1,721,140 research outputs found
Dynamic flexibility in the structure and function of photosystem II in higher plant thylakoid membranes: The grana enigma
No full textGrana are not essential for photosynthesis, yet they are ubiquitous in higher plants and in the recently evolved Charaphyta algae; hence grana role and its need is still an intriguing enigma. This article discusses how the grana provide integrated and multifaceted functional advantages, by facilitating mechanisms that fine-tune the dynamics of the photosynthetic apparatus, with particular implications for photosystem II (PSII). This dynamic flexibility of photosynthetic membranes is advantageous in plants responding to ever-changing environmental conditions, from darkness or limiting light to saturating light and sustained or intermittent high light. The thylakoid dynamics are brought about by structural and organizational changes at the level of the overall height and number of granal stacks per chloroplast, molecular dynamics within the membrane itself, the partition gap between appressed membranes within stacks, the aqueous lumen encased by the continuous thylakoid membrane network, and even the stroma bathing the thylakoids. The structural and organizational changes of grana stacks in turn are driven by physicochemical forces, including entropy, at work in the chloroplast. In response to light, attractive van der Waals interactions and screening of electrostatic repulsion between appressed grana thylakoids across the partition gap and most probably direct protein interactions across the granal lumen (PSII extrinsic proteins OEEp-OEEp, particularly PsbQ-PsbQ) contribute to the integrity of grana stacks. We propose that both the light-induced contraction of the partition gap and the granal lumen elicit maximisation of entropy in the chloroplast stroma, thereby enhancing carbon fixation and chloroplast protein synthesizing capacity. This spatiotemporal dynamic flexibility in the structure and function of active and inactive PSIIs within grana stacks in higher plant chloroplasts is vital for the optimization of photosynthesis under a wide range of environmental and developmental conditions. © 2008 Springer Science+Business Media B.V.Australian Research Council for financial support through Discovery Project Grant DP0664719.Peer Reviewe
Bioinformatic strategies to analyse multiple cancer subtypes and build associated gene networks using genomic profiling: integrative studies on hematological malignancies
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APID: Agile protein interaction DataAnalyzer
No full textThe online version of this article has been published under an open access model.Agile Protein Interaction DataAnalyzer (APID) is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore >35 000 different proteins and 111 000 different proven interactions. The web includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Such parameters are for the 'proteins': connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; and for the 'interactions': number of methods, GO overlapping, iPfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. The application is available open access at http://bioinfow.dep.usal. es/apid/. © The Author 2006. Published by Oxford University Press. All rights reserved.We acknowledge the funding and support provided by the Spanish Ministerio de Sanidad y Consumo, ISCIII (research grant ref. PI030920), Junta de Castilla y Leon (research grant ref. SA104/03) and Fundación BBVA (Bioinformatics Grants Program). C.P. holds a research grant for PhD from Junta de Castilla y Leon (ref. BOCyL no. 119, EDU/777/2005).Peer Reviewe
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Desarrollo y aplicación de métodos estadísticos basados en recortes imparciales a datos de expresión génica de alta dimensionalidad
No full textTesis Doctoral presentada por Itziar Fernández Martínez para optar al grado de Doctor por la Universidad de Valladolid (Departamento de Estadística e Investigación Operativa).En esta Tesis proponemos la utilización de métodos estadísticos basados en recortes imparciales [Gordaliza, 1991] que, aplicados a matrices de datos de expresión génica de alta dimensionalidad, permiten obtener estimadores con funcionamiento robusto mediante la eliminación de un porcentaje de individuos. La aplicación de este tipo de estrategias nos va a permitir caracterizar el nivel de expresión típico de cada gen en medidas de escala genómica (genome-wide) como el que aparece asociado al comportamiento de una mayoría de condiciones, utilizando una adaptación del estimador smart [Cuesta-Albertos et al, 2008] a una situación unidimensional. Nuestra aproximación plantea utilizar como procedimiento de recorte de partida el estimador MCD de [Rousseeuw, 1985], lo que permite obtener una representación simplificada para el estimador smart y la obtención de un algoritmo más eficiente que el disponible actualmente. La estimación de los parámetros que describen el comportamiento típico de un gen, va a permitir identificar mejor condiciones que manifiestan expresión diferencial y nuevas definiciones para caracterizar genes que muestran comportamientos de expresión generalizada (tipo gen housekeeping). El estimador propuesto será la base de estadísticos para identificar comportamientos atípicos en muestras clasificadas inicialmente como homogéneas, y también para contrastar expresión diferencial entre condiciones diferentes. Basado en los mismos principios, proponemos la utilización de metodología para encontrar grupos de genes (clústers) que co-expresan y para encontrar agrupaciones conjuntas de genes y de condiciones que comparten patrones de co-expresión. Los procedimientos de agrupación propuestos incorporan el recorte de un porcentaje de genes y de condiciones para aumentar la robustez de la clasificación propuesta. Para todos los procedimientos propuestos se han desarrollado funciones, algoritmos y programas de R [R Development Core Team, 2011] que los implementan. El funcionamiento de los métodos se ha ilustrado utilizando datos simulados y sobre todo utilizando varios conjuntos de datos reales correspondientes a experimentos y estudios biológicos con microarrays de oligonucleótidos de alta densidad, que es una de las tecnologías genómicas de gran escala más utilizadas para el estudio de la expresión génica.Peer Reviewe
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