Multiple verification in computational modeling of bone pathologies

We introduce a model checking approach to diagnose the emerging of bone pathologies. The implementation of a new model of bone remodeling in PRISM has led to an interesting characterization of osteoporosis as a defective bone remodeling dynamics with respect to other bone pathologies. Our approach allows to derive three types of model checking-based diagnostic estimators. The first diagnostic measure focuses on the level of bone mineral density, which is currently used in medical practice. In addition, we have introduced a novel diagnostic estimator which uses the full patient clinical record, here simulated using the modeling framework. This estimator detects rapid (months) negative changes in bone mineral density. Independently of the actual bone mineral density, when the decrease occurs rapidly it is important to alarm the patient and monitor him/her more closely to detect insurgence of other bone co-morbidities. A third estimator takes into account the variance of the bone density, which could address the investigation of metabolic syndromes, diabetes and cancer. Our implementation could make use of different logical combinations of these statistical estimators and could incorporate other biomarkers for other systemic co-morbidities (for example diabetes and thalassemia). We are delighted to report that the combination of stochastic modeling with formal methods motivate new diagnostic framework for complex pathologies. In particular our approach takes into consideration important properties of biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could be further expanded, inching towards the complexity of human diseases. Finally, we briefly introduce self-adaptiveness in formal methods which is a key property in the regulative mechanisms of biological systems and well known in other mathematical and engineering areas.Comment: In Proceedings CompMod 2011, arXiv:1109.104

A Quantitative Methodology to Measure Injector Fouling Through Image Analysis

Abstract The use of vegetables oils in a compression ignited internal combustion engine presents some critical issues as the large amount of carbon deposits on the tip of injectors, which significantly influence emissions and engine performance. A previous draft methodology was developed by the authors, based on images capture and post-processing. The carbon deposit was correlated with the number of pixels in the gray scale, so it was possible to determine a Fouling Index. First results showed interesting perspectives and some limits: the aim of the present work is the optimization of the test bench and methodology. At first an improvement of image acquisition, increasing sampling frequency and image resolution, is performed, replacing the old camera with a digital microscope and improving both injector and microscope positioning. The test bench prototype has been realized with the aid of 3D printing, obtaining fundamental mechanical components. Also an alternative methodology is proposed to evaluate carbon deposits volume through a Volumetric Index. The new methodology validation was done using images sampled with the previous test bench. The performances of the Fouling index and of the new Volumetric Index were compared and fouling was examined in the real case of a diesel engine, fed with diesel and sunflower oil. Results show a greater reliability of the new Volumetric Index

Pyrolysis of Olive Stone for Energy Purposes

Abstract Pyrolysis of biomass is a promising technology for the production of distributed and renewable energy on small and micro-scale since it produces a gas with relatively high calorific value, which can be burned in an internal combustion engine or in a microturbine; pyrolysis also generates by products (char and tar) which can be used to provide energy to the process or for cogeneration purposes. This research is aimed at the exploitation of waste from agricultural production processes, in particular olive mill wastes whose management has critical environmental and disposal costs; the yields of pyrogas, tar and char obtained from the pyrolysis of olive stone in a batch reactor was measured. Pyrogas produced is sampled through a line for the sampling of condensable substances in accordance with existing regulations, CEN/TS 15439, and once purified from water vapor and tars is analyzed with micro-GC. The data collected is used to perform mass and energy balances and to determine the content of tars and the Low Heating Value (LHV) of the gas produced

i rexfo life an innovative business model to reduce food waste

Abstract Every year the food produced and wasted consumes a volume of water equal to 250 km3, requires around 30% of the world agricultural land, and it is responsible for the emission of 3,3 billion tons of greenhouse gases. The direct economic consequences of food waste are ranging around 750 billion dollars per year (FAO source). i-REXFO designs an innovative business model with the objective of reducing significantly the amount of landfilled food waste. The actions are economically sustained by public incentives, tax reductions and private revenues from energy valorization of residual food waste. Uptaking the good practices from other EU countries (Denmark) the project will develop a tool to design the integrated model, optimize it from a technical, economic and environmental point of view and transfer it to other EU regions. i-REXFO will increase consumer awareness on food waste reduction in retail malls and HORECA while facilitating the sale and donation to charities and food banks of close to expiration and aesthetically not adequate food; it will also remove the barriers that hamper the use of food residues in biogas plants. The actions are economically sustained from energy valorization of food waste in biogas plant that use the digestate as fertilizer, closing the cycle. I-REXFO will achieve an overall reduction of 17000 tons/year of food waste landfilled during the project duration and in the after life phase. This will correspond to an overall reduction of 41000 tons of CO2 equivalent emissions

Modelling the effect of gap junctions on tissue-level cardiac electrophysiology

When modelling tissue-level cardiac electrophysiology, continuum approximations to the discrete cell-level equations are used to maintain computational tractability. One of the most commonly used models is represented by the bidomain equations, the derivation of which relies on a homogenisation technique to construct a suitable approximation to the discrete model. This derivation does not explicitly account for the presence of gap junctions connecting one cell to another. It has been seen experimentally [Rohr, Cardiovasc. Res. 2004] that these gap junctions have a marked effect on the propagation of the action potential, specifically as the upstroke of the wave passes through the gap junction. In this paper we explicitly include gap junctions in a both a 2D discrete model of cardiac electrophysiology, and the corresponding continuum model, on a simplified cell geometry. Using these models we compare the results of simulations using both continuum and discrete systems. We see that the form of the action potential as it passes through gap junctions cannot be replicated using a continuum model, and that the underlying propagation speed of the action potential ceases to match up between models when gap junctions are introduced. In addition, the results of the discrete simulations match the characteristics of those shown in Rohr 2004. From this, we suggest that a hybrid model -- a discrete system following the upstroke of the action potential, and a continuum system elsewhere -- may give a more accurate description of cardiac electrophysiology.Comment: In Proceedings HSB 2012, arXiv:1208.315

Efficiency Enhancement for an S-Band Axial Vircator Using 5-Stage Two-Step Tapered Radiators

An S-band multistage axial virtual cathode oscillator with efficiency enhancement for high pulsed power electromagnetic applications is presented. The Particle-in-Cell (PIC) results of the designed 5-stage Vircator, with two-step negative tapering in the reflectors, carried out by CST Studio suite 2021 simulation code show a peak power value of 5.54 GW and an efficiency value of 13.65% at 2.45 GHz, under a beam voltage and current equal to 520 kV and 20 kA, respectively

Chlorinated hydrocarbons in Coastal Lagoon of the Pacific Coast of Nicaragua

A screening for persistent chlorinated hydrocarbons was carried out in December 1995 in the main coastal lagoons on the Pacific side of Nicaragua, where most of the country’s agriculture and pesticide use has been taking place for decades. Results for a wide range of organochlorine pesticides in lagoon sediments show levels that generally were very low in Estero Real, Estero Padre Ramos, and estuary of San Juan del Sur. For example, total DDTs in these lagoons averaged 4.5 6 3.4 ng g21 dry weight, which may be considered a baseline level for the region. Other compounds such as HCHs, BHC, endosulfan, heptachlor, endrin, toxaphene, and aroclors were present in concentrations even lower, generally below 1 ng g21 dry weight. However, sediments of the Esteros Naranjo–Paso Caballos system at Chinandega district contained pesticide residues in much higher levels, attaining maximum values of 1,420 ng g21 and 270 ng g21 dry weight, respectively, for toxaphene and total DDTs. Other compounds such as aroclors, chlordane, endosulfan, and dieldrin were also present in the sediments of this lagoon system, but in lower concentrations. The very high concentrations of toxaphene and DDTs in this lagoon are a result of the intensive use of these pesticides in cotton growing in the district of Chinandega. Due to the long environmental half-lives of these compounds (t1⁄2 . 10 years in temperate soils), their concentrations in lagoon sediments will likely remain high for years to come. Based on these results, the development of the new shrimp farming activities in the Pacific coastal lagoons should be restricted to selected areas. The intensive use of pesticides in Nicaragua, which for decades has been one of the biggest pesticide importers and users in Central America (Appel 1991; Castillo et al. 1997), is likely to cause severe contamination of aquatic systems. In particular halogenated hydrocarbons, including chlorinated pesticides and industrial chemicals such as the polychlorinated biphenyls (PCBs), are lipophilic toxic compounds that bioaccumulate and transfer in the food chain. Introduced in aquatic environments these chemicals may compromise the health of the ecosystems (Tardiff 1991). This is the case for the coastal lagoons of the Pacific coast of Nicaragua, where most of the country’s agriculture and population have been concentrated. In particular, cotton growing, a pesticide intensive agriculture started in the 1950s, was developed in this region of Nicaragua (Appel 1991). The degradation of these coastal lagoon systems, especially the reduction of mangrove forest and overexploitation of fishery resources, has received focused attention from national authorities. Agrochemical residues are suspected in the degradation of these lagoons, but have not been investigated. Furthermore, with the plans for developing shrimp rearing farms in these coastal lagoons (esteros), contamination by agrochemical residues becomes a matter of much concern for the future of this industry. To provide information on the potential impacts from agriculture and urban development, a screening of the contaminants was carried out in the main lagoons of the Pacific coast. This paper presents the results of the analyses of chlorinated hydrocarbons in lagoon sediments and discusses the ecotoxicological hazard posed by the current levels of persistent pesticide residues to aquatic biota

Design and preliminary operation of a gasification plant for micro-CHP with internal combustion engine and SOFC

A gasification plant was designed and built to test syngas production from biomass for electricity generation on microscale. The plant is mainly composed by a downdraft reactor, a gas cleaning section with a cyclone and a wet scrubber, a blower for syngas extraction and an ICE (Internal Combustion Engine, Lombardini LGA 340), equipped with an alternator. A small quantity of producer was also eventually sent to a button cell SOFC (Solid Oxide Fuel Cell) for preliminary characterization. The plant was tested in a preliminary experimental campaign to evaluate mass and energy balances and process efficiency. Woody biomass was used and the producer gas firstly passed through impingers bottles, to condense and measure tar concentration (according to CEN/TS 15439), and then the remaining uncondensed gas was analyzed with a micro-GC (Gas Chromatograph). The paper presents and discusses the results of the preliminary tests carried out

Biowep: a workflow enactment portal for bioinformatics applications

<p>Abstract</p> <p>Background</p> <p>The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing.</p> <p>Results</p> <p>We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved.</p> <p>Conclusion</p> <p>We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO.</p

Bounded Model Checking for Probabilistic Programs

In this paper we investigate the applicability of standard model checking approaches to verifying properties in probabilistic programming. As the operational model for a standard probabilistic program is a potentially infinite parametric Markov decision process, no direct adaption of existing techniques is possible. Therefore, we propose an on-the-fly approach where the operational model is successively created and verified via a step-wise execution of the program. This approach enables to take key features of many probabilistic programs into account: nondeterminism and conditioning. We discuss the restrictions and demonstrate the scalability on several benchmarks