Patient-based Literature Retrieval and Integration: A Use Case for Diabetes and arterial Hypertension

Specialized search engines such as PubMed, MedScape or Cochrane have increased dramatically the visibility of biomedical scientific results. These web-based tools allow physicians to access scientific papers instantly. However, this decisive improvement had not a proportional impact in clinical practice due to the lack of advanced search methods. Even queries highly specified for a concrete pathology frequently retrieve too many information, with publications related to patients treated by the physician beyond the scope of the results examined. In this work we present a new method to improve scientific article search using patient information. Two pathologies have been used within the project to retrieve relevant literature to patient data and to be integrated with other sources. Promising results suggest the suitability of the approach, highlighting publications dealing with patient features and facilitating literature search to physicians.

Growth data from a field trial of Quercus suber plants regenerated from selected trees and their half-sib progenies by somatic embryogenesis

The development of reliable clonal propagation technologies is a requisite for performing Multi-Varietal Forestry (MVF). Somatic embryogenesis is considered the tissue culture based method more suitable for operational breeding of forest trees. Vegetative propagation is very difficult when tissues are taken from mature donors, making clonal propagation of selected trees almost impossible. We have been able to induce somatic embryogenesis in leaves taken from mature oak trees, including cork oak (Quercus suber). This important species of the Mediterranean ecosystem produces cork regularly, conferring to this species a significant economic value. In a previous paper we reported the establishment of a field trial to compare the growth of plants of somatic origin vs zygotic origin, and somatic plants from mature trees vs somatic plants from juvenile seedlings. For that purpose somatic seedlings were regenerated from five selected cork oak trees and from young plants of their half-sib progenies by somatic embryogenesis. They were planted in the field together with acorn-derived plants of the same families. After the first growth period, seedlings of zygotic origin doubled the height of somatic seedlings, showing somatic plants of adult and juvenile origin similar growth. Here we provide data on height and diameter increases after two additional growth periods. In the second one, growth parameters of zygotic seedlings were also significantly higher than those of somatic ones, but there were not significant differences in height increase between seedlings and somatic plants of mature origin. In the third growth period, height and diameter increases of somatic seedlings cloned from the selected trees did not differ from those of zygotic seedlings, which were still higher than data from plants obtained from somatic embryos from the sexual progeny. Therefore, somatic seedlings from mature origin seem not to be influenced by a possible ageing effect, and plants from somatic embryos tend to minimize the initial advantage of plants from acorns

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a huge number of publications. Against this backdrop, novel information retrieval methods are even more necessary. While web search engines are widespread in many areas, facilitating access to all kinds of information, additional tools are required to automatically link information retrieved from these engines to specific biomedical applications. In the case of clinical environments, this also means considering aspects such as patient data security and confidentiality or structured contents, e.g., electronic health records (EHRs). In this scenario, we have developed a new tool to facilitate query building to retrieve scientific literature related to EHRs. Results: We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches. Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific literature search in these documents, i.e., Medical Subject Headings (MeSH), automatically driven by the CDAPubMed configuration, which advanced users can optimize to adapt to each specific situation, and (iii) generate and launch literature search queries to a major search engine, i.e., PubMed, to retrieve citations related to the EHR under examination. Conclusions: CDAPubMed is a platform-independent tool designed to facilitate literature searching using keywords contained in specific EHRs. CDAPubMed is visually integrated, as an extension of a widespread web browser, within the standard PubMed interface. It has been tested on a public dataset of HL7-CDA documents, returning significantly fewer citations since queries are focused on characteristics identified within the EHR. For instance, compared with more than 200,000 citations retrieved by breast neoplasm, fewer than ten citations were retrieved when ten patient features were added using CDAPubMed. This is an open source tool that can be freely used for non-profit purposes and integrated with other existing systems.

The evolution of the laws of software evolution. A discussion based on a systematic literature review

After more than 40 years of life, software evolution should be considered as a mature field. However, despite such a long history, many research questions still remain open, and controversial studies about the validity of the laws of software evolution are common. During the first part of these 40 years the laws themselves evolved to adapt to changes in both the research and the software industry environments. This process of adaption to new paradigms, standards, and practices stopped about 15 years ago, when the laws were revised for the last time. However, most controversial studies have been raised during this latter period. Based on a systematic and comprehensive literature review, in this paper we describe how and when the laws, and the software evolution field, evolved. We also address the current state of affairs about the validity of the laws, how they are perceived by the research community, and the developments and challenges that are likely to occur in the coming years.

Negative density dependence and environmental heterogeneity effects on tree ferns across succession in a tropical montane forest.

Although tree ferns are an important component of temperate and tropical forests, very little is known about their ecology. Their peculiar biology (e.g., dispersal by spores and two-phase life cycle) makes it difficult to extrapolate current knowledge on the ecology of other tree species to tree ferns. In this paper, we studied the effects of negative density dependence (NDD) and environmental heterogeneity on populations of two abundant tree fern species, Cyathea caracasana and Alsophila engelii, and how these effects change across a successional gradient. Species patterns harbor information on processes such as competition that can be easily revealed using point pattern analysis techniques. However, its detection may be difficult due to the confounded effects of habitat heterogeneity. Here, we mapped three forest plots along a successional gradient in the montane forests of Southern Ecuador. We employed homogeneous and inhomogeneous K and pair correlation functions to quantify the change in the spatial pattern of different size classes and a case-control design to study associations between juvenile and adult tree ferns. Using spatial estimates of the biomass of four functional tree types (short- and long-lived pioneer, shade- and partial shade-tolerant) as covariates, we fitted heterogeneous Poisson models to the point pattern of juvenile and adult tree ferns and explored the existence of habitat dependencies on these patterns. Our study revealed NDD effects for C. caracasana and strong environmental filtering underlying the pattern of A. engelii. We found that adult and juvenile populations of both species responded differently to habitat heterogeneity and in most cases this heterogeneity was associated with the spatial distribution of biomass of the four functional tree types. These findings show the effectiveness of factoring out environmental heterogeneity to avoid confounding factors when studying NDD and demonstrate the usefulness of covariate maps derived from mapped communities.

The trade credit in the Spanish agrofood industry

Selling on credit is rather frequent in Mediterranean countries. Its generalized use can lead to excessive enlargements of the payment periods and consequently can deteriorate the profitability of firms. In spite of the relevance of this problem there are few empirical researches. This work intends to fill this gap and to shed light on the factors related to the extension of trade credit. In the theoretical and empirical literature, different motives have been proposed to explain this issue: a mechanism to reduce transaction costs, a financial alternative to the bank system and an additional tool to improve commercial activities. To contrast these ideas a panel of 388 firms of the Spanish agrofood industry has been taken, and static and dynamic regression models have been estimated by using robust methods to heteroskedasticity, autocorrelation and endogeneity of the explanatory variables. The results confirm that trade credit receivable is associated with more active firms and with cheaper bank financing. Other factors with positive relationships are short-term bank debts and accounts payable. These findings are consistent with commercial motives, rather than a pure financial view, in the sense that financial distressed producers extend trade credit as a way of promoting their products and in turn increasing their sales.

Mobile devices: dominant design as a goal

Since the beginning of the smartphones in the 80s, the mobile device market has grown and evolved towards devices connected everywhere, with hardware more and more close to computers and laptops than a classic mobile telephone. Nowadays, this market seems to be crowded and some companies seem not to know exactly which step is next. In this manner, a concept appears in the market as a solution or a difficulty to overcome: the dominant design. The thesis aims to establish an analysis and definition of what a dominant design is and how we should understand this concept: which are the costumers’ demands and needs? How can we relate this information with the dominant design? What is the strategy of the firm before designing a device? Do they use a concept similar to a dominant design?. The research base its analysis in a theoretical framework based in innovation and marketing literature, to then compare the model studied with data collected from surveys made to customers, interviews made to workers of the mobile device market, and different new projects on the market. The research finishes with a discussion about the theoretical and the empirical frameworks, and concludes replying the research questions, and defining a dominant design and its current situation in the market. RESUMEN. Desde la aparición de los Smartphones en los años 80, el mercado de los dispositivos móviles ha crecido y evolucionado hacia dispositivos cada vez más conectados, con hardware cada vez más cercano a los ordenadores de sobremesa y portátiles que al clásico teléfono móvil. A día de hoy, el mercado está saturado y algunas compañías parecen dubitativas ante el próximo paso a seguir. De esta manera, el concepto del diseño dominante aparece en el mercado como una solución a esta dificultad. El primer capítulo de este estudio se centra en establecer, a modo de introducción, los antecedentes al caso a estudiar, el objetivo de la tesis con sus limitaciones y delimitaciones, así como la metodología utilizada. También se plantean las preguntas principales (Research Questions) sobre el objetivo de la tesis, las cuales darán respuesta en la conclusión final al caso de estudio. Este proyecto tiene como objetivo establecer un análisis y definición sobre que es un diseño dominante y qué deberíamos entender como tal: ¿cuáles son las necesidades y las exigencias de los clientes? ¿Cómo se puede relacionar esta información con el diseño dominante en el sector tecnológico? ¿Cuáles son las estrategias de las empresas antes de diseñar un nuevo dispositivo? ¿Usan un concepto o modelos similares a un diseño dominante? Posteriormente, el segundo capítulo expone la bibliografía utilizada, y el enfoque analítico que se llevará a cabo con las 3 principales fuentes de datos. La investigación enfoca su análisis en un marco teórico, basado en publicaciones y bibliografía relacionadas con la innovación y el marketing, para luego comparar el modelo estudiado con un marco empírico: datos obtenidos de encuestas a consumidores, entrevistas a profesionales del sector de los dispositivos móviles, y diferentes prototipos y nuevos proyectos en este mercado. Entre esta literatura se encuentran manuales de marketing como “22 Immutable laws of Marketing” (de Al Ries & Jack Trout), publicaciones sobre el sector industrial de la tecnología y negocios: “Crossing the Chasm” de Geoffrey A. Moore y modelos de innovación entre otros como “Mastering the Dynamics of Innovation” de James M. Utterback. El tercer capítulo corresponde al estudio del marco teórico de la tesis, donde se analizará principalmente el modelo de innovación utilizado (el modelo cíclico de Utterback) y varios principios de marketing aplicados a este sector. Se plantean las bases de este modelo, la definición que el propio Utterback ofrece sobre el diseño dominante, y las 3 fases del proceso del mismo (Fluid Phase, Transitional Phase y Specific Phase), donde las empresas cambian de estrategia según las circunstancias evolutivas del dispositivo, su posición respecto el líder del mercado, o los procesos de estandarización y de costes. Por último se plantea la base para el desarrollo del diseño dominante en un ciclo evolutivo constante en el tiempo. Respecto a la parte más analítica de la tesis, el cuarto capítulo se desarrolla a partir de los datos obtenidos de las fuentes de información en el marco empírico de estudio. Se obtienen conclusiones sobre los datos realizados en ambas encuestas (en Español e Inglés) y sobre la relevancia de esta información; se estudian uno por uno hasta cuatro casos de nuevos dispositivos a corto-medio plazo en el mercado y se obtienen unas conclusiones globales sobre las entrevistas realizadas a los profesionales del sector y la relevancia de todas estas informaciones. En el quinto capítulo de la tesis se desarrolla la discusión en torno a los marcos teórico y empírico utilizados, para concluir respondiendo a las “Research Questions”, definiendo de esta manera el concepto de diseño dominante y comparando esta definición con la situación real del mercado. Se contrastan las bases del modelo de Utterback con los datos obtenidos en el capítulo cuarto, enfatizando la comparación entre las fases de este modelo con la realidad obtenida a través del estudio. Las encuestas realizadas a los consumidores se enmarcan en la segunda y tercera fase del ciclo, donde el desarrollo del diseño dominante ya está establecido y más desarrollado, mientras que las entrevistas unifican varios puntos clave a tener en cuenta en la primera y segunda fases, orientándose a las capas previas del proceso. Después se comparan uno a uno los 4 dispositivos analizados, a fin de establecer su jerarquía dentro del mercado, como posibles nuevos diseños dominantes o evoluciones especializadas de otros que ya aparecieron en el mercado con anterioridad. Así mismo, en esta parte final del estudio se comparan entre sí los resultados similares entre las tres fuentes de datos, y se analiza la veracidad de todas las fuentes consultadas. Finalmente, se han registrado en un sexto capítulo todas las referencias utilizadas en este proyecto, tanto publicaciones bibliográficas, entrevistas, citas de personajes relevantes del sector y enlaces en la red sobre noticias relevantes. En el apartado de apéndices se adjuntan tres anexos, donde se adjunta información utilizada en el caso de estudio, y la cual se ha obviado del texto principal con el objetivo de agilizar la lectura y la comprensión del mismo. Estos tres apéndices corresponden a las dos encuestas realizadas en ambos idiomas y la entrevista realizada a los profesionales del sector de los dispositivos móviles.

Estructura espacial y dinámica del bosque montano del sur del Ecuador. Interacciones bióticas y limitaciones abióticas

Muchos estudios han descrito la composición y diversidad de los bosques montanos tropicales, pero los patrones espaciales y las diferentes tipos de relaciones de estos, entre especies o entre grupos funcionales ha sido poco documentada. El presente trabajo se realizó en tres parcelas completamente censadas del bosque de la Estación Biológica “Chamusquin” (Zamora Chinchipe, Ecuador), y se plantea como objetivo principal conocer la estructura espacial y dinámica del bosque montano tropical del sur del Ecuador, así como las interacciones bióticas y limitaciones abióticas que influyen en esta dinámica, para ello se planteó cuatro objetivos de estudio que son: conocer los patrones espaciales de los gremios ecológicos dentro de la zona de estudio; conocer la influencia de la dependencia negativa de la densidad sobre dos especies de helechos arborescentes (Cyatheaceae); conocer si existen especies o grupos ecológicos acumuladoras o repulsoras de diversidad en el área de estudio; y conocer cómo influyen la diversidad filogenética y la densidad del vecindario en la incidencia de herbivoría y parasitismo sobre las fases iniciales del establecimiento forestal (brinzales) así como en la supervivencia de los mismos Como paso previo para el análisis del resto de objetivos, dentro de cada parcela se marcaron todos los individuos con DAP ≥5 cm y se tomaron sus coordenadas (X, Y). Además se tomaron datos de variables superficiales y muestras del suelo. Las especies encontradas se clasificaron de acuerdo a sus características biológicas, asignándolas a cada uno de los cuatro gremios forestales usualmente distinguidos en los bosques tropicales: tolerantes a la sombra (TS), tolerantes parciales a la sombra (TPS), pioneras de vida larga (PVL) y pioneras de vida corta (PVC). Para el estudio del primer objetivo tas se emplearon funciones K de Ripley inhomogéneas, ajustando la heterogeneidad en base a la variación espacial de las variables ambientales registradas . Los resultados demostraron que tanto la frecuencia relativa como el patrón espacial de las diferentes estrategias funcionales varían a lo largo de la sucesión y que éste además está influido por la variación ambiental. En adición, tanto el patrón espacial como la respuesta a la variación ambiental de los diferentes gremios es distinta entre adultos y juveniles. Todo ello sugiere que el ensamblaje de la diversidad en los bosque montanos andinos está controlado por procesos deterministas más que por procesos neutrales. Para responder el segundo objetivo se estudiaron los efectos de la dependencia negativa de la densidad (DND) y la heterogeneidad ambiental en las poblaciones de dos especies de helechos arborescentes abundantes, Cyathea caracasana y Alsophila engelii, y cómo estos efectos cambian a través de un gradiente sucesional. Los patrones de especies albergan información sobre procesos tales como la competencia que puede ser revelado fácilmente utilizando técnicas de análisis de patrones punto. Sin embargo, su detección puede ser difícil debido a los efectos de factores de confusión heterogeneidad del hábitat. Aquí, empleamos funciones K y funciones de correlación de par homogéneas y no homogéneas para cuantificar el cambio en el patrón espacial de diferentes clases de tamaño con un diseño de casos-controles para estudiar las asociaciones entre helechos arborescentes jóvenes y adultos. Usando estimaciones espaciales de la biomasa de los cuatro tipos de gremios ecológicos (PVC, PVL, TPS, TS) como covariables, hemos ajustado modelos de Poisson heterogéneos a los patrones de puntos de de los helechos juveniles y los adultos y hemos explorado además la existencia de dependencia del hábitat en estos patrones. Nuestro estudio reveló efectos de la DND para C. caracasana y un fuerte filtrado ambiental que subyace al patrón de A. engelii. Encontramos también que las poblaciones de adultos y juveniles de ambas especies respondieron de manera diferente a la heterogeneidad del hábitat y en la mayoría de los casos esta heterogeneidad se asoció con la distribución espacial de la biomasa de los cuatro tipos de gremios. Estos resultados muestran la eficacia de controlar los efectos de la heterogeneidad ambiental para evitar su confusión con los patrones derivados de interacciones biológicas cuando se estudia la DND y demuestran la utilidad de los mapas de covariables derivados de comunidades biológicas como resumen de la heterogeneidad ambiental. Para nuestro tercer objetivo nos centramos en explorar cómo influyen las especies más abundantes en la organización espacial de la diversidad a lo largo de un gradiente sucesional en el bosque montano del sur del Ecuador. Para ello utilizamos la función ISAR (Individual Species Area Relationship). Encontramos que la frecuencia de especies neutras, repulsoras y acumuladoras de diversidad taxonómica varía dependiendo del grado de sucesión. Además se comprobó que la mayoría de los gremios forestales se comportó de forma neutral, pero la proporción de acumuladores, aumentó al avanzar la sucesión hacia estados más maduros, lo que indica el establecimiento de fuertes procesos competitivos a medida que avanza la sucesión y la mayor importancia del papel de las especies individuales en dichos estados. Finalmente, examinamos el efecto de la vecindad taxonómica y filogenética, así como la estrategia de vida, sobre la incidencia de la herbivoría y el parasitismo en las poblaciones de brinzales de tres fragmentos forestales en una secuencia sucesional del bosque montano húmedo. Evaluamos además los efectos de herbivoría, parasitismo, estrategia de vida y diferentes indicadores de la vecindad sobre la supervivencia de los brinzales. Por último contrastamos la posible existencia de una tendencia compensatoria de la comunidad (CCT) a nivel de fragmento forestal. Nuestros análisis no consiguieron detectar una CCT pero si pusieron de manifiesto la existencia de efectos locales de dependencia negativa de la densidad. Por ejemplo, la presencia de herbivoría y parasitismo sobre los brinzales se relacionó significativamente con una menor supervivencia de estos. Por otro lado, indicadores del efecto de la vecindad como la densidad de brinzales del mismo género y el área basal de árboles vecinos del mismo género incrementaron la prevalencia de la herbivoría o el parasitismo en los brinzales. El incremento de la incidencia de la herbivoría o el parasitismo no está exclusivamente ligado a tener una vecindad taxonómicamente idéntica (vecinos de la misma especie) sino que categorías taxonómicas más laxas como el "género" o simplemente relaciones de semejanza filogenética son capaces de predecir los efectos negativos de la vecindad. Los efectos detectados variaron en los diferentes grupos funcionales distinguidos. Los resultados que hemos obtenido en este trabajo parecen indicar que el funcionamiento de las comunidades de brinzales del bosque montano tropical no difiere mucho del reportado para comunidades de plántulas en otros bosques tropicales y cumple las predicciones de la hipótesis de Janzen y Connell, aunque matizadas por la mayor resistencia de los brinzales al efecto de herbivoría y parasitismo. ABSTRACT Many studies have described the composition and diversity of tropical montane forests, but the different spatial patterns and types of relationships between species or between functional groups has been poorly documented. This work was made in three completely surveyed forest plots at Biological Station "Chamusquin" (Zamora Chinchipe, Ecuador). Our main objective was to know the spatial structure and dynamics of the tropical montane forest in southern Ecuador, as well as the biotic interactions and abiotic constraints affecting this dynamic. More specifically, we aimed to understand the spatial patterns of ecological guilds; to explore the influence of negative density dependence on two species of tree ferns (Cyatheaceae); to determine whether some species or ecological groups structure spatially plant diversity in these forests; and to test the effects of biological neighborhood on the incidence of herbivory and parasitism and on the survival of saplings. We mapped within each plot all trees with DBH ≥5 cm. Besides, surface data variables and soil samples they were taken. The species found were classified according to their biological characteristics in four forest guilds: shade-tolerant (ST), partial shade tolerant (PST), long-lived pioneer (LLP) and short-lived pioneer (SLP). To analyze the spatial patterns of the ecological guilds, we employed the inhomogeneous version of Ripley's K-function and adjusted heterogeneity surfaces based on the spatial variation of the measured environmental variables. The results showed that both the relative frequency of each functional guild as well as their spatial pattern varied throughout succession and that the spatial pattern is explained by environmental variation. In addition, both spatial pattern and the response to spatial variation of each guild varied throughout ontogeny. All in all suggest that diversity assembly in the studied forests is ruled by deterministic instead of neutral processes. We also addressed the negative effects of density dependence (NDD) and environmental heterogeneity in populations of two species of abundant tree ferns, Cyathea caracasana and Alsophila engelii, and how these effects change across a successional gradient.. Here, we used homogeneous and inhomogeneous K and pair-correlation functions to quantify the change in the spatial pattern of different size classes with a case-control design to study associations between young and adult tree ferns. Using spatial estimates of the biomass of the four types of ecological guilds (SLP, LLP, PST, ST) as co-variables, we fitted heterogeneous Poisson models to juvenile and adult tree fern point patterns and explored the existence of habitat dependence. Our study revealed NDD effects for C. caracasana and strong environmental filtering underlying the pattern of A. engelii. We found that adult and juvenile populations of both species responded differently to habitat heterogeneity and in most cases this heterogeneity was associated with the spatial distribution of biomass of the four functional tree types. These findings show the effectiveness of factoring out environmental heterogeneity to avoid confounding factors when studying NDD and demonstrate the usefulness of covariate maps derived from mapped communities. For our third objective we focused on exploring how the most abundant species influence the spatial organization of tree diversity in these forests. For this, we used the individual species-area relationship function (ISAR). We found that the proportion of accumulator, repeller and neutral species, varied depending on the degree of succession. We found also that most guilds behaved neutrally but the proportion of accumulator guilds increased as succession advanced to more mature stages. This point, to the existence of strong competitive effects mediated by individual species in these mature forests. Finally, we examined the effects of life strategies and taxonomic and phylogenetic neighborhood on the incidence of herbivory and parasitism in the communities of saplings in the same forest fragments. We evaluated also the effects of life strategies, herbivory, parasitism and some indicators of neighborhood on sapling survival. Finally we tested for the existences of a compensatory community trend at plot scale. We did not found a CCT but we found proof of local NND effects. For instance, the prevalence of herbivory and parasitism were related to lower sapling survival. On the other hand the density of con-generic saplings and the basal area of neighbor con-generic trees were related to a higher prevalence of herbivory or parasitism in the saplings. We demonstrated that the increase in the prevalence of herbivory or parasitism it s not exclusive of a conspecific neighborhood but instead larger taxonomic categories such as "genus" or simple phylogenetic relationships are also able to predict NND effects. The NND effects varied among functional guilds. Our results show that the dynamic of sapling communities in Ecuadorian montane forests is similar to seedling dynamics in other tropical forest and follows the predictions of Janzen-Connell hypothesis, although softened by the strong resilience of saplings in comparison to seedlings.

Barriers to the adoption of photovoltaic systems: The state of the art

Although photovoltaic (PV) systems have become much more competitive, the diffusion of PV systems still remains low in comparison to conventional energy sources. What are the current barriers hindering the diffusion of PV systems? In order to address this, we conducted an extensive and systematic literature review based on the Web of Science database. Our state-of-the-art review shows that, despite the rapid development and maturity of the technology during the past few years, the adoption of PV systems still faces several barriers. The wide adoption of PV systems-either as a substitute for other electricity power generation systems in urban areas or for rural electrification-is a challenging process. Our results show that the barriers are evident for both low- and high-income economies, encompassing four dimensions: sociotechnical, management, economic, and policy. Although the barriers vary across context, the lessons learned from one study can be valuable to others. The involvement of all stakeholders-adopters, local communities, firms, international organizations, financial institutions, and government-is crucial to foster the adoption.