tratamiento e interpretación que se le dio en cada una de las obras.Sophonisba was a young Carthaginian girl who lived during the Second Punic War and whose vicissitudes were narrated by the historians Titus Livy, Apian and Polybius. Her unique experience, her patriotism, fortitude and her dignified and courageous acceptance of her early and tragic death made her the protagonist of numerous tragedies since the Renaissance. This article analyses the Italian tragedies centred on this character and the different treatment and interpretation given to her in each of the works

Differential in vitro and in vivo effect of barley cysteine and serine protease inhibitors on phytopathogenic microorganisms

Protease inhibitors from plants have been involved in defence mechanisms against pests and pathogens. Phytocystatins and trypsin/α-amylase inhibitors are two of the best characterized protease inhibitor families in plants. In barley, thirteen cystatins (HvCPI-1 to 13) and the BTI-CMe trypsin inhibitor have been previously studied. Their capacity to inhibit pest digestive proteases, and the negative in vivo effect caused by plants expressing these inhibitors on pests support the defence function of these proteins. Barley cystatins are also able to inhibit in vitro fungal growth. However, the antifungal effect of these inhibitors in vivo had not been previously tested. Moreover, their in vitro and in vivo effect on plant pathogenous bacteria is still unknown. In order to obtain new insights on this feature, in vitro assays were made against different bacterial and fungal pathogens of plants using the trypsin inhibitor BTI-CMe and the thirteen barley cystatins. Most barley cystatins and the BTI-CMe inhibitor were able to inhibit mycelial growth but no bacterial growth. Transgenic Arabidopsis plants independently expressing the BTI-CMe inhibitor and the cystatin HvCPI-6 were tested against the same bacterial and fungal pathogens. Neither the HvCPI-6 expressing transgenic plants nor the BTI-CMe ones were more resistant to plant pathogen fungi and bacteria than control Arabidopsis plants. The differences observed between the in vitro and in planta assays against phytopathogenic fungi are discusse

El derecho comparado sobre el regimen aduanero de adhesion temporal para perfeccionamiento activo

La maestrante entrega tres ejemplares empastados de su tesis y tres CD con el contenido de la misma en Word y en formato PDFEsta Tesis pretende revelar el uso que tiene el régimen aduanero de “admisión temporal para perfeccionamiento activo” para incrementar las exportaciones en especial para los MIPYMES, como primera solución, hasta que el país tenga liquidez y tecnología suficientes para reducir la importación de materia prima, insumos, productos intermedios, partes y piezas, para incorporarlas en su proceso productivo y, de esta manera, fomentar e incrementar las exportaciones. En su desarrollo se podrá observar las normas legales y las exportaciones que tienen cuatro países de América al usar el referidorégimen aduanero de admisión temporal para perfeccionamiento activo. La temática desarrollada explica el uso del régimen aduanero de admisión temporal para perfeccionamiento activo para que las MIPYMES puedan utilizar el referido régimen en su proceso productivo y que lleven con éxito las exportaciones, como uno de los caminos para cumplir con la nueva matriz productiva que tiene como antecedente el Plan Nacional del Buen Vivir, buscando una gestión incluyente, articulada y participativa. Concluye la tesis con la propuesta que es un manual de procedimiento básico para que las MIPYMES puedan tener como referencia y, en un solo documento, contar con todos los pasos que deben tener presente y las normas legales vigentes para la aplicación del referido régimen aduanero de admisión temporal para perfeccionamiento activo.This thesis aims to reveal the use having the customs regime of temporary admission for inward to increase exports especially for MIPYMEs, like first solution, until the country has sufficient liquidity and enough technology to not need to import raw material inputs, intermediate products and parts, to be incorporated in the production process and, thus, promote and increase exports.In its development we can observe the laws and exports have four Latin using the said customs regime of temporary admission for inward processing. The theme developed explains the use of the customs procedure of temporary admission for inward for MIPYMEs to use such a scheme in their production process and with successful exports, as one way to meet the new production matrix having the background of the National Plan for Good Living, seeking an inclusive, coordinated and participatory management. Thesis concludes with the proposal is a basic procedure manual for MIPYMEs can have as a reference and, in one document, all steps have to be aware of and legal norms for the application of such customs procedure of admission time for inward

Pensando sobre si mesmos : o que adolescentes em situação de vulnerabilidade social aprendem ao enfrentar adversidades

Orientadora: Helga LoosDissertação (mestrado) - Universidade Federal do Paraná, Setor de Educação, Programa de Pós-Graduação em Educação. Defesa: Curitiba, 2008Inclui bibliografia e anexosResumo: As situaÁ?es de risco social s"o cada vez mais comuns, e para muitas crianÁas e adolescentes essas situaÁ?es n"o s"o fatos isolados, mas vivÍncias di·rias, que podem afetar seu desenvolvimento moral, fÌsico, emocional e cognitivo. O foco principal desta pesquisa est· no interjogo entre as crenÁas auto-referenciadas de um indivÌduo e a maneira como enfrenta, e eventualmente supera, as situaÁ?es adversas que se d"o, especificamente, em contextos de aprendizagem. Partindo do pressuposto que neste interjogo h· peÁas-chave para se compreender melhor o desenvolvimento de adolescentes expostos a situaÁ?es de risco, esta pesquisa visou analisar o conjunto das suas crenÁas auto-referenciadas, as estratÈgias utilizadas para lidar com a adversidade e os mecanismos de autoregulaÁ"o utilizados para repensar as crenÁas apÛs esse enfrentamento. Para isto, foram utilizados quatro instrumentos de coleta de dados: a escala de auto-estima de Rosenberg (1965), escala de autoconceito de Piers-Harris (1984), escala de auto-efic·cia de Bandura (1990) e uma entrevista semi-estruturada elaborada especificamente para esta pesquisa. Os participantes foram 25 adolescentes, do sexo masculino, com idades entre 15 e 18 anos que se encontram abrigados em uma ONG localizada na regi"o metropolitana de Curitiba, Paran·. Os resultados indicam que a maioria dos adolescentes do grupo pesquisado possui um nÌvel de auto-estima mediano, um autoconceito positivo e uma auto-efic·cia positiva, porÈm destaca-se que seu grau de auto-efic·cia para a regulaÁ"o da prÛpria conduta È baixo em comparaÁ"o com os dados encontrados na revis"o de literatura. A an·lise das entrevistas aponta a utilizaÁ"o de diversas estratÈgias de coping (aÁ"o direta, aÁ"o agressiva e busca de apoio social foram as mais mencionadas); o emprego de alguns mecanismos de autoregulaÁ"o tanto para estabelecer, empreender, avaliar e modificar a prÛpria conduta em funÁ"o dos resultados desejados, como tambÈm na reconstruÁ"o das prÛprias crenÁas. Os estudos de caso realizados com sete dos adolescentes do grupo, os quais englobam os principais resultados de todos os instrumentos aplicados, destacam o papel das crenÁas de autoestima, autoconceito e, sobretudo, da auto-efic·cia ao lidar com a adversidade e como esta forma de lidar realimenta as prÛprias crenÁas. Em funÁ"o destes resultados considera-se importante o papel que os educadores e cuidadores destes adolescentes tÍm na construÁ"o das suas crenÁas auto-referenciadas, assim como na educaÁ"o a respeito das diversas estratÈgias de coping e nos mecanismos de regulaÁ"o da conduta necess·rios para que eles se sintam mais preparados para enfrentar e superar as adversidades. Por fim, destaca-se que a maioria obteve escores altos na dimens"o da felicidade e satisfaÁ"o com a vida prÛpria da escala de autoconceito, o que evidencia, possivelmente, o grande potencial de resiliÍncia que demonstram estes adolescentes, ao se considerarem felizes e satisfeitos, apesar dos fatos e circunst‚ncias adversas a que estiveram e est"o expostos.Abstract: Social risk situations are no longer unusual, and to many children and adolescents those situations are not isolated facts, but day-to-day experiences that may affect their moral, physical, emotional, and cognitive development. The main focus of this research is in the interplay between the self-beliefs and the way that the individual follows to cope with, and eventually overcome, the risk situations that could happen in a learning context. With the hypothesis that in this interplay are key- to a better understanding of the adolescentsí development exposed to risky situations, this research aimed to analyze the self-beliefs set, the strategies used to cope with adversity, and the self-regulation mechanisms used to rethink the beliefs after the whole process. For this purpose 4 instruments were used: The Rosenberg Self-Esteem Scale (1965), the Piers-Harris SelfConcept Scale (1984), Bandura Self-Efficacy Scale for Children and Adolescents (1990) and an interview elaborated for this study. The participants were 25 male adolescents from 15 to 18 years old that are sheltered in a Non Governmental Organization in the metropolitan region of Curitiba, Paran·. The results informed that most of these adolescents have a middle level of self-esteem, a positive self-concept, and also a positive self-efficacy, although the level of self-efficacy for regulation of the own behavior is low in comparison with other studies. The interviewsí analyses point out the utilization of different coping strategies (taking action, seeking help and aggressive conducts were the most mentioned among all), the use of several mechanisms of selfregulation to establish, engage and evaluate the followed conduct, and also to rethink their self-beliefs. The cases of seven adolescents belonging to the group were deeply analyzed using all the instruments applied, and there were found that self-esteem, selfconcept and most of all the self-efficacy beliefs have a prominent role in coping with adversity, and how the coping stile feedback the self-beliefs. The results allow some considerations about the role of the teachers and caregivers of these adolescents in the construction of their self-beliefs, and in the education in terms of coping abilities and mechanisms of self-regulation, because they are basic resources to deal well, and eventually overcome, the adversities. Finally, it is interesting to consider that most of the participant subjects got a high score in the ìhappiness and satisfaction with themselves and their own lifeî, a dimension of the self-concept scale. This may reveal the big resilient potential that these adolescents showed up, as they consider themselves happy and satisfied, despite of all adverse facts and circumstances they have been exposed to