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Maggioli, F.; Mancini, T.; Tronci, E. |
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Title |
SBML2Modelica: Integrating biochemical models within open-standard simulation ecosystems |
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Journal Article |
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2019 |
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Bioinformatics |
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36 |
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7 |
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2165–2172 |
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SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g., enable in-silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models.Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems.In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2 -compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate, and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialised SBML simulators.SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica |
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1367-4803 |
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MCLab @ davi @ ref10.1093/bioinformatics/btz860 |
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179 |
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Leeners, B.; Kruger, T.H.C.; Geraedts, K.; Tronci, E.; Mancini, T.; Ille, F.; Egli, M.; Röblitz, S.; Saleh, L.; Spanaus, K.; Schippert, C.; Zhang, Y.; Hengartner, M.P. |
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Title |
Lack of Associations between Female Hormone Levels and Visuospatial Working Memory, Divided Attention and Cognitive Bias across Two Consecutive Menstrual Cycles |
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2017 |
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Frontiers in Behavioral Neuroscience |
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11 |
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120 |
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Background: Interpretation of observational studies on associations between prefrontal cognitive functioning and hormone levels across the female menstrual cycle is complicated due to small sample sizes and poor replicability. Methods: This observational multisite study comprised data of n=88 menstruating women from Hannover, Germany, and Zurich, Switzerland, assessed during a first cycle and n=68 re-assessed during a second cycle to rule out practice effects and false-positive chance findings. We assessed visuospatial working memory, attention, cognitive bias and hormone levels at four consecutive time-points across both cycles. In addition to inter-individual differences we examined intra-individual change over time (i.e., within-subject effects). Results: Oestrogen, progesterone and testosterone did not relate to inter-individual differences in cognitive functioning. There was a significant negative association between intra-individual change in progesterone and change in working memory from pre-ovulatory to mid-luteal phase during the first cycle, but that association did not replicate in the second cycle. Intra-individual change in testosterone related negatively to change in cognitive bias from menstrual to pre-ovulatory as well as from pre-ovulatory to mid-luteal phase in the first cycle, but these associations did not replicate in the second cycle. Conclusions: There is no consistent association between women's hormone levels, in particular oestrogen and progesterone, and attention, working memory and cognitive bias. That is, anecdotal findings observed during the first cycle did not replicate in the second cycle, suggesting that these are false-positives attributable to random variation and systematic biases such as practice effects. Due to methodological limitations, positive findings in the published literature must be interpreted with reservation. |
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1662-5153 |
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Sapienza @ mari @ ref10.3389/fnbeh.2017.00120 |
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167 |
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Leeners, B.; Krueger, T.H.C.; Geraedts, K.; Tronci, E.; Mancini, T.; Egli, M.; Roeblitz, S.; Saleh, L.; Spanaus, K.; Schippert, C.; Zhang, Y.; Ille, F. |
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Associations Between Natural Physiological and Supraphysiological Estradiol Levels and Stress Perception |
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2019 |
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Frontiers in Psychology |
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10 |
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1296 |
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Stress is a risk factor for impaired general, mental and reproductive health. The role of physiological and supraphysiological estradiol concentrations in stress perception and stress processing is less well understood. We therefore, conducted a prospective observational study to investigate the association between estradiol, stress perception and stress-related cognitive performance within serial measurements either during the natural menstrual cycle or during fertility treatment, where estradiol levels are strongly above the physiological level of a natural cycle and consequently, represent a good model to study dose-dependent effects of estradiol. Data from 44 women receiving in vitro fertilization at the Department of Reproductive Endocrinology in Zurich, Switzerland was compared to data from 88 women with measurements during their natural menstrual cycle. The german version of the Perceived Stress Questionnaire (PSQ) and the Cognitive Bias Test (CBT), in which cognitive performance is tested under time stress were used to evaluate subjective and functional aspects of stress. Estradiol levels were investigated at four different time points during the menstrual cycle and at two different time points during a fertility treatment. Cycle phase were associated with PSQ worry and cognitive bias in normally cycling women, but different phases of fertility treatment were not associated with subjectively perceived stress and stress-related cognitive bias. PSQ lack of joy and PSQ demands related to CBT in women receiving fertility treatment but not in women with a normal menstrual cycle. Only strong changes of the estradiol level during fertility treatment were weakly associated with CBT, but not with subjectively experienced stress. Our research emphasises the multidimensional character of stress and the necessity to adjust stress research to the complex nature of stress perception and processing. Infertility is associated with an increased psychological burden in patients. However, not all phases of the process to overcome infertility do significantly increase patient stress levels. Also, research on the psychological burden of infertility should consider that stress may vary during the different phases of fertility treatment. |
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1664-1078 |
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MCLab @ davi @ ref10.3389/fpsyg.2019.01296 |
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178 |
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Leeners, B.; Krueger, T.; Geraedts, K.; Tronci, E.; Mancini, T.; Ille, F.; Egli, M.; Roeblitz, S.; Wunder, D.; Saleh, L.; Schippert, C.; Hengartner, M.P. |
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Title |
Cognitive function in association with high estradiol levels resulting from fertility treatment |
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Journal Article |
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2021 |
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Hormones and Behavior |
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130 |
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104951 |
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Cognition, Estrogen, Estradiol, Fertility treatment, Attention, Cognitive bias |
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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. |
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0018-506x |
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MCLab @ davi @ Leeners2021104951 |
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Lanotte, Ruggero; Maggiolo-Schettini, Andrea; Tini, Simone; Troina, Angelo; Tronci, Enrico |
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Automatic Covert Channel Analysis of a Multilevel Secure Component |
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2004 |
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Information and Communications Security, 6th International Conference, ICICS 2004, Malaga, Spain, October 27-29, 2004, Proceedings |
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249-261 |
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The NRL Pump protocol defines a multilevel secure component whose goal is to minimize leaks of information from high level systems to lower level systems, without degrading average time performances. We define a probabilistic model for the NRL Pump and show how a probabilistic model checker (FHP-mur$\varphi$) can be used to estimate the capacity of a probabilistic covert channel in the NRL Pump. We are able to compute the probability of a security violation as a function of time for various configurations of the system parameters (e.g. buffer sizes, moving average size, etc). Because of the model complexity, our results cannot be obtained using an analytical approach and, because of the low probabilities involved, it can be hard to obtain them using a simulator. |
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Springer |
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Lopez, J.; Qing, S.; Okamoto, E. |
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Lecture Notes in Computer Science |
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3269 |
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Sapienza @ mari @ icics04 |
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34 |
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Lanotte, Ruggero; Maggiolo-Schettini, Andrea; Tini, Simone; Troina, Angelo; Tronci, Enrico |
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Automatic Analysis of the NRL Pump |
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2004 |
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Electr. Notes Theor. Comput. Sci. |
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99 |
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245-266 |
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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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Sapienza @ mari @ entcs04 |
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36 |
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Intrigila, Benedetto; Magazzeni, Daniele; Melatti, Igor; Tronci, Enrico |
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A Model Checking Technique for the Verification of Fuzzy Control Systems |
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2005 |
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CIMCA '05: Proceedings of the International Conference on Computational Intelligence for Modelling, Control and Automation and International Conference on Intelligent Agents, Web Technologies and Internet Commerce Vol-1 (CIMCA-IAWTIC'06) |
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536-542 |
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Fuzzy control is well known as a powerful technique for designing and realizing control systems. However, statistical evidence for their correct behavior may be not enough, even when it is based on a large number of samplings. In order to provide a more systematic verification process, the cell-to-cell mapping technology has been used in a number of cases as a verification tool for fuzzy control systems and, more recently, to assess their optimality and robustness. However, cell-to-cell mapping is typically limited in the number of cells it can explore. To overcome this limitation, in this paper we show how model checking techniques may be instead used to verify the correct behavior of a fuzzy control system. To this end, we use a modified version of theMurphi verifier, which ease the modeling phase by allowing to use finite precision real numbers and external C functions. In this way, also already designed simulators may be used for the verification phase. With respect to the cell mapping technique, our approach appears to be complementary; indeed, it explores a much larger number of states, at the cost of being less informative on the global dynamic of the system. |
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IEEE Computer Society |
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Washington, DC, USA |
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0-7695-2504-0-01 |
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Sapienza @ mari @ Immt05 |
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75 |
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Hengartner, M. P.; Kruger, T. H. C.; Geraedts, K.; Tronci, E.; Mancini, T.; Ille, F.; Egli, M.; Röblitz, S.; Ehrig, R.; Saleh, L.; Spanaus, K.; Schippert, C.; Zhang, Y.; Leeners, B. |
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Negative affect is unrelated to fluctuations in hormone levels across the menstrual cycle: Evidence from a multisite observational study across two successive cycles |
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2017 |
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Journal of Psychosomatic Research |
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99 |
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21-27 |
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Hayes, B. P. ; Melatti, I.; Mancini, T.; Prodanovic, M.; Tronci, E. |
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Residential Demand Management using Individualised Demand Aware Price Policies |
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2017 |
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IEEE Transactions On Smart Grid |
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8 |
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3 |
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1284-1294 |
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MCLab @ davi @ |
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Gribaudo, Marco; Horváth, Andras; Bobbio, Andrea; Tronci, Enrico; Ciancamerla, Ester; Minichino, Michele |
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Fluid Petri Nets and hybrid model checking: a comparative case study |
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2003 |
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Int. Journal on: Reliability Engineering & System Safety |
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81 |
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3 |
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239-257 |
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The modeling and analysis of hybrid systems is a recent and challenging research area which is actually dominated by two main lines: a functional analysis based on the description of the system in terms of discrete state (hybrid) automata (whose goal is to ascertain conformity and reachability properties), and a stochastic analysis (whose aim is to provide performance and dependability measures). This paper investigates a unifying view between formal methods and stochastic methods by proposing an analysis methodology of hybrid systems based on Fluid Petri Nets (FPNs). FPNs can be analyzed directly using appropriate tools. Our paper shows that the same FPN model can be fed to different functional analyzers for model checking. In order to extensively explore the capability of the technique, we have converted the original FPN into languages for discrete as well as hybrid as well as stochastic model checkers. In this way, a first comparison among the modeling power of well known tools can be carried out. Our approach is illustrated by means of a ’real world’ hybrid system: the temperature control system of a co-generative plant. |
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Elsevier |
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Sapienza @ mari @ ress03 |
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40 |
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