M. Pennisi - Academia.edu (original) (raw)
Papers by M. Pennisi
We present a preliminary ODE model to sketch the immune response of cytotoxic T cells against can... more We present a preliminary ODE model to sketch the immune response of cytotoxic T cells against cancer through the use of pulsed autologous dendritic cells. The model is partially based on data coming from experiments that are presently in progress in the wet lab of our collaborators, but it can be applied in principle to different tumors. To this end,
ABSTRACT Cited By (since 1996):1, Export Date: 19 September 2014
Lecture Notes in Computer Science, 2010
BioMed Research International, 2014
Several components that interact with each other to evolve a complex, and, in some cases, unexpec... more Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide ra...
IEEE Engineering in Medicine and Biology Magazine, 2009
Bioinformatics, 2014
Motivation: Although results from phase III clinical trials substantially support the use of prop... more Motivation: Although results from phase III clinical trials substantially support the use of prophylactic and therapeutic vaccines against cancer, what has yet to be defined is how many and how frequent boosts are needed to sustain a long-lasting and protecting memory T-cell response against tumor antigens. Common experience is that such preclinical tests require the sacrifice of a relatively large number of animals, and are particularly time- and money-consuming. Results: As a first step to overcome these hurdles, we have developed an ordinary differential equation model that includes all relevant entities (such as activated cytotoxic T lymphocytes and memory T cells), and investigated the induction of immunological memory in the context of wild-type mice injected with a dendritic cell-based vaccine. We have simulated the biological behavior both in the presence and in the absence of memory T cells. Comparing results of ex vivo and in silico experiments, we show that the model is a...
Bioinformatics, 2008
Summary: Since few years the problem of finding optimal solutions for drug or vaccine protocols h... more Summary: Since few years the problem of finding optimal solutions for drug or vaccine protocols have been tackled using system biology modeling. These approaches are usually computationally expensive. Our previous experiences in optimizing vaccine or drug protocols using genetic algorithms required the use of a high performance computing infrastructure for a couple of days. In the present article we show that by an appropriate use of a different optimization algorithm, the simulated annealing, we have been able to downsize the computational effort by a factor102. The new algorithm requires computational effort that can be achieved by current generation personal computers. Availability: Software and additional data can be found at http://www.immunomics.eu/SA/ Contact: francesco@dmi.unict.it
Mathematical Modelling of Natural Phenomena, 2012
Journal of Circuits, Systems and Computers, 2009
Many human tumors cannot easily be avoided. In most cases a prophylactic vaccination prevents the... more Many human tumors cannot easily be avoided. In most cases a prophylactic vaccination prevents the tumor growth. In particular the Triplex vaccine prevented mammary carcinoma formation using a Chronic schedule, but it is not known if this schedule is minimal. A computational model named SimTriplex was able to reproduce in silico the in vivo experiments. The combination of SimTriplex and Genetic Algorithms (GA), produced a minimal vaccination schedule capable to guarantee in silico survival. This process required the use of a High Performance Computing (HPC) infrastructure for several days. In this paper we show another optimization procedure based on simulated annealing approach used to get a faster algorithm response.
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2010
The ultimate aim of the EU-funded ImmunoGrid project is to develop a natural-scale model of the h... more The ultimate aim of the EU-funded ImmunoGrid project is to develop a natural-scale model of the human immune system-that is, one that reflects both the diversity and the relative proportions of the molecules and cells that comprise it-together with the grid infrastructure necessary to apply this model to specific applications in the field of immunology. These objectives present the ImmunoGrid Consortium with formidable challenges in terms of complexity of the immune system, our partial understanding about how the immune system works, the lack of reliable data and the scale of computational resources required. In this paper, we explain the key challenges and the approaches adopted to overcome them. We also consider wider implications for the present ambitious plans to develop natural-scale, integrated models of the human body that can make contributions to personalized health care, such as the European Virtual Physiological Human initiative. Finally, we ask a key question: How long will it take us to resolve these challenges and when can we expect to have fully functional models that will deliver health-care benefits in the form of personalized care solutions and improved disease prevention?
Meccanica, 2014
ABSTRACT Export Date: 19 September 2014, Article in Press
dmi.unict.it
Abstract. Atherosclerosis is a pathology where the immune system control plays a relevant role. W... more Abstract. Atherosclerosis is a pathology where the immune system control plays a relevant role. We present studies on the increased atherosclerosis risk using an agent based model of atherogenesis. It is well known that the major risk in atherosclerosis is the persistent ...
We present a preliminary ODE model to sketch the immune response of cytotoxic T cells against can... more We present a preliminary ODE model to sketch the immune response of cytotoxic T cells against cancer through the use of pulsed autologous dendritic cells. The model is partially based on data coming from experiments that are presently in progress in the wet lab of our collaborators, but it can be applied in principle to different tumors. To this end,
ABSTRACT Cited By (since 1996):1, Export Date: 19 September 2014
Lecture Notes in Computer Science, 2010
BioMed Research International, 2014
Several components that interact with each other to evolve a complex, and, in some cases, unexpec... more Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide ra...
IEEE Engineering in Medicine and Biology Magazine, 2009
Bioinformatics, 2014
Motivation: Although results from phase III clinical trials substantially support the use of prop... more Motivation: Although results from phase III clinical trials substantially support the use of prophylactic and therapeutic vaccines against cancer, what has yet to be defined is how many and how frequent boosts are needed to sustain a long-lasting and protecting memory T-cell response against tumor antigens. Common experience is that such preclinical tests require the sacrifice of a relatively large number of animals, and are particularly time- and money-consuming. Results: As a first step to overcome these hurdles, we have developed an ordinary differential equation model that includes all relevant entities (such as activated cytotoxic T lymphocytes and memory T cells), and investigated the induction of immunological memory in the context of wild-type mice injected with a dendritic cell-based vaccine. We have simulated the biological behavior both in the presence and in the absence of memory T cells. Comparing results of ex vivo and in silico experiments, we show that the model is a...
Bioinformatics, 2008
Summary: Since few years the problem of finding optimal solutions for drug or vaccine protocols h... more Summary: Since few years the problem of finding optimal solutions for drug or vaccine protocols have been tackled using system biology modeling. These approaches are usually computationally expensive. Our previous experiences in optimizing vaccine or drug protocols using genetic algorithms required the use of a high performance computing infrastructure for a couple of days. In the present article we show that by an appropriate use of a different optimization algorithm, the simulated annealing, we have been able to downsize the computational effort by a factor102. The new algorithm requires computational effort that can be achieved by current generation personal computers. Availability: Software and additional data can be found at http://www.immunomics.eu/SA/ Contact: francesco@dmi.unict.it
Mathematical Modelling of Natural Phenomena, 2012
Journal of Circuits, Systems and Computers, 2009
Many human tumors cannot easily be avoided. In most cases a prophylactic vaccination prevents the... more Many human tumors cannot easily be avoided. In most cases a prophylactic vaccination prevents the tumor growth. In particular the Triplex vaccine prevented mammary carcinoma formation using a Chronic schedule, but it is not known if this schedule is minimal. A computational model named SimTriplex was able to reproduce in silico the in vivo experiments. The combination of SimTriplex and Genetic Algorithms (GA), produced a minimal vaccination schedule capable to guarantee in silico survival. This process required the use of a High Performance Computing (HPC) infrastructure for several days. In this paper we show another optimization procedure based on simulated annealing approach used to get a faster algorithm response.
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2010
The ultimate aim of the EU-funded ImmunoGrid project is to develop a natural-scale model of the h... more The ultimate aim of the EU-funded ImmunoGrid project is to develop a natural-scale model of the human immune system-that is, one that reflects both the diversity and the relative proportions of the molecules and cells that comprise it-together with the grid infrastructure necessary to apply this model to specific applications in the field of immunology. These objectives present the ImmunoGrid Consortium with formidable challenges in terms of complexity of the immune system, our partial understanding about how the immune system works, the lack of reliable data and the scale of computational resources required. In this paper, we explain the key challenges and the approaches adopted to overcome them. We also consider wider implications for the present ambitious plans to develop natural-scale, integrated models of the human body that can make contributions to personalized health care, such as the European Virtual Physiological Human initiative. Finally, we ask a key question: How long will it take us to resolve these challenges and when can we expect to have fully functional models that will deliver health-care benefits in the form of personalized care solutions and improved disease prevention?
Meccanica, 2014
ABSTRACT Export Date: 19 September 2014, Article in Press
dmi.unict.it
Abstract. Atherosclerosis is a pathology where the immune system control plays a relevant role. W... more Abstract. Atherosclerosis is a pathology where the immune system control plays a relevant role. We present studies on the increased atherosclerosis risk using an agent based model of atherogenesis. It is well known that the major risk in atherosclerosis is the persistent ...