A combined measure for quantifying and qualifying the topology preservation of growing self-organizing maps

The Self-OrganizingMap (SOM) is a neural network model that performs an ordered projection of a high dimensional input space in a low-dimensional topological structure. The process in which such mapping is formed is defined by the SOM algorithm, which is a competitive, unsupervised and nonparametric method, since it does not make any assumption about the input data distribution. The feature maps provided by this algorithm have been successfully applied for vector quantization, clustering and high dimensional data visualization processes. However, the initialization of the network topology and the selection of the SOM training parameters are two difficult tasks caused by the unknown distribution of the input signals. A misconfiguration of these parameters can generate a feature map of low-quality, so it is necessary to have some measure of the degree of adaptation of the SOM network to the input data model. The topologypreservation is the most common concept used to implement this measure. Several qualitative and quantitative methods have been proposed for measuring the degree of SOM topologypreservation, particularly using Kohonen's model. In this work, two methods for measuring the topologypreservation of the Growing Cell Structures (GCSs) model are proposed: the topographic function and the topology preserving map

Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra.

Reviewing technical approaches for sharing and preservation of experimental data

Empirical Software Engineering (ESE) replication researchers need to store and manipulate experimental data for several purposes, in particular analysis and reporting. Current research needs call for sharing and preservation of experimental data as well. In a previous work, we analyzed Replication Data Management (RDM) needs. A novel concept, called Experimental Ecosystem, was proposed to solve current deficiencies in RDMapproaches. The empirical ecosystem provides replication researchers with a common framework that integrates transparently local heterogeneous data sources. A typical situation where the Empirical Ecosystem is applicable, is when several members of a research group, or several research groups collaborating together, need to share and access each other experimental results. However, to be able to apply the Empirical Ecosystem concept and deliver all promised benefits, it is necessary to analyze the software architectures and tools that can properly support it.

Balancing management and preservation of mediterranean scattered oak woodlands (Dehesas) in human-dominated landscapes

Los sistemas agroforestales mediterráneos tienen una gran importancia ecológica y socioeconómica, y mantienen altos valores medioambientales y de diversidad biológica a la vez que producen importantes servicios ecosistémicos. Estos sistemas han sido testigos de diversos cambios rápidos y drásticos en su gestión y aprovechamiento durante el último siglo. La mayor parte de la investigación desarrollada en esta tesis doctoral ha sido llevada a cabo en las dehesas españolas. Esta tesis nos muestra: i) la evidencia de la existencia de un cambio global del estrato arbóreo y del manejo del pastoreo en el todo el área de distribución de la dehesa durante los últimos 60 años; ii) la importancia del papel que juega el arbolado disperso y el adecuado manejo del ganado en la mejora de la producción, calidad y diversidad de las comunidades herbáceas, que a su vez, un pasto herbáceo bien desarrollado es importante para la rentabilidad del sistema, evaluando estos efectos bajo distintos escenarios de clima y calidad de estación; y iii) la evidencia de la falta de regeneración en sistemas agroforestales mediterráneos bajo distintos tipos de manejo del pastoreo, y además se evalúa el crecimiento y desarrollo de las pocas plántulas existentes que serán las que aseguren la viabilidad y persistencia y de estos sistemas. El arbolado disperso de estos sistemas ha experimentado una reducción importante en su densidad arbórea y fracción de cabida cubierta durante el periodo entre 1950-1980 donde tuvieron lugar importantes transformaciones en la actividad agropecuaria. La cabaña ganadera de ovino disminuyó drásticamente en los años 70 en comparación a la de bovino que desde entonces ha aumentado progresivamente hasta la actualidad. Por otro lado, el mismo tipo de manejo del ganado doméstico (especialmente bovino) durante bastante tiempo (mínimo 30 años) provocó una reducción significativa de la densidad de las plántulas. Además la probabilidad de ocurrencia y la intensidad de daños por herbivoría fue mayor bajo pastoreo bovino (con daños más intensos y consistentes) que bajo pastoreo ovino o sin pastoreo doméstico (presencia de ciervos). También el patrón de crecimiento de las plantas jóvenes estuvo afectado por el tipo de manejo, generando plántulas achaparradas en el caso del bovino y plántulas esbeltas favoreciendo el crecimiento en altura en el caso del ovino. La presencia de un arbolado disperso generó una mayor diversidad y variación en la producción de las comunidades herbáceas según las condiciones de disponibilidad de agua. Especialmente, el ecotono como microhábitat sostuvo altos valores de diversidad herbácea. La presencia del ganado bajo pastoreo continuo de intensidad moderada a alta, especialmente el bovino, incrementó los rendimientos de producción y diversidad del estrato herbáceo. Los resultados de esta tesis nos muestran la importancia que tiene la existencia de un equilibrio entre la producción y la conservación de los sistemas agroforestales mediterráneos para obtener una producción sostenible de servicios ecosistémicos mientras se asegura la perpetuación del sistema a largo plazo. Es crucial diseñar planes de gestión incorporando objetivos de conservación que integren técnicas silvopastorales apropiadas para poder aplicar en los sistemas agroforestales mediterráneos. ABSTRACT Mediterranean scattered oak woodlands have great ecological and socio-economic importance, supporting high environmental and amenity values, and relatively rich biological diversity while producing important ecosystem services. They have been witnesses of different and fast changes developed in the last century. Most of the research developed in this dissertation has conducted within dehesas. This thesis provides: i) the global change evidence of the tree layer and grazing management experienced in the land-use range of a Mediterranean scattered oak woodland (dehesa) over the last 60 years; ii) the important role of scattered trees and adequate management grazing in the improvement of grassland yield, quality and diversity - which it is important, in turn, for the system profitability - under different climate scenarios and site quality; and iii) the lack of oak regeneration evidence under some given representative management regimes and how is the growth development of these plants to assure the viability and persistence of Mediterranean scattered oak woodlands. Tree layer experienced a significant reduction in dehesas during 1950-1980 period where the highest human impacts took place. Sheep herd decreased drastically during the 1970s and, in contrast, cattle have been increasing gradually since then. On the other hand, same livestock grazing management (especially cattle) during long time (minimum 30 years) within Mediterranean scattered oak woodlands reduced strongly the density of young oak plants and showed high probability of herbivory occurrence and intensity. Young plant growth pattern was greatly modified by livestock. Cattle grazing generated stunted plants and sheep grazing generated slender plants favoring the height growth. Microsites created by large trees modified the herbaceous yield according the water availability of the year and generated high plant diversity within herbaceous communities. Especially, ecotone microsite supported high values of herbaceous diversity. The presence of livestock species increased the herbaceous yield and maintained a more diverse community under continuous grazing at both moderate and high intensities; especially cattle. Thus, around the influence of scattered trees there is a high amount of different interactions among livestock, trees and grasslands maintaining and enhancing the quality of whole dehesa system. The results of this thesis highlight how important is balancing management and preservation of Mediterranean scattered oak woodlands to obtain the optimum ecosystem services while the system conservation is assured for a long-term. It is crucial to design management plans with conservation goals that include appropriate silvopastoral practices in Mediterranean scattered oak woodlands.

Balancing management and preservation of mediterranean scattered oak woodlands (Dehesas) in human-dominated landscapes

Los sistemas agroforestales mediterráneos tienen una gran importancia ecológica y socioeconómica, y mantienen altos valores medioambientales y de diversidad biológica a la vez que producen importantes servicios ecosistémicos. Estos sistemas han sido testigos de diversos cambios rápidos y drásticos en su gestión y aprovechamiento durante el último siglo. La mayor parte de la investigación desarrollada en esta tesis doctoral ha sido llevada a cabo en las dehesas españolas. Esta tesis nos muestra: i) la evidencia de la existencia de un cambio global del estrato arbóreo y del manejo del pastoreo en el todo el área de distribución de la dehesa durante los últimos 60 años; ii) la importancia del papel que juega el arbolado disperso y el adecuado manejo del ganado en la mejora de la producción, calidad y diversidad de las comunidades herbáceas, que a su vez, un pasto herbáceo bien desarrollado es importante para la rentabilidad del sistema, evaluando estos efectos bajo distintos escenarios de clima y calidad de estación; y iii) la evidencia de la falta de regeneración en sistemas agroforestales mediterráneos bajo distintos tipos de manejo del pastoreo, y además se evalúa el crecimiento y desarrollo de las pocas plántulas existentes que serán las que aseguren la viabilidad y persistencia y de estos sistemas. El arbolado disperso de estos sistemas ha experimentado una reducción importante en su densidad arbórea y fracción de cabida cubierta durante el periodo entre 1950-1980 donde tuvieron lugar importantes transformaciones en la actividad agropecuaria. La cabaña ganadera de ovino disminuyó drásticamente en los años 70 en comparación a la de bovino que desde entonces ha aumentado progresivamente hasta la actualidad. Por otro lado, el mismo tipo de manejo del ganado doméstico (especialmente bovino) durante bastante tiempo (mínimo 30 años) provocó una reducción significativa de la densidad de las plántulas. Además la probabilidad de ocurrencia y la intensidad de daños por herbivoría fue mayor bajo pastoreo bovino (con daños más intensos y consistentes) que bajo pastoreo ovino o sin pastoreo doméstico (presencia de ciervos). También el patrón de crecimiento de las plantas jóvenes estuvo afectado por el tipo de manejo, generando plántulas achaparradas en el caso del bovino y plántulas esbeltas favoreciendo el crecimiento en altura en el caso del ovino. La presencia de un arbolado disperso generó una mayor diversidad y variación en la producción de las comunidades herbáceas según las condiciones de disponibilidad de agua. Especialmente, el ecotono como microhábitat sostuvo altos valores de diversidad herbácea. La presencia del ganado bajo pastoreo continuo de intensidad moderada a alta, especialmente el bovino, incrementó los rendimientos de producción y diversidad del estrato herbáceo. Los resultados de esta tesis nos muestran la importancia que tiene la existencia de un equilibrio entre la producción y la conservación de los sistemas agroforestales mediterráneos para obtener una producción sostenible de servicios ecosistémicos mientras se asegura la perpetuación del sistema a largo plazo. Es crucial diseñar planes de gestión incorporando objetivos de conservación que integren técnicas silvopastorales apropiadas para poder aplicar en los sistemas agroforestales mediterráneos. ABSTRACT Mediterranean scattered oak woodlands have great ecological and socio-economic importance, supporting high environmental and amenity values, and relatively rich biological diversity while producing important ecosystem services. They have been witnesses of different and fast changes developed in the last century. Most of the research developed in this dissertation has conducted within dehesas. This thesis provides: i) the global change evidence of the tree layer and grazing management experienced in the land-use range of a Mediterranean scattered oak woodland (dehesa) over the last 60 years; ii) the important role of scattered trees and adequate management grazing in the improvement of grassland yield, quality and diversity - which it is important, in turn, for the system profitability - under different climate scenarios and site quality; and iii) the lack of oak regeneration evidence under some given representative management regimes and how is the growth development of these plants to assure the viability and persistence of Mediterranean scattered oak woodlands. Tree layer experienced a significant reduction in dehesas during 1950-1980 period where the highest human impacts took place. Sheep herd decreased drastically during the 1970s and, in contrast, cattle have been increasing gradually since then. On the other hand, same livestock grazing management (especially cattle) during long time (minimum 30 years) within Mediterranean scattered oak woodlands reduced strongly the density of young oak plants and showed high probability of herbivory occurrence and intensity. Young plant growth pattern was greatly modified by livestock. Cattle grazing generated stunted plants and sheep grazing generated slender plants favoring the height growth. Microsites created by large trees modified the herbaceous yield according the water availability of the year and generated high plant diversity within herbaceous communities. Especially, ecotone microsite supported high values of herbaceous diversity. The presence of livestock species increased the herbaceous yield and maintained a more diverse community under continuous grazing at both moderate and high intensities; especially cattle. Thus, around the influence of scattered trees there is a high amount of different interactions among livestock, trees and grasslands maintaining and enhancing the quality of whole dehesa system. The results of this thesis highlight how important is balancing management and preservation of Mediterranean scattered oak woodlands to obtain the optimum ecosystem services while the system conservation is assured for a long-term. It is crucial to design management plans with conservation goals that include appropriate silvopastoral practices in Mediterranean scattered oak woodlands.

Preservation of myocardial β-adrenergic receptor signaling delays the development of heart failure after myocardial infarction

When the heart fails, there is often a constellation of biochemical alterations of the β-adrenergic receptor (βAR) signaling system, leading to the loss of cardiac inotropic reserve. βAR down-regulation and functional uncoupling are mediated through enhanced activity of the βAR kinase (βARK1), the expression of which is increased in ischemic and failing myocardium. These changes are widely viewed as representing an adaptive mechanism, which protects the heart against chronic activation. In this study, we demonstrate, using in vivo intracoronary adenoviral-mediated gene delivery of a peptide inhibitor of βARK1 (βARKct), that the desensitization and down-regulation of βARs seen in the failing heart may actually be maladaptive. In a rabbit model of heart failure induced by myocardial infarction, which recapitulates the biochemical βAR abnormalities seen in human heart failure, delivery of the βARKct transgene at the time of myocardial infarction prevents the rise in βARK1 activity and expression and thereby maintains βAR density and signaling at normal levels. Rather than leading to deleterious effects, cardiac function is improved, and the development of heart failure is delayed. These results appear to challenge the notion that dampening of βAR signaling in the failing heart is protective, and they may lead to novel therapeutic strategies to treat heart disease via inhibition of βARK1 and preservation of myocardial βAR function.

Telomerase expression and activity are coupled with myocyte proliferation and preservation of telomeric length in the failing heart

The role and even the existence of myocyte proliferation in the adult heart remain controversial. Documentation of cell cycle regulators, DNA synthesis, and mitotic images has not modified the view that myocardial growth can only occur from hypertrophy of an irreplaceable population of differentiated myocytes. To improve understanding the biology of the heart and obtain supportive evidence of myocyte replication, three indices of cell proliferation were analyzed in dogs affected by a progressive deterioration of cardiac performance and dilated cardiomyopathy. The magnitude of cycling myocytes was evaluated by the expression of Ki67 in nuclei. Ki67 labeling of left ventricular myocytes increased 5-fold, 12-fold, and 17-fold with the onset of moderate and severe ventricular dysfunction and overt failure, respectively. Telomerase activity in vivo is present only in multiplying cells; this enzyme increased 2.4-fold and 3.1-fold in the decompensated heart, preserving telomeric length in myocytes. The contribution of cycling myocytes to telomerase activity was determined by the colocalization of Ki67 and telomerase in myocyte nuclei. More than 50% of Ki67-positive cells expressed telomerase in the overloaded myocardium, suggesting that these myocytes were the morphological counterpart of the biochemical assay of enzyme activity. Moreover, we report that 20–30% of canine myocytes were telomerase competent, and this value was not changed by cardiac failure. In conclusion, the enhanced expression of Ki67 and telomerase activity, in combination with Ki67-telomerase labeling of myocyte nuclei, support the notion that myocyte proliferation contributes to cardiac hypertrophy of the diseased heart.