Benedetto Intrigila, Igor Melatti, Alberto Tofani, and Guido Macchiarelli. "Computational models of myocardial endomysial collagen arrangement." Computer Methods and Programs in Biomedicine 86, no. 3 (2007): 232–244. Elsevier North-Holland, Inc.. ISSN: 0169-2607. DOI: 10.1016/j.cmpb.2007.03.004.
Abstract: Collagen extracellular matrix is one of the factors related to high passive stiffness of cardiac muscle. However, the architecture and the mechanical aspects of the cardiac collagen matrix are not completely known. In particular, endomysial collagen contribution to the passive mechanics of cardiac muscle as well as its micro anatomical arrangement is still a matter of debate. In order to investigate mechanical and structural properties of endomysial collagen, we consider two alternative computational models of some specific aspects of the cardiac muscle. These two models represent two different views of endomysial collagen distribution: (1) the traditional view and (2) a new view suggested by the data obtained from scanning electron microscopy (SEM) in NaOH macerated samples (a method for isolating collagen from the other tissue). We model the myocardial tissue as a net of spring elements representing the cardiomyocytes together with the endomysial collagen distribution. Each element is a viscous elastic spring, characterized by an elastic and a viscous constant. We connect these springs to imitate the interconnections between collagen fibers. Then we apply to the net of springs some external forces of suitable magnitude and direction, obtaining an extension of the net itself. In our setting, the ratio forces magnitude /net extension is intended to model the stress /strain ratio of a microscopical portion of the myocardial tissue. To solve the problem of the correct identification of the values of the different parameters involved, we use an artificial neural network approach. In particular, we use this technique to learn, given a distribution of external forces, the elastic constants of the springs needed to obtain a desired extension as an equilibrium position. Our experimental findings show that, in the model of collagen distribution structured according to the new view, a given stress /strain ratio (of the net of springs, in the sense specified above) is obtained with much smaller (w.r.t. the other model, corresponding to the traditional view) elasticity constants of the springs. This seems to indicate that by an appropriate structure, a given stiffness of the myocardial tissue can be obtained with endomysial collagen fibers of much smaller size.
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Giuseppe Della Penna, Antinisca Di Marco, Benedetto Intrigila, Igor Melatti, and Alfonso Pierantonio. "Interoperability mapping from XML schemas to ER diagrams." Data Knowl. Eng. 59, no. 1 (2006): 166–188. Elsevier Science Publishers B. V.. ISSN: 0169-023x. DOI: 10.1016/j.datak.2005.08.002.
Abstract: The eXtensible Markup Language (XML) is a de facto standard on the Internet and is now being used to exchange a variety of data structures. This leads to the problem of efficiently storing, querying and retrieving a great amount of data contained in XML documents. Unfortunately, XML data often need to coexist with historical data. At present, the best solution for storing XML into pre-existing data structures is to extract the information from the XML documents and adapt it to the data structures’ logical model (e.g., the relational model of a DBMS). In this paper, we introduce a technique called Xere (XML entity–relationship exchange) to assist the integration of XML data with other data sources. To this aim, we present an algorithm that maps XML schemas into entity–relationship diagrams, discuss its soundness and completeness and show its implementation in XSLT.
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Giuseppe Della Penna, Benedetto Intrigila, Daniele Magazzeni, Igor Melatti, and Enrico Tronci. "CGMurphi: Automatic synthesis of numerical controllers for nonlinear hybrid systems." European Journal of Control 19, no. 1 (2013): 14–36. Elsevier North-Holland, Inc.. ISSN: 0947-3580. DOI: 10.1016/j.ejcon.2013.02.001.
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Ruggero Lanotte, Andrea Maggiolo-Schettini, Simone Tini, Angelo Troina, and Enrico Tronci. "Automatic Analysis of the NRL Pump." Electr. Notes Theor. Comput. Sci. 99 (2004): 245–266. DOI: 10.1016/j.entcs.2004.02.011.
Abstract: We define a probabilistic model for the NRL Pump and using FHP-mur$\varphi$ show experimentally that there exists a probabilistic covert channel whose capacity depends on various NRL Pump parameters (e.g. buffer size, number of samples in the moving average, etc).
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T. Mancini, F. Mari, A. Massini, I. Melatti, I. Salvo, and E. Tronci. "On minimising the maximum expected verification time." Information Processing Letters (2017). DOI: 10.1016/j.ipl.2017.02.001.
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T. Mancini, F. Mari, A. Massini, I. Melatti, and E. Tronci. "On Checking Equivalence of Simulation Scripts." Journal of Logical and Algebraic Methods in Programming (2021): 100640. ISSN: 2352-2208. DOI: 10.1016/j.jlamp.2021.100640.
Abstract: To support Model Based Design of Cyber-Physical Systems (CPSs) many simulation based approaches to System Level Formal Verification (SLFV) have been devised. Basically, these are Bounded Model Checking approaches (since simulation horizon is of course bounded) relying on simulators to compute the system dynamics and thereby verify the given system properties. The main obstacle to simulation based SLFV is the large number of simulation scenarios to be considered and thus the huge amount of simulation time needed to complete the verification task. To save on computation time, simulation based SLFV approaches exploit the capability of simulators to save and restore simulation states. Essentially, such a time saving is obtained by optimising the simulation script defining the simulation activity needed to carry out the verification task. Although such approaches aim to (bounded) formal verification, as a matter of fact, the proof of correctness of the methods to optimise simulation scripts basically relies on an intuitive semantics for simulation scripting languages. This hampers the possibility of formally showing that the optimisations introduced to speed up the simulation activity do not actually omit checking of relevant behaviours for the system under verification. The aim of this paper is to fill the above gap by presenting an operational semantics for simulation scripting languages and by proving soundness and completeness properties for it. This, in turn, enables formal proofs of equivalence between unoptimised and optimised simulation scripts.
Keywords: Formal verification, Simulation based formal verification, Formal Verification of cyber-physical systems, System-level formal verification
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M. P. Hengartner, T. H. C. Kruger, K. Geraedts, E. Tronci, T. Mancini, F. Ille, M. Egli, S. Röblitz, R. Ehrig, L. Saleh et al. "Negative affect is unrelated to fluctuations in hormone levels across the menstrual cycle: Evidence from a multisite observational study across two successive cycles." Journal of Psychosomatic Research 99 (2017): 21–27. DOI: 10.1016/j.jpsychores.2017.05.018.
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T. Mancini, F. Mari, A. Massini, I. Melatti, and E. Tronci. "Anytime system level verification via parallel random exhaustive hardware in the loop simulation." Microprocessors and Microsystems 41 (2016): 12–28. ISSN: 0141-9331. DOI: 10.1016/j.micpro.2015.10.010.
Abstract: Abstract System level verification of cyber-physical systems has the goal of verifying that the whole (i.e., software + hardware) system meets the given specifications. Model checkers for hybrid systems cannot handle system level verification of actual systems. Thus, Hardware In the Loop Simulation (HILS) is currently the main workhorse for system level verification. By using model checking driven exhaustive HILS, System Level Formal Verification (SLFV) can be effectively carried out for actual systems. We present a parallel random exhaustive HILS based model checker for hybrid systems that, by simulating all operational scenarios exactly once in a uniform random order, is able to provide, at any time during the verification process, an upper bound to the probability that the System Under Verification exhibits an error in a yet-to-be-simulated scenario (Omission Probability). We show effectiveness of the proposed approach by presenting experimental results on SLFV of the Inverted Pendulum on a Cart and the Fuel Control System examples in the Simulink distribution. To the best of our knowledge, no previously published model checker can exhaustively verify hybrid systems of such a size and provide at any time an upper bound to the Omission Probability.
Keywords: Model Checking of Hybrid Systems; Model checking driven simulation; Hardware in the loop simulation
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S. Sinisi, V. Alimguzhin, T. Mancini, and E. Tronci. "Reconciling interoperability with efficient Verification and Validation within open source simulation environments." Simulation Modelling Practice and Theory (2021): 102277. ISSN: 1569-190x. DOI: 10.1016/j.simpat.2021.102277.
Abstract: A Cyber-Physical System (CPS) comprises physical as well as software subsystems. Simulation-based approaches are typically used to support design and Verification and Validation (V&V) of CPSs in several domains such as: aerospace, defence, automotive, smart grid and healthcare. Accordingly, many simulation-based tools are available to support CPS design. This, on one side, enables designers to choose the toolchain that best suits their needs, on the other side poses huge interoperability challenges when one needs to simulate CPSs whose subsystems have been designed and modelled using different toolchains. To overcome such an interoperability problem, in 2010 the Functional Mock-up Interface (FMI) has been proposed as an open standard to support both Model Exchange (ME) and Co-Simulation (CS) of simulation models created with different toolchains. FMI has been adopted by several modelling and simulation environments. Models adhering to such a standard are called Functional Mock-up Units (FMUs). Indeed FMUs play an essential role in defining complex CPSs through, e.g., the System Structure and Parametrization (SSP) standard. Simulation-based V&V of CPSs typically requires exploring different simulation scenarios (i.e., exogenous input sequences to the CPS under design). Many such scenarios have a shared prefix. Accordingly, to avoid simulating many times such shared prefixes, the simulator state at the end of a shared prefix is saved and then restored and used as a start state for the simulation of the next scenario. In this context, an important FMI feature is the capability to save and restore the internal FMU state on demand. This is crucial to increase efficiency of simulation-based V&V. Unfortunately, the implementation of this feature is not mandatory and it is available only within some commercial software. As a result, the interoperability enabled by the FMI standard cannot be fully exploited for V&V when using open-source simulation environments. This motivates developing such a feature for open-source CPS simulation environments. Accordingly, in this paper, we focus on JModelica, an open-source modelling and simulation environment for CPSs based on an open standard modelling language, namely Modelica. We describe how we have endowed JModelica with our open-source implementation of the FMI 2.0 functions needed to save and restore internal states of FMUs for ME. Furthermore, we present experimental results evaluating, through 934 benchmark models, correctness and efficiency of our extended JModelica. Our experimental results show that simulation-based V&V is, on average, 22 times faster with our get/set functionality than without it.
Keywords: Simulation, Verification and Validation, Interoperability, FMI/FMU, Model Exchange, Cyber-Physical Systems
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B. Leeners, T. Krueger, K. Geraedts, E. Tronci, T. Mancini, F. Ille, M. Egli, S. Roeblitz, D. Wunder, L. Saleh et al. "Cognitive function in association with high estradiol levels resulting from fertility treatment." Hormones and Behavior 130 (2021): 104951. ISSN: 0018-506x. DOI: 10.1016/j.yhbeh.2021.104951.
Abstract: The putative association between hormones and cognitive performance is controversial. While there is evidence that estradiol plays a neuroprotective role, hormone treatment has not been shown to improve cognitive performance. Current research is flawed by the evaluation of combined hormonal effects throughout the menstrual cycle or in the menopausal transition. The stimulation phase of a fertility treatment offers a unique model to study the effect of estradiol on cognitive function. This quasi-experimental observational study is based on data from 44 women receiving IVF in Zurich, Switzerland. We assessed visuospatial working memory, attention, cognitive bias, and hormone levels at the beginning and at the end of the stimulation phase of ovarian superstimulation as part of a fertility treatment. In addition to inter-individual differences, we examined intra-individual change over time (within-subject effects). The substantial increases in estradiol levels resulting from fertility treatment did not relate to any considerable change in cognitive functioning. As the tests applied represent a broad variety of cognitive functions on different levels of complexity and with various brain regions involved, we can conclude that estradiol does not show a significant short-term effect on cognitive function.
Keywords: Cognition, Estrogen, Estradiol, Fertility treatment, Attention, Cognitive bias
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