A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification

This article is available from: http://www.biomedcentral.com/1471-2105/8/442[Background] Classification procedures are widely used in phylogenetic inference, the analysis of expression profiles, the study of biological networks, etc. Many algorithms have been proposed to establish the similarity between two different classifications of the same elements. However, methods to determine significant coincidences between hierarchical and non-hierarchical partitions are still poorly developed, in spite of the fact that the search for such coincidences is implicit in many analyses of massive data.[Results] We describe a novel strategy to compare a hierarchical and a dichotomic non-hierarchical classification of elements, in order to find clusters in a hierarchical tree in which elements of a given "flat" partition are overrepresented. The key improvement of our strategy respect to previous methods is using permutation analyses of ranked clusters to determine whether regions of the dendrograms present a significant enrichment. We show that this method is more sensitive than previously developed strategies and how it can be applied to several real cases, including microarray and interactome data. Particularly, we use it to compare a hierarchical representation of the yeast mitochondrial interactome and a catalogue of known mitochondrial protein complexes, demonstrating a high level of congruence between those two classifications. We also discuss extensions of this method to other cases which are conceptually related.[Conclusion] Our method is highly sensitive and outperforms previously described strategies. A PERL script that implements it is available at http://www.uv.es/~genomica/treetracker.Our group is supported by Grant SAF2006-08977 (Ministerio de Educación y Ciencia [MEC], Spain). A.M. was the recipient of a predoctoral fellowship from the MEC.Peer reviewe

How Athila retrotransposons survive in the Arabidopsis genome

<p>Abstract</p> <p>Background</p> <p>Transposable elements are selfish genetic sequences which only occasionally provide useful functions to their host species. In addition, models of mobile element evolution assume a second type of selfishness: elements of different familes do not cooperate, but they independently fight for their survival in the host genome.</p> <p>Results</p> <p>We show that recombination events among distantly related Athila retrotransposons have led to the generation of new Athila lineages. Their pattern of diversification suggests that Athila elements survive in <it>Arabidopsis </it>by a combination of selfish replication and of amplification of highly diverged copies with coding potential. Many Athila elements are non-autonomous but still conserve intact open reading frames which are under the effect of negative, purifying natural selection.</p> <p>Conclusion</p> <p>The evolution of these mobile elements is far more complex than hitherto assumed. Strict selfish replication does not explain all the patterns observed.</p

Solar Corona. Espacio ciudadano en el barrio del Carmen, Valencia.

Entrevista realizada por Teresa Marín García y Enrique Salom Marco (Petit Comité de Resistencia Audiovisual) a dos miem- bros de la asamblea del Solar Corona, un espacio autogestio- nado recuperado por la ciudadanía. Extracto que forma parte del proyecto en proceso Cultura Colectiva de la Comunidad Valenciana (CCCv)

Smart kitchen for Ambient Assisted Living

El envejecimiento de la población es una realidad en todos los países desarrollados. Las predicciones de crecimiento de esta población son alarmantes, planteando un reto para los servicios sociales y sanitarios. Las personas ancianas padecen diversas discapacidades que se van acentuando con la edad, siendo más propensas a sufrir accidentes domésticos, presentando problemas para realizar tareas cotidianas, etc. Esta situación conlleva a una pérdida paulatina de capacidades que en muchas ocasiones acaba con la vida autónoma de la persona. En este contexto, las Tecnologías de la Información y Comunicación (TIC) aplicadas al entorno doméstico pueden jugar un papel importante, permitiendo que las personas ancianas vivan más tiempo, de forma independiente en su propio hogar, presentando, por tanto, una alternativa a la hospitalización o institucionalización de las mismas. Este trabajo da un paso más en este sentido, presentando el diseño y desarrollo de un Ambiente Inteligente en la cocina, que ayuda a las personas ancianas y/o con discapacidad a desempeñar sus actividades de la vida diaria de una forma más fácil y sencilla. Esta tesis realiza sus principales aportaciones en dos campos: El metodológico y el tecnológico. Por un lado se presenta una metodología sistemática para extraer necesidades de colectivos específicos a fin de mejorar la información disponible por el equipo de diseño del producto, servicio o sistema. Esta metodología se basa en el estudio de la interacción Hombre-Máquina en base a los paradigmas y modelos existentes y el modelado y descripción de las capacidades del usuario en la misma utilizado el lenguaje estandarizado propuesto en la Clasificación Internacional del Funcionamiento, de la Discapacidad y de la Salud (CIF). Adicionalmente, se plantea el problema de la evaluación tecnológica, diseñando la metodología de evaluación de la tecnología con la finalidad de conocer su accesibilidad, funcionalidad y usabilidad del sistema desarrollado y aplicándola a 61 usuarios y 31 profesionales de la gerontología. Desde un punto de vista técnico, se afronta el diseño de un ambiente asistido inteligente (Ambient Assisted Living, AAL) en la cocina, planteando y definiendo la arquitectura del sistema. Esta arquitectura, basada en OSGi (Open Services Gateway initiative), oferta un sistema modular, con altas capacidades de interoperabilidad y escalabilidad. Además, se diseña e implementa una red de sensores distribuida en el entorno con el fin de obtener la mayor información posible del contexto, presentando distintos algoritmos para obtener información de alto nivel: detección de caídas o localización. Todos los dispositivos presentes en el entorno han sido modelados utilizando la taxonomía propuesta en OSGi4AmI, extendiendo la misma a los electrodomésticos más habituales de la cocina. Finalmente, se presenta el diseño e implementación de la inteligencia del sistema, que en función de la información procedente del contexto y de las capacidades del usuario da soporte a las principales actividades de la vida diaria (AVD) en la cocina

3D mapping of the SPRY2 domain of ryanodine receptor 1 by single-particle Cryo-EM

The type 1 skeletal muscle ryanodine receptor (RyR1) is principally responsible for Ca(2+) release from the sarcoplasmic reticulum and for the subsequent muscle contraction. The RyR1 contains three SPRY domains. SPRY domains are generally known to mediate protein-protein interactions, however the location of the three SPRY domains in the 3D structure of the RyR1 is not known. Combining immunolabeling and single-particle cryo-electron microscopy we have mapped the SPRY2 domain (S1085-V1208) in the 3D structure of RyR1 using three different antibodies against the SPRY2 domain. Two obstacles for the image processing procedure; limited amount of data and signal dilution introduced by the multiple orientations of the antibody bound in the tetrameric RyR1, were overcome by modifying the 3D reconstruction scheme. This approach enabled us to ascertain that the three antibodies bind to the same region, to obtain a 3D reconstruction of RyR1 with the antibody bound, and to map SPRY2 to the periphery of the cytoplasmic domain of RyR1. We report here the first 3D localization of a SPRY2 domain in any known RyR isoform.The authors want to thank the Brigham and Women’s Hospital Biomedical Research Institute (to MS), the Australian National Health and the Medical Research Council (471418 to AD, MC and PB), and the European Commission (Marie Curie Action PIOF-GA-2009-237120 to AP-M)

Los colectivos artísticos: microcosmos y motor del procomún de las artes

The collective artistic activity can be seen as a metaphor for the small-scale cultural commons. In its processes and strategies can be traced many of the key issues and conflicts that make the keys of the commons in regard to the arts, as cultural and intangible. The artistic groups are also essential elements for building assets/goods and resources that make up the cultural structure, very particular local contexts, while having great potential as builders of larger scale networks. After a brief discussion of these issues is presented an initiative of a collaborative platform project, CCCV, starting from the reality of a local context arises the objective of generating a network-file-laboratory to create and share knowledge about the collective culture.La actividad de los colectivos artísticos pueden entenderse como una metáfora del procomún cultural a pequeña escala. En sus procesos y estrategias puede rastrearse muchas de las cuestiones esenciales y conflictos que conforman las claves del procomún en lo que respecta a las artes, como bien cultural e intangible. Los colectivos artísticos, son además elementos esenciales para la construcción de bienes y recursos que conforman el tejido cultural, de forma muy particular en los contextos locales, al tiempo que tienen un gran potencial como constructores de redes a mayor escala. Tras un breve análisis de estos aspectos se presenta una iniciativa de un proyecto de plataforma colaborativa CCCV, que partiendo de la realidad de un contexto local se plantea el objetivo de generar un archivo-red-laboratorio para crear y compartir conocimientos en torno a la cultura colectiva

APROXIMACIÓN AL TURISMO DE SALUD DESDE LA GEOGRAFÍA. DEFINICIÓN Y CAMPO DE ESTUDIO

Since ancient history, human beings have travelled to other places in search of remedies to improve their health or find a cure for their disease. In the last decades, the number of people traveling in search of medical and wellness treatments and interventions has grown significantly, making health tourism an important sector of the global economy. Therefore, health tourism, due to its potential, represents a great opportunity for business, wealth, and employment development. Spain, thanks to its geographical position and a series of environmental, climatic, cultural and lifestyle characteristics, has become the second most visited country by tourists. Its wide range of health services and its availability of resources have made it one of the main tourist destinations for medical and/or wellness reasons. Despite the innumerable benefits of international health tourism, the development of this tourism typology can also have adverse effects. These disadvantages must be overcome through healthcare strategies - by the responsible governments and institutions - to guarantee and accredit the veracity and quality of these services in the visited countries. This would give greater certainty and trust to health tourists without affecting access and health care for residents in the receiving country.Desde la antigüedad, los seres humanos han viajado a otros lugares en busca de remedios para mejorar su salud o encontrar una cura a su enfermedad. En las últimas décadas, el número de personas que viajan en busca de tratamientos e intervenciones médicas y de bienestar ha crecido notablemente, convirtiendo al turismo de salud en un importante sector de la economía mundial. Por ello, el turismo de salud, debido a su potencial, representa una gran oportunidad de negocio, creación de riqueza y empleo. España, gracias a su posición geográfica y a una serie de características ambientales, climáticas, culturales y estilos de vida se ha convertido en el segundo país más visitado por los turistas. Su amplia oferta de servicios sanitarios y su disponibilidad de recursos la han convertido en uno de los principales destinos turísticos por motivos médicos y/o de bienestar. A pesar de los innumerables beneficios del turismo de salud internacional, el desarrollo de esta tipología también puede tener efectos adversos, tanto en el país receptor, como en el país emisor. Estos inconvenientes deben superarse mediante estrategias sanitarias - por parte de los gobiernos y las instituciones responsables - que permitan garantizar y acreditar la veracidad y calidad de estas prestaciones en los países receptores. De este modo, se daría mayor tranquilidad y confianza a los turistas de salud sin que ello repercuta en el acceso y la atención sanitaria por parte de los residentes en el país receptor

Subsistence of early anatomically modern humans in Europe as evidenced in the Protoaurignacian occupations of Fumane Cave, Italy

Documenting the subsistence strategies developed by early modern humans is relevant for understanding the success of their dispersal throughout Eurasia. Today, we know that there was not a single colonization event and that the process was progressive while coping with the MIS3 abrupt climatic oscillations. Modern humans expanded into the continent by adapting to different topographic situations and by exploiting resources in diverse ecological niches. The northern part of Italy is one of the first European regions where early modern humans are documented. Here, we present the subsistence regimen adopted by the Protoaurignacian groups in two different levels in Fumane Cave based on archaeozoological data. New radiocarbon dates confirm an overlap between Uluzzian and Protoaurignacian occupations, around 42 and 41,000 cal BP, and reveal that modern humans occupied the cave from GI10 to GS9, the last level coinciding with the Heinrich Event 4. The data indicate seasonal site occupations during late spring/summer and that prey exploitation was focused mostly on ibex and chamois, killed in nearby areas. The whole faunal assemblage suggests the presence of early modern humans in a cold environment with mostly open landscapes and patchy woodlands. The estimation of net primary productivity (NPP) in Fumane, compared with other contemporaneous Italian sites, reflects how the NPP fluctuations in the Prealpine area, where Fumane is located, affected the biotic resources in contrast to known Mediterranean sites. From a pan- European perspective, the spatiotemporal fluctuation of the NPP versus the subsistence strategies adopted by Protoaurignacian groups in the continent supports rapid Homo sapiens dispersal and resilience in a mosaic of environments that were affected by significant climate changes.This research is funded by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 818299‐SUBSILIENCE project (https:// www. subsi lience. eu). G. T. and M.V.C. were funded by the former project and later by a Juan de la Cierva Formación Grant (Ref: FJC2019-040637-I and FJC2021-047601-I) funded by the Spanish Ministry of Science and Innovation. Research and fieldwork at Fumane Cave are coordinated by the University of Ferrara (M. Peresani) in the framework of a project supported by the Ministry of Culture—SAPAB Archaeological Superintendence, public institutions (Lessinia-Regional Natural Park, B.I.M. Adige, Fumane Municipality), private associations and companies, and in collaboration with Italian and European research centres. The authors thank all the colleagues from EvoAdapta Group for the constant enriching discussions and Prof. L. G. Straus for his edition of the English in the accepted version. Finally, we are grateful to two anonymous reviewers for their valuable comments and suggestions which have helped us to improve the manuscript

Approaches to health tourism from the geography. Definition and study field

Desde la antigüedad, los seres humanos han viajado a otros lugares en busca de remedios curativos para mejorar su salud o encontrar una cura a su enfermedad. En las últimas décadas, el número de personas que viajan en busca de tratamientos e intervenciones médicas y de bienestar ha crecido notablemente, convirtiendo al turismo de salud en un importante sector de la economía mundial. Por ello, el turismo de salud, debido a su potencial, representa una gran oportunidad de negocio, creación de riqueza y empleo. España, gracias a su posición geográfica y a una serie de características ambientales, climáticas, culturales y estilos de vida se ha con-vertido en el segundo país más visitado por los turistas. Su amplia oferta de servicios sanitarios y su disponibilidad de recursos la han convertido en uno de los principales destinos turísticos por motivos médicos y/o de bienestar. A pesar de los innumerables beneficios del turismo de salud internacional, el desarrollo de esta tipología también puede tener efectos adversos, tanto en el país receptor, como en el país emisor. Estos inconvenientes deben superarse mediante estrategias sanitarias - por parte de los gobiernos y las instituciones responsables - que permitan garantizar y acreditar la veracidad y calidad de estas prestaciones en los países receptores. De este modo, se daría mayor tranquilidad y confianza a los turistas de salud sin que ello repercuta en el acceso y la atención sanitaria por parte de los residentes en el país receptorSince ancient history, human beings have traveled to other places in search of healing remedies to improve their health or find a cure for their disease. In the last decades, the number of people traveling in search of medical and wellness treatments and interventions has grown significantly, making health tourism an important sector of the global economy. Therefore, health tourism, due to its potential, represents a great opportunity for business, wealth, and employment development. Spain, thanks to its geographical location and a series of environmental, climatic, cultural and lifestyle characteristics, has become the second most visited country by tourists. Its wide range of health services and its availability of resources have made it one of the main tourist destinations for medical and/or wellness rea-sons. Despite the innumerable benefits of international health tourism, the development of this tourism typology can also have adverse effects. These disadvantages must be overcome through healthcare strategies - by the responsible governments and institutions - to guarantee and accredit the veracity and quality of these services in the visited countries. This would give greater safety and security to health tourists without affecting access and health care for residents in the receiving countr

Protocol and Architecture to Bring Things into Internet of Things

The Internet of Things (IoT) concept proposes that everyday objects are globally accessible from the Internet and integrate into new services having a remarkable impact on our society. Opposite to Internet world, things usually belong to resource-challenged environmentswhere energy, data throughput, and computing resources are scarce. Building upon existing standards in the field such as IEEE1451 and ZigBee and rooted in context semantics, this paper proposes CTP (Communication Things Protocol) as a protocol specification to allow interoperability among things with different communication standards as well as simplicity and functionality to build IoT systems. Also, this paper proposes the use of the IoT gateway as a fundamental component in IoT architectures to provide seamless connectivity and interoperability among things and connect two different worlds to build the IoT: the Things world and the Internet world. Both CTP and IoT gateway constitute a middleware content-centric architecture presented as the mechanism to achieve a balance between the intrinsic limitations of things in the physical world and what is required fromthem in the virtual world. Said middleware content-centric architecture is implemented within the frame of two European projects targeting smart environments and proving said CTP’s objectives in real scenarios