BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.

Division of labor in frontal eye field neurons during presaccadic remapping of visual receptive fields.

Our percept of visual stability across saccadic eye movements may be mediated by presaccadic remapping. Just before a saccade, neurons that remap become visually responsive at a future field (FF), which anticipates the saccade vector. Hence, the neurons use corollary discharge of saccades. Many of the neurons also decrease their response at the receptive field (RF). Presaccadic remapping occurs in several brain areas including the frontal eye field (FEF), which receives corollary discharge of saccades in its layer IV from a collicular-thalamic pathway. We studied, at two levels, the microcircuitry of remapping in the FEF. At the laminar level, we compared remapping between layers IV and V. At the cellular level, we compared remapping between different neuron types of layer IV. In the FEF in four monkeys (Macaca mulatta), we identified 27 layer IV neurons with orthodromic stimulation and 57 layer V neurons with antidromic stimulation from the superior colliculus. With the use of established criteria, we classified the layer IV neurons as putative excitatory (n = 11), putative inhibitory (n = 12), or ambiguous (n = 4). We found that just before a saccade, putative excitatory neurons increased their visual response at the RF, putative inhibitory neurons showed no change, and ambiguous neurons increased their visual response at the FF. None of the neurons showed presaccadic visual changes at both RF and FF. In contrast, neurons in layer V showed full remapping (at both the RF and FF). Our data suggest that elemental signals for remapping are distributed across neuron types in early cortical processing and combined in later stages of cortical microcircuitry.

INNOVATIONS IN FRENCH CHAMBER MUSIC AND MÉLODIE (1886 – 1962) – A COLLABORATIVE PIANIST’S PERSPECTIVE

French chamber music in the last quarter of the nineteenth century displayed significant advances in musical innovations and technical developments. As the Parisian public began to favor instrumental music and mélodie over opera, vocal and chamber music with piano became one of the main genres to express French composers’ creativity and individuality. The composers Franck, Debussy, Fauré, Duparc, Ravel, Chausson and Poulenc were the major contributors to this unusually creative period in French music. French mélodies of this period blend precision with lyricism, and demand the performer’s elegance and wit. They show careful settings of the French language’s rhythmic subtleties and increased expressiveness in and importance of the piano accompaniment. The chamber works of this period demanded superior pianistic and instrumental virtuosity while displaying wide ranges of sonority, multiple tone colors, and rhythmic fluidity. The three recitals which comprise this dissertation project were performed at the University of Maryland Gildenhorn Recital Hall on 27 October 2006, All Nations Mission Church (Dayton, NJ) on 5 December 2009, and the Leah M. Smith Lecture Hall of the University of Maryland on 11 May 2010. The repertoire included Poulenc’s Sonata for Oboe and Piano (1962) with oboist Yeongsu Kim, French mélodies by Fauré, Chausson, Debussy, Ravel and Duparc with soprano Jung-A Lee and baritone Hyun-Oh Shin, Poulenc’s Sextet for Piano, Flute, Oboe, Clarinet, Bassoon and Horn (1932-1939) with flutist Katrina Smith, clarinetist Jihoon Chang, bassoonist Erich Heckscher, hornist Heidi Littman and oboist Yeongsu Kim, Debussy’s Sonata for Cello and Piano (1915) with cellist Ji-Sook Shin, Poulenc’s Sonata for Violin and Piano (1942-1949) with violinist Ji-Hee Lim, Franck’s Sonata for Violin and Piano (1886) with violinist Na-Young Cho, Ravel’s Piano Trio (1915) with cellist Ji-Sook Shin and violinist Yu-Jeong Lee and Ravel’s Sonata for Violin and Piano (1927) with violinist Yu-Jeong Lee. The recitals were recorded on compact discs and are archived within the Digital Repository at the University of Maryland (DRUM).

Algae-Based Purification of Landfill Biogas Using a CO2 Removal System and Helical Photobioreactor in Series

Biogas is a mixture of methane and other gases. In its crude state, it contains carbon dioxide (CO2) that reduces its energy efficiency and hydrogen sulfide (H2S) that is toxic and highly corrosive. Because chemical methods of removal are expensive and environmentally hazardous, this project investigated an algal-based system to remove CO2 from biogas. An anaerobic digester was used to mimic landfill biogas. Iron oxide and an alkaline spray were used to remove H2S and CO2 respectively. The CO2-laden alkali solution was added to a helical photobioreactor where the algae metabolized the dissolved CO2 to generate algal biomass. Although technical issues prevented testing of the complete system for functionality, cost analysis was completed and showed that the system, in its current state, is not economically feasible. However, modifications may reduce operation costs.

Validation of the NEMO-ERSEM operational ecosystem model for the North West European Continental Shelf

This paper details updates to the Met Office's operational coupled hydrodynamic-ecosystem model from the 7 km Medium-Resolution Continental Shelf – POLCOMS-ERSEM (MRCS-PE) system (Siddorn et al., 2007) to the 7 km Atlantic Margin Model NEMO-ERSEM (AMM7-NE) system. We also provide a validation of the ecosystem component of the new operational system. Comparisons have been made between the model variables and available in situ, satellite and climatological data. The AMM7-NE system has also been benchmarked against the MRCS-PE system. The transition to the new AMM7-NE system was successful and it has been running operationally since March 2012 and has been providing products through MyOcean (http://www.myocean.eu.org) since that time. The results presented herein show the AMM7-NE system performs better than the MRCS-PE system with the most improvement in the model nutrient fields. The problem of nutrient accumulation in the MRCS-PE system appears to be solved in the new AMM7-NE system with nutrient fields improved throughout the domain as discussed in Sect. 4. Improvements in model chlorophyll are also seen but are more modest.

Lecanora rhizinata spec. nova, liquen taxonómicamente aislado, sobre fisuras de rocas exfoliables, en España

Se describe una nueva especie de Lecanora Ach. (L. rhizinata Poetl., Barreno & Rico) de la alta montaña del Centro de España, que se desarrolla sobre rocas metamórficas fácilmente exfoliables. La especie puede encuadrarse dentro de la subsección Concolores Poelt (sect. Petrasterion Poelt, subgen. Placodium (Pers.) Poelt) del género Lecanora. Sin embargo, la compleja estructura anatómica del talo, en la que se diferencian fascículos de hifas fuertemente conglutinadas, que partiendo del córtex penetran hacia la médula llegando, en ocasiones, hasta el límite inferior de la escuámula e intercalándose con la capa gonidial a la que disgregan en glomérulos, unido a la presencia de cordones rizinales («Rhizinenstränge»), hacen que la nueva especie tenga una posición aislada dentro del grupo Concolores y pudiera reclamar un estatus distinto. Asimismo se hace una comparación con otras especies de la citada subsect. Concolores y con otros géneros de Lecanoraceae.

Revisión del género Angelica L (Umbelliferae) en la Península Ibérica

Se ha realizado la revisión de las especies ibéricas del género Angelica L. (Umbelliferae), todas ellas pertenecientes al subgen. Angelica, sect. Angelica. Se reconocen cuatro especies, tres de ellas endémicas de la Península y Pirineos. Se añade una clave para la determinación de las especies y la descripción de cada una de ellas, con indicación del nombre correcto y sinonimias comprobadas, tipo y distribución en la Península, en base al material estudiado.

New wild Brassica oleracea L. germplasm at its western distribution limit in the Iberian Peninsula

An exploration and collection mission for wild Brassica oleracea populations was carried out in spring and summer of 2013. The aim of this collection was to expand the number of accessions of wild Brassica oleracea available for basic and applied research in plant breeding. In this paper we report a new accession of wild Brassica oleracea in an unexplored coastal area of Galicia, NW Iberian Peninsula. Details of population ecology and vegetation, soil, climate and geographic data were recorded for this population. The “Endangered” threat category for the region is proposed, and actions for in situ and ex situ conservation are proposed. Seeds will be added to the germplasm collections of University of Santiago de Compostela and Misión Biológica de Galicia (CSIC) for further research on diverse aspects of the dynamics and ecophysiology of the population along with characterization and evaluation of useful traits.

Identidad territorial y paisaje. Evolución morfológica de los núcleos en Castilla y León.

Este estudio intenta esclarecer las transformaciones físicas y socioeconómicas de los asentamientos rurales de la región española de Castilla y León, durante la segunda mitad del siglo XX. Se analiza la evolución temporal de la forma urbana a través de un Sistema de Información Geográfico (SIG), calculando unos índices métricos y comparándolos con la información demográfica histórica. Los resultados pretenden mostrar los efectos de la especialización funcional económica, causada por la integración en las jerarquías productivas globales, sobre la estructura urbana. La pérdida gradual de las características tradicionales de los pueblos castellanos, como la compacidad y la integración en el entorno, debido a la pérdida o degradación de la arquitectura popular y la construcción de nuevas edificaciones industriales, supone un riesgo para las futuras políticas de desarrollo local. Se considera necesario preservar la identidad paisajística y evitar la destrucción del patrimonio cultural para poder revitalizar estos territorios.

'Not Forsworn with Pink Ribbons': Hannah More, Thomas De Quincey, and the Literature of Power

De Quincey's conception of the literature of "power" as opposed to that of "knowledge," has proved to be one of the most influential of romantic theories of literature, playing no small part in the canonization of Wordsworth. De Quincey's early acquaintance with the Lyrical Ballads was made through the Evangelical circles of his mother, who was a follower of Hannah More and a member of the Clapham sect. In later years, however, De Quincey repudiated his early Evangelical upbringing and wrote quite scathingly of the literary pretensions of Hannah More. This paper attempts to uncover the revisionary nature of De Quincey's later reminiscences of More and to indicate thereby the covert influence of Evangelical thinking on his literary theorizing. Far from absolving literature of politics, however, colonialist and nationalist imperatives typical of Evangelical thinking may be seen to operate within the spiritualized and aesthetic sphere to which literary power is arrogated by De Quincey.