Fibroblast protein profile analysis highlights the role of oxidative stress and vitamin K recycling in the pathogenesis of pseudoxanthoma elasticum

Pseudoxanthoma elasticum (PXE) is a genetic disorder associated to mutations in the ABCC6 gene; however, the pathogenetic mechanisms leading to elastic fibre calcifications and to clinical manifestations are still unknown. Dermal fibroblasts, directly involved in the production of the extracellular milieu, have been isolated from healthy subjects and from patients affected by PXE, cultured in vitro and characterized for their ability to produce reactive oxygen species, for structural and functional properties of their cell membranes, for changes in their protein profile. Data demonstrate that oxidative stress has profound and endurable consequences on PXE fibroblast phenotype being responsible for: reduced levels of global DNA methylation, increased amount of carbonylated proteins and of lipid peroxidation products, altered structural properties of cell membranes, modified protein expression. Data shed new light on the pathogenetic pathways in PXE, by identifying a network of proteins affecting elastic fibre calcification through inefficient vitamin K recycling, and highlight the role of differentially expressed proteins as targets for validating the efficacy of future therapeutic strategies aiming to delay and/or revert the pathologic phenotype of PXE fibroblasts. Moreover, data open new perspectives for investigating PXE-like phenotypes in the absence of ABCC6 mutations.     

Secondary bioreceptivity of granite: effect of salt weathering on subaerial biofilm growth

Salt crystallisation is a very common and powerful weathering agent that can modify the petrophysical properties of building stone such as granite. In addition, the weathering can affect the susceptibility of the stone to biological colonisation. The aims of the present study were to examine the properties of a granite weathered by sodium chloride crystallisation and to evaluate the effects of the weathering on the secondary bioreceptivity of the stone to subaerial phototrophic biofilms. For this purpose, granite samples were subjected to a laboratory-based accelerated salt weathering test, and changes in weight, open porosity, bulk density, capillary water content, abrasion pH and surface roughness of the samples were determined. Samples of both weathered and non-weathered granite were then inoculated with a multi-species phototrophic culture derived from a natural subaerial biofilm and incubated under standardised laboratory conditions for 3 months. The weight loss produced by the weathering process was consistent with significant changes in abrasion pH and surface roughness. The bioreceptivity of the stone was also altered. According to the bioreceptivity index, the granite under study was characterised by ‘mild primary bioreceptivity’, but ‘high secondary bioreceptivity’ after the salt weathering process. Study of the secondary bioreceptivity of stone materials can provide very useful information about response to weathering effects, and the findings can be used to improve the selection of materials for building purposes.     

Global estimates of evapotranspiration and gross primary production based on MODIS and global meteorology data

The simulation of gross primary production (GPP) at various spatial and temporal scales remains a major challenge for quantifying the global carbon cycle. We developed a light use efficiency model, called EC-LUE, driven by only four variables: normalized difference vegetation index (NDVI), photosynthetically active radiation (PAR), air temperature, and the Bowen ratio of sensible to latent heat flux. The EC-LUE model may have the most potential to adequately address the spatial and temporal dynamics of GPP because its parameters (i.e., the potential light use efficiency and optimal plant growth temperature) are invariant across the various land cover types. However, the application of the previous EC-LUE model was hampered by poor prediction of Bowen ratio at the large spatial scale. In this study, we substituted the Bowen ratio with the ratio of evapotranspiration (ET) to net radiation, and revised the RS-PM (Remote Sensing-Penman Monteith) model for quantifying ET. Fifty-four eddy covariance towers, including various ecosystem types, were selected to calibrate and validate the revised RS-PM and EC-LUE models. The revised RS-PM model explained 82% and 68% of the observed variations of ET for all the calibration and validation sites, respectively. Using estimated ET as input, the EC-LUE model performed well in calibration and validation sites, explaining 75% and 61% of the observed GPP variation for calibration and validation sites respectively.Global patterns of ET and GPP at a spatial resolution of 0.5° latitude by 0.6° longitude during the years 2000-2003 were determined using the global MERRA dataset (Modern Era Retrospective-Analysis for Research and Applications) and MODIS (Moderate Resolution Imaging Spectroradiometer). The global estimates of ET and GPP agreed well with the other global models from the literature, with the highest ET and GPP over tropical forests and the lowest values in dry and high latitude areas. However, comparisons with observed GPP at eddy flux towers showed significant underestimation of ET and GPP due to lower net radiation of MERRA dataset. Applying a procedure to correct the systematic errors of global meteorological data would improve global estimates of GPP and ET. The revised RS-PM and EC-LUE models will provide the alternative approaches making it possible to map ET and GPP over large areas because (1) the model parameters are invariant across various land cover types and (2) all driving forces of the models may be derived from remote sensing data or existing climate observation networks.     

Knowledge-based sense disambiguation (almost) for all structures

Structural disambiguation is acknowledged as a very real and frequent problem for many semantic-aware applications. In this paper, we propose a unified answer to sense disambiguation on a large variety of structures both at data and metadata level such as relational schemas, XML data and schemas, taxonomies, and ontologies. Our knowledge-based approach achieves a general applicability by converting the input structures into a common format and by allowing users to tailor the extraction of the context to the specific application needs and structure characteristics. Flexibility is ensured by supporting the combination of different disambiguation methods together with different information extracted from different sources of knowledge. Further, we support both assisted and completely automatic semantic annotation tasks, while several novel feedback techniques allow us to improve the initial disambiguation results without necessarily requiring user intervention. An extensive evaluation of the obtained results shows the good effectiveness of the proposed solutions on a large variety of structure-based information and disambiguation requirements.     

Performance evaluation of a region growing procedure for mammographic breast lesion identification

At present, mammography is the most effective examination for an early diagnosis of breast cancer. Nevertheless, the detection of cancer signs in mammograms is a difficult procedure owing to the great number of non-pathological structures which are also present in the image. Recent statistics show that in current breast cancer screenings 10%-25% of the tumors are missed by the radiologists. For this reason, a lot of research is currently being done to develop systems for Computer Aided Detection (CADe). Probably, some causes of the false-negative screening examinations are that tumoral masses have varying dimension and irregular shape, their borders are often ill-defined and their contrast is very low, thus making difficult the discrimination from parenchymal structures. Therefore, in a CADe system a preliminary segmentation procedure has to be implemented in order to separate the mass from the background tissue. In this way, various characteristics of the segmented mass can be evaluated and used in a classification step to discriminate benign and malignant cases. In this paper, we describe an effective algorithm for massive lesions segmentation based on a region-growing technique and we provide full details the performance evaluation procedure used in this specific context.     

Integrating web service and semantic dialogue model for user models interoperability on the web

Nowadays there is a great number of Web information systems that build a model of the user and adapt their services according to the needs and preferences maintained by the user model (UM). One of the most challenging issues of this scenario is the possibility to enable different systems to cooperate in order to exchange the available information about a user. Our aim is to create rich (and scalable) communication protocols and infrastructures to enable consumers and providers of UM data to interact. Our solution for dealing with such an issue is to exploit Web standards for interoperability (i.e. Semantic Web and Web Services) for implementing simple atomic communication, and a dialogue model for implementing enhanced communication capabilities. In particular, two systems can start a semantics-enhanced Dialogue Game as a form of negotiation to clarify the meaning of the requested concepts when a shared knowledge model does not exist, and to approximate the response when the exact one is not available. We propose a distributed semantic conversation framework based on the Sesame semantic environment for the exchange of user model knowledge on the Web. Systems have to expose their user model data as a Web Service, and to exploit a public dialogue knowledge base to start the dialogue. The main advantage of the approach is to allow systems to deal with difficult situations by starting an appropriate dialogue game instead of stopping the communication as in the traditional “all-or-nothing” Web Service approach. On the basis of a preliminary evaluation, the approach has shown an improvement of the adaptation results provided by the systems we tested.     

Bio-PEPA: A framework for the modelling and analysis of biological systems

In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use of general kinetic laws. Bio-PEPA may be seen as an intermediate, formal, compositional representation of biological systems, on which different kinds of analyses can be carried out. Bio-PEPA is enriched with some notions of equivalence. Specifically, the isomorphism and strong bisimulation for PEPA have been considered and extended to our language. Finally, we show the translation of a biological model into the new language and we report some analysis results.     

High-Energy Physics on the Grid: the ATLAS and CMS Experience

In this paper we present the experience of the ATLAS and CMS High-Energy Physics (HEP) experiments at the Large Hadron Collider (LHC) with the LCG/EGEE Grid infrastructure. The activity developed around the following two main lines: large-scale physics and detector simulations and end-user analysis. The LCG/EGEE Grid infrastructure offers a large amount of computing and storage resources and is growing very rapidly. It provides the natural environment for large-scale physics and detector simulations. Also, the analysis of these detector simulation data (and in the near future of the reconstructed data from physics collisions) requires efficient end-users access to Grid resources. In this paper, the main findings and lessons learned in terms of performance, robustness and scalability of the whole system are discussed in detail.     

Designing a personal informatics system for users without experience in self-tracking: a case study

Thanks to the advancements in ubiquitous and wearable technologies, Personal Informatics (PI) systems can now reach a larger audience of users. However, it is not still clear whether this kind of tool can fit the needs of their daily lives. Our research aims at identifying specific barriers that may prevent the widespread adoption of PI and finding solutions to overcome them. We requested users without competence in self-tracking to use different PI instruments during their daily practices, identifying five user requirements by which to design novel PI tools. On such requirements, we developed a new system that can stimulate the use of these technologies, by enhancing the perceived benefits of collecting personal data. Then, we explored how naïve and experienced users differently explore their personal data in our system through a user trial. Results showed that the system was successful at helping individuals manage and interpret their own data, validated the usefulness of the requirements found and inspired three further design opportunities that could orient the design of future PI systems.     

The evaluation of a social adaptive website for cultural events

In this paper, we present an evaluation of a social adaptive website in the domain of cultural events, iCITY DSA, which provides information about cultural resources and events that promote the cultural heritage in the city of Turin. Using this evaluation, our objective was to investigate the actual usage of a social adaptive website, in an effort to discover the real behavior of users, the unforeseen correlations among user actions and the consequent interactive behavior, the accuracy of both system and social recommendations and their impact on the users themselves, and the role of tagging in the user modeling process. The major contributions of the paper are manifold: insights into user interactions with social adaptive systems; guidelines for future designs; evaluation of the tagging activity and tag meanings in relation to the application domain and thus their impact on the representation of the user model; and a demonstration of how a combination and interplay of evaluation methodologies (e.g., quantitative and qualitative) can enhance our comprehension of evaluation data.