Epigenetics: Biology's Quantum Mechanics

The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920s and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene – the molecular biological view and the epigenetic view – are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider

Knowledge-Rich Self-Supervision for Biomedical Entity Linking

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision ($\tt KRISS$) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces $\tt KRISSBERT$, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy

RETOS Y EXPERIENCIAS PROFESIONALES DE UNA PROFESORA VISITANTE EN EE.UU.

   El objetivo de este trabajo es mostrar algunas de las dinámicas desarrolladas en la clase de Español como segunda lengua y de Ciencias Sociales en español, dentro del programa bilingüe implantado en la primera Academia Internacional de Español en EEUU, como resultado de la experiencia profesional como profesora visitante. El modelo de enseñanza-aprendizaje que se propone parte de una instrucción multidireccional, participativa y activa, de la contextualización del saber, del fomento de la creatividad y del pensamiento, así como de la estimulación del interés a través del juego y la competición. Por tanto, explicaremos brevemente en qué consiste el programa de profesores visitantes y cuál es el contexto sociocultural del estado en que tuvo lugar la estancia profesional; a continuación, analizaremos el tipo de programa bilingüe del centro norteamericano; y finalmente, nos centraremos en cuál era el perfil del alumnado del centro, en cómo era conveniente organizar cada periodo de clase y cuáles fueron algunas de las dinámicas de clase que favorecieron su aprendizaje

Educación, democracia y ciudadanía en el siglo XXI desde el proyecto político educativo de Paulo Freire

This article has two main purposes: first, to reflect on the possibilities of education in the forming process of citizenship, and second, analyze the relationship between democracy, citizenship and education from a critical and reflective educator Paulo Freire, one of the principal educational thinkers in the educational politics worldwide. His valuable contributions have been breaking new ways in the educational area using as tool of social transformation in the construction of really democratic and participative societies. It also puts in evidence the relationship between education and citizenship, and political nature and training to create critical citizens, responsible and active. From this perspective, the education is synonymous of formative practice and implies a way of intervening and transforming the world by individuals through their own knowledge. His model of education for freedom as a precondition for democracy has managed to influence the new liberating ideas and the pedagogic European renovations, establishing solid bases on the cultural, social and economic reality which it is contextualized.El presente artículo tiene dos propósitos fundamentales: primero, reflexionar sobre las posibilidades de la educación en el proceso de conformación de la ciudadanía; y, segundo, analizar la relación entre educación, democracia y ciudadanía desde la mirada crítica y reflexiva del pedagogo Paulo Freire, uno de los principales pensadores educacionales y referentes en las políticas educativas a nivel mundial. Sus valiosas aportaciones han logrado abrir nuevos caminos en el ámbito educativo sirviendo de herramienta de transformación social en la construcción de sociedades verdaderamente democráticas y participativas. Asimismo, pone en evidencia la relación de la educación con la ciudadanía, y su carácter político y formativo para crear ciudadanos críticos, responsables y activos. Desde este prisma, la educación es sinónimo de praxis formativa e implica una forma de intervenir y de transformar el mundo, por parte de los individuos a través de sus propios conocimientos. Su modelo de educación para la libertad como condición previa para lograr la democracia ha logrado influir en las nuevas ideas liberadoras y en las renovaciones pedagógicas europeas, estableciendo bases sólidas basadas en la realidad cultural, social y económica donde se contextualizado

Honduras 2013 : proceso electoral, financiamiento y transparencia. Informe de monitoreo

El proceso electoral que concluyó con la celebración de las elecciones generales el domingo 24 de noviembre del año 2013, fue un proceso especial y de gran significado en la historia de la transición política hacia la democracia en la sociedad hondureña. A lo largo de esta transición, a veces tan errática y difícil como incierta y prolongada, los hondureños hemos ido a las urnas en una decena de veces para escoger a nuestros gobernantes. Pero nunca antes el torneo electoral había sido tan abierto y plural, así como tan reñido y polarizado ideológicamente, como lo ha sido en esta ocasión. Marcadas por la impronta del reciente golpe de Estado perpetrado el 28 de junio del año 2009, las elecciones de 2013 se llevaron a cabo en medio de un clima de mucha expectación ciudadana y grandes posibilidades de llevar a cabo cambios políticos importantes en la vida de la nación. Nunca antes el status quo había sido tan cuestionado y puesto en duda como en el proceso electoral del año 2013

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Next-generation sequencing and bioinformatic approaches to detect and analyze influenza virus in ferret

Origin and evolution of the nuclear auxin response system.

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal

Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis.

Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure-function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4-β-xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. Of the 12 known gene classes involved in 1,4-β-xylan formation, XYS1/IRX10 in plants, IRX7, IRX8, IRX9, IRX14 and GUX occurred for the first time in charophyte algae. An XYS1/IRX10 ortholog from Klebsormidium flaccidum, designated K. flaccidumXYLAN SYNTHASE-1 (KfXYS1), possesses 1,4-β-xylan synthase activity, and 1,4-β-xylan occurs in the K. flaccidum cell wall. These data suggest that plant 1,4-β-xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide-based plant cell walls

The ReAS Algorithm

<p>We start by computing <i>K-</i>mer depth, which is the number of times that a <i>K-</i>mer appears in the shotgun data. Copy number refers to how often a <i>K-</i>mer appears in the assembled genome. Depth divided by copy number is the coverage. We seed the process using a randomly chosen high-depth <i>K-</i>mer. All shotgun reads containing this <i>K-</i>mer are retrieved and trimmed into 100-bp segments centered at that <i>K-</i>mer. When the sequence identity between them exceeds a preset threshold, they are assembled into an ICS using ClustalW. We perform an iterative extension by selecting high-depth <i>K-</i>mers at both ends of the ICS and repeating the above procedure. After all such extensions are done, clone-end pairing information is used to resolve ambiguous joins and to break misassemblies, but not to join fragmented assemblies. The final consensus is our ReAS TE.</p