Advances in computational immunology

Published versio

Optimal vaccination schedules using simulated annealing

Abstract 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: [email protected]

Corpo, tecnologia, ambiente. Nuove tendenze naturalistiche dell’esperienza estetica

In this article we propose to overlap aesthetic experience with medial experience, starting from the assumption that every aesthetic experience is always a medial experience. Adopting a naturalistic approach, in which we explain what we mean with the term naturalization, we suggest a partial review of the issue. First, we state that human natural language is a kind of technology, made possible by certain physical, cognitive and social features; this sort of biological technology must be considered as an underlying condition for aesthetic experience. Secondly, we suggest the importance of social relationships among various species, demonstrating the role played by this relationships in natural selection: a new perspective will emerge. Thirdly, we explain in more detail why aesthetic experience can be likened to medial experience; in doing so, we offer an epistemological comparison between evolutionary theory and Marshall McLuhan’s approach to media studies. Resulting comparison will offer an original definition of aesthetic experience which rises through the interaction engaged by our natural technologies interacting prosthetically with environment

Computational modelling approaches to vaccinology

Excepting the Peripheral and Central Nervous Systems, the Immune System is the most complex of somatic systems in higher animals. This complexity manifests itself at many levels from the molecular to that of the whole organism. Much insight into this confounding complexity can be gained through computational simulation. Such simulations range in application from epitope prediction through to the modelling of vaccination strategies. In this review, we evaluate selectively various key applications relevant to computational vaccinology: these include technique that operates at different scale that is, from molecular to organisms and even to population level

Gene expression and pathway bioinformatics analysis detect a potential predictive value of MAP3K8 in thyroid cancer progression

Thyroid cancer is the commonest endocrine malignancy. Mutation in the BRAF serine/threonine kinase is the most frequent genetic alteration in thyroid cancer. Target therapy for advanced and poorly differentiated thyroid carcinomas include BRAF pathway inhibitors. Here, we evaluated the role of MAP3K8 expression as a potential driver of resistance to BRAF inhibition in thyroid cancer. By analyzing Gene Expression Omnibus data repository, across all thyroid cancer histotypes, we found that MAP3K8 is up-regulated in poorly differentiated thyroid carcinomas and its expression is related to a stem cell like phenotype and a poorer prognosis and survival. Taken together these data unravel a novel mechanism for thyroid cancer progression and chemo-resistance and confirm previous results obtained in cultured thyroid cancer stem cellsComment: 5 page

Update on intensive motor training in spinocerebellar ataxia: time to move a step forward?:

Some evidence suggests that high-intensity motor training slows down the severity of spinocerebellar ataxia. However, whether all patients might benefit from these activities, and by which activity, and the underlying mechanisms remain unclear. We provide an update on the effect and limitations of different training programmes in patients with spinocerebellar ataxias. Overall, data converge of the finding that intensive training is still based either on conventional rehabilitation protocols or whole-body controlled videogames ("exergames"). Notwithstanding the limitations, short-term improvement is observed, which tends to be lost once the training is stopped. Exergames and virtual reality can ameliorate balance, coordination, and walking abilities, whereas the efficacy of adapted physical activity, gym, and postural exercises depends on the disease duration and severity. In conclusion, although a disease-modifying effect has not been demonstrated, constant, individually tailored, high-intensity motor training might be effective in patients with degenerative ataxia, even in those with severe disease. These approaches may enhance the remaining cerebellar circuitries or plastically induce compensatory networks. Further research is required to identify predictors of training success, such as the type and severity of ataxia and the level of residual functioning

Agent Based Modeling of Lung Metastasis-Immune System Competition,

Extended Abstract The Triplex vaccine is a cell vaccine developed as an immunopreventive approach to breast cancer. Recent studies showed that the same vaccine has a considerable therapeutic effect against lung metastases derived by mammary carcinoma Using three different signals (the target antigen, interleukin-12 (IL-12) and allogeneic MHC molecules) it stimulates immune system response in many ways. The "in vivo" experiment lasts for 32 days. For the induction of lung micrometastasis, all mice received an intravenous injection of 2.5·10 4 metastatic cells at day 0. In standard "in vivo" experiments it is considered common practice to use multiple sets of mice, each treated with a different protocol. One of these sets (the control set) is usually treated with a placebo solution in order to study/represen