Internet y África: de la brecha a la esperanza digital. Redes, libertades y comunicación

With a critical and comparative perspective, the article outlines the digital universe reality in Africa, taking into account regional differences. Descriptively, we are interested in issues such as Internet access situation, policies and existing regulatory infrastructure, the digital economy, the impact of new media, e-government initiatives and digital citizen participation, together with some aspects of the cultural colonization that may occur as a result of the universalization of a clearly westernized Internet. Con una mirada crítica y comparativa se esboza la realidad del universo digital en África, teniendo en cuenta las diferencias regionales existentes. De modo descriptivo, nos interesamos por cuestiones como la situación del acceso a Internet, las políticas de infraestructuras y regulatorias existentes, la economía digital, el impacto de los nuevos medios, las iniciativas de gobierno electrónico y participación ciudadana digital, y algunos aspectos de la colonización cultural que se puede producir a cuentas de una red claramente occidentalizada

Emergent patterns in protein, microbial and mutualistic systems

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 17-04-2015In this thesis we analyse emergent patterns in complex biological systems. We say that these patterns emerge, given that they result from behaviours of the system that are di cult to explain starting from a microscopic description. These behaviours are strongly dependent on the interactions between elements, and thus our research focuses on the identi cation and evaluation of interaction networks. In particular, we have analysed interactions that may re ect the response of the system to long term conditions, whose analysis may be compatible with an evolutionary interpretation. The methodological and conceptual framework needed for the development of our research is complex. This is the reason why the rst part of the thesis is devoted to clarify the epistemological approximation we have followed. In subsequent chapters, we present our research results, which have been developed around three systems with notable di erences among them. The rst system considers a representative subset of all the protein structures known up to date. We develop a method that objectively demonstrates the existence of structural protein classes known as folds, de ning conserved interaction patterns between amino-acids. We go deeper into the evolutionary interpretation of this result investigating the role of protein function in the structural conservation and divergence. Second, we analyse high-throughput sequencing experiments collecting the presence of bacterial taxa in di erent environments. From this data we infer aggregation and segregation patterns suggesting that bacterial mutualistic interactions are very relevant, and whose functional role is explored in more detail analysing the bacterial assembly process in a group of infants during their development. Last, we have considered mutualistic communities of plants and pollinators. We predict the structural stability of this system de ning two magnitudes: the e ective interspeci c competition and the propagation of perturbations. These magnitudes rationalize the relative e ect of competition versus mutualism and, in particular, of the di erent mutualistic networks in the structural stability, which we show has a main role for sustaining biodiversityEn esta tesis analizamos patrones emergentes en sistemas biológicos complejos. Estos patrones los cali camos como emergentes porque son el resultado de comportamientos del sistema difíciles de caracterizar partiendo de una descripción microscópica. Dichos comportamientos son fuertemente dependientes de las interacciones entre elementos, por lo que nos centramos en la identi cación y evaluación de redes de interacción. En particular, hemos analizado interacciones que esperamos que re ejen la respuesta del sistema a condiciones relevantes en escalas de tiempo largas, cuyo análisis puede ser compatible con una interpretación evolutiva. El marco metodológico y conceptual necesario para el desarrollo de nuestra investigación es complejo. Por ello, la primera parte de la tesis está orientada a clari car la aproximación epistemológica que hemos seguido. En los siguientes capítulos presentamos el resultado de nuestra investigación, desarrollada alrededor de tres sistemas con notables diferencias entre ellos. El primer sistema considera un conjunto representativo de todas las estructuras de proteínas conocidas hasta la fecha. Desarrollamos un método que demuestra objetivamente la existencia de clases estructurales de proteí- nas conocidas como folds, que de nen patrones de interacción entre aminoácidos. Profundizamos en la interpretación evolutiva del resultado investigando el rol de la función de proteínas en la conservación o divergencia estructural. En segunda lugar analizamos experimentos de secuenciación masiva que recogen la presencia de taxones bacterianos en distintos ambientes. De estos datos inferimos patrones de agregación y segregación que sugieren que las interacciones mutualistas entre bacterias son muy relevantes, y cuyo rol funcional es explorado en más detalle analizando el proceso de ensamblaje bacteriano en un grupo de bebés durante su desarrollo. Por último, hemos considerado comunidades mutualistas de plantas y polinizadores. Predecimos la estabilidad estructural de este sistema de niendo dos magnitudes: la competición efectiva interespecí ca y la propagación de las perturbaciones. Estas magnitudes permiten racionalizar el efecto relativo de la competición versus el mutualismo y, en particular, de las distintas redes mutualistas en la estabilidad estructural, cuyo papel mostramos que es esencial en el sostenimiento de la biodiversida

11 - Modelos simplificados de plegamiento de proteínas

Chapter 11 of the book "Bioinformática con Ñ" a project aiming to provide specialized educational bibliography on Bioinformatics for Spanish speakers. The result consists on more than 500 pages where the following matters are covered: biomedical databases, sequence analysis, phylogeny and evolution, structural biology, including diverse topics such as docking, virtual screening or molecular dynamics, statistics and R, systems biology, programming skills, data mining, parallel computation, bibliography management and science article writing. Note: Exercises related with the contents of this section can be found in: Nido GS, Bachschmid-Romano L, Bastolla U, Pascual-García A. (2016) Learning structural bioinformatics and evolution with a snake puzzle. PeerJ Computer Science 2:e100 10.7717/peerj-cs.10

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.phpThis work was supported by the Ramon y Cajal program of the Spanish Science Ministry of Education and Science, Project ‘Centrosoma 3DBioinformatics’ of the program Consolider-Ingenio 2010 of the Spanish Ministry of Education and Science, Project BIO2005-0576 from the Spanish Ministry of Education and Science, Project 200520M157 from the Comunidad de Madrid, and Research Foundation ‘‘Ramon Areces’’.Peer reviewe

Use of Diagnostic and Therapeutic Resources in Patients Hospitalized for Heart Failure: Influence of Admission Ward Type (INCARGAL Study)

[Resumen] Antecedentes. La insuficiencia cardíaca es la enfermedad cardiológica de más crecimiento en las naciones desarrolladas, y supone ya la primera causa de ingreso en ancianos. No se ha estudiado bien la diferencia que el servicio de ingreso supone en cuanto al manejo de la insuficiencia cardíaca ni los factores que condicionan el servicio de ingreso. Objetivos. Establecer si existen diferencias de manejo pronóstico en función del servicio de ingreso (cardiología frente a medicina interna y geriatría) en pacientes con insuficiencia cardíaca. Pacientes y método. Estudio transversal en que 951 pacientes (505 varones y 446 mujeres) ingresados consecutivamente por insuficiencia cardíaca en los servicios de cardiología (n = 364), medicina interna y geriatría (n = 587) de 14 hospitales de Galicia fueron reclutados durante un período máximo de 6 meses, registrándose en el momento del ingreso las principales variables epidemiológicas y clínicas, complicaciones, tratamientos y situación en el momento del alta. Resultados. Los pacientes con insuficiencia cardíaca tenían una edad media de 75,5 ± 12,4 años (78,5 ± 10,6 en mujeres y 72,7 ± 13,5 en varones). La estancia media fue de 11 ± 8 días, con un 50,8% de primeros ingresos, siendo la mortalidad global hospitalaria del 6,8%. El 58,9% de los pacientes tenía hipertensión arterial, el 31,8% cardiopatía isquémiea, el 27,7% valvulopatía, el 28,4% diabetes mellitus y el 32,5% EPOC. Por servicios, los pacientes atendidos en servicios de cardiología son más jóvenes (72,5 ± 13,3 frente a 77,4 ± 11,4 años; p < 0,005), con más varones (51,9 frente a 3,7%; p < 0,01), mayor proporción de primeros ingresos (54,8 frente a 48,4; p < 0,05) Y de edema agudo de pulmón (22,8 frente a 9,2%; P < 0,001). Las odds ratio (y sus intervalos de confianza [IC] del 95%) de realización de procedimientos diagnósticos y terapéuticos en función del servicio de ingreso (el grupo de referencia es medicina interna-geriatría), ajustando por edad, sexo, función sistólica, número de ingresos y antecedentes personales de demencia, hipertensión arterial, EPOC, infarto agudo de miocardio, valvulopatía, arteriopatía periférica y cardiopatía isquémica, son: ecocardiograma, 3,31 (2,42-4,52); cateterismo, 6,61 (2,78-15,73); ingreso en UCI, 3,4 (1,48-7,8); revascularización, 2,93 (0,54-15,74), y tratamiento con bloqueado res beta 2,87 (1,37-6,04). No se observaron diferencias en la mortalidad temprana (6,6% en cardiología frente a 7% en medicina interna-geriatría) ni en la estancia media. Conclusiones. El servicio de ingreso determinó una clara diferencia en el manejo de la insuficiencia cardíaca, con una mayor adhesión a los protocolos de tratamiento y uso de recursos por parte de los cardiólogos que no se tradujo en diferencias en la mortalidad temprana. Se precisa un seguimiento de los pacientes para evaluar el impacto de estas diferencias en el pronóstico y la evolución de la insuficiencia cardíaca a medio y largo plazos, así como la relación coste-beneficio en una población de edad media avanzada.[Abstract] Background. Heart failure (HF) is the most rapidly growing cardiac pathology in industrialized countries, and already the primary cause of hospital admissions of elderly people. Outside the field of clinical trials, there have not been many studies in Spain of the influence of the admission department on diagnostic and therapeutic management, whether this affects short-term and long-term prognosis, and the factors that determine the department the patient is admitted to. Objectives. To analyze whether management and prognosis of patients admitted with heart failure differ depending on the admission ward (cardiology versus internal medicine-geriatrics). Patients and method. Cross-sectional study of 951 patients (505 men and 446 women) consecutively hospitalized for HF in the cardiology (n = 363) and internal medicine-geriatrics (n = 588) wards of 12 hospitals of Galicia and recruited over a maximum period of 6 months. The main epidemiological and clinical variables were recorded at admission, and the complications, treatments, and clinical status were recorded at release. Results. HF patients had a mean age of 75.5 ± 12 years (women 78.5 years and men 72.6 years). The average hospitalization time was 11 ± 8 days and 50.8% were first admissions. Total hospital mortality was 6.8%. Fifty-nine percent (58.9%) of patients had arterial hypertension, 31.9% ischemic heart disease, 27.6% cardiac valve disease, 28.5% diabetes mellitus, and 32.5% chronic obstructive pulmonary disease (COPO). The patients admitted to cardiology ward were younger (72.5 ± 13 vs 77.4 ± 11 years; p < 0.005), more frequently men (51.9 vs 43.7%; P < 0.005), more often first hospitalizations (54.8 vs 48.4%; P < 0.005), and acute pulmonary edema was more common (22.8 vs 9.2%; P < 0.005). The odds ratio (and 95% CI) for therapeutic and diagnostic procedures in relation to admission ward (reference group internal medicine-geriatrics), adjusted for age, sex, systolic function, number of hospitalizations, and history of dementia, hypertension, COPO, AMI, valve disease and ischemic heart disease, are: echocardiogram, 3.49 (2.58-4.73); catheterization, 6.42 (3.29-12.55), admission to intensive care, 3.94 (2.15-7.25), revascularization, 2.15 (0.57-8.08), and beta-blocker treatment, 3.39 (1.93-5.97). No differences in hospital mortality (6.6% in cardiology vs 7% in internal medicine-geriatrics) or average hospitalization time were found between departments. Conclusions. The admission ward was related with a clear difference in HF management, with better adherence to guidelines and more use of resources by cardiologists. This was unrelated with differences in hospital mortality so a longer follow-up of these patients is required to evaluate the impact of these therapeutic measures on the prognosis and evolution of HF, as well as the cost-benefit relation in an elderly patient population

A passive available bandwidth estimation methodology

The Available Bandwidth (AB) of an end-to-end path is its remaining capacity and it is an important metric for several applications such as overlay routing and P2P networking. That is why many AB estimation tools have been published recently. Most of these tools use the Probe Rate Model, which requires sending packet trains at a rate matching the AB. Its main issue is that it congests the path under measurement. We present a different approach: a novel passive methodology to estimate the AB that does not introduce probe traffic. Our methodology, intended to be applied between two separate nodes, estimates the path’s AB by analyzing specific parameters of the traffic exchanged. The main challenge is that we cannot rely on any given rate of this traffic. Therefore we rely on a different model, the Utilization Model. In this paper we present our passive methodology and a tool (PKBest) based on it. We evaluate its applicability and accuracy using public NLANR data traces. Our results -more than 300Gb- show that our tool is more accurate than pathChirp, a state-of-the-art active PRM-based tool. At the best of the authors’ knowledge this is the first passive AB estimation methodology.Preprin

Redes sociales en la radio española. Facebook, Twitter y Community Management

The social network burst in the Spanish Radio in the period between 2009-2010, transforming profoundly the relation with the listeners, and enriching significally the emission. The purpose of this study is to analyze the results of this symbiosis among media, in addition to the disparate benefit among various distant channels regarding this new tool. We will test out this decisive use, but incipient, and the clear superiority of Facebook over Twitter, the two most used platforms. Regarding the profile of whom they manage today the network in the Radio Station, it is notable that there is a lack of specific training in the community management.; Las redes sociales irrumpen en la radio española en la temporada 2009-10, transformando profundamente la relación con sus oyentes y enriqueciendo de forma notable la emisión. El propósito de este estudio es analizar los frutos de esta simbiosis entre medios y el aprovechamiento dispar que hacen las distintas cadenas generalistas de estas nuevas herramientas. Comprobamos un uso decidido, pero incipiente, y una clara primacía de Facebook sobre Twitter, las dos plataformas más usadas. Respecto del perfil de quienes hoy gestionan las redes sociales en las emisoras de radio, se constata su falta de formación específica en community management.; Sare sozialak 2009-10 denboraldian hasiko dira irrati espainiarrean presentzia izaten, entzuleekin harremana errotik eraldatuz eta emisioa nabarmen aberastuz. Ikerketa honen helburua komunikabideen arteko sinbiosi honen fruituak eta informazio orokorreko kate ezberdinek tresna berri hauetaz baliatzeko dituzten modu anitzak aztertzea da. Erabilera honen aldeko apustu argi baina hasiberria hautematen dugu, eta Facebook-en nagusitasuna Twiter-ekiko, bi plataforma erabilienen artean. Irrati emisoretan sare sozialak maneiatzen dituztenen perfilari dagokionez, community management gisa trebakuntza espezifikorik ez dutela ikusi da

Redes sociales en la radio española. Facebook, Twitter y Community Management

The social network burst in the Spanish Radio in the period between 2009-2010, transforming profoundly the relation with the listeners, and enriching significally the emission. The purpose of this study is to analyze the results of this symbiosis among media, in addition to the disparate benefit among various distant channels regarding this new tool. We will test out this decisive use, but incipient, and the clear superiority of Facebook over Twitter, the two most used platforms. Regarding the profile of whom they manage today the network in the Radio Station, it is notable that there is a lack of specific training in the community management.; Las redes sociales irrumpen en la radio española en la temporada 2009-10, transformando profundamente la relación con sus oyentes y enriqueciendo de forma notable la emisión. El propósito de este estudio es analizar los frutos de esta simbiosis entre medios y el aprovechamiento dispar que hacen las distintas cadenas generalistas de estas nuevas herramientas. Comprobamos un uso decidido, pero incipiente, y una clara primacía de Facebook sobre Twitter, las dos plataformas más usadas. Respecto del perfil de quienes hoy gestionan las redes sociales en las emisoras de radio, se constata su falta de formación específica en community management.; Sare sozialak 2009-10 denboraldian hasiko dira irrati espainiarrean presentzia izaten, entzuleekin harremana errotik eraldatuz eta emisioa nabarmen aberastuz. Ikerketa honen helburua komunikabideen arteko sinbiosi honen fruituak eta informazio orokorreko kate ezberdinek tresna berri hauetaz baliatzeko dituzten modu anitzak aztertzea da. Erabilera honen aldeko apustu argi baina hasiberria hautematen dugu, eta Facebook-en nagusitasuna Twiter-ekiko, bi plataforma erabilienen artean. Irrati emisoretan sare sozialak maneiatzen dituztenen perfilari dagokionez, community management gisa trebakuntza espezifikorik ez dutela ikusi da

Optical transitions and excitonic recombination in InAs/InP self-assembled quantum wires

InAs self-assembled quantum wire structures have been grown on InP substrates and studied by means of photoluminescence and polarized-light absorption measurements. According to our calculations, the observed optical transitions in each sample are consistent with wires of different heights, namely from 6 to 13 monolayers. The nonradiative mechanism limiting the emission intensity at room temperature is related to thermal escape of carriers out of the wires.This work has been supported under project No. TIC99-1035-C02 of the Spanish CICYT.Peer reviewe