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Search Results: 1 - 10 of 5409 matches for " Luca Simonelli "
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Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin
Mattia Pedotti,Luca Simonelli,Elsa Livoti,Luca Varani
International Journal of Molecular Sciences , 2011, DOI: 10.3390/ijms12010226
Abstract: Antibodies play an increasingly important role in both basic research and the pharmaceutical industry. Since their efficiency depends, in ultimate analysis, on their atomic interactions with an antigen, studying such interactions is important to understand how they function and, in the long run, to design new molecules with desired properties. Computational docking, the process of predicting the conformation of a complex from its separated components, is emerging as a fast and affordable technique for the structural characterization of antibody-antigen complexes. In this manuscript, we first describe the different computational strategies for the modeling of antibodies and docking of their complexes, and then predict the binding of two antibodies to the stalk region of influenza hemagglutinin, an important pharmaceutical target. The purpose is two-fold: on a general note, we want to illustrate the advantages and pitfalls of computational docking with a practical example, using different approaches and comparing the results to known experimental structures. On a more specific note, we want to assess if docking can be successful in characterizing the binding to the same influenza epitope of other antibodies with unknown structure, which has practical relevance for pharmaceutical and biological research. The paper clearly shows that some of the computational docking predictions can be very accurate, but the algorithm often fails to discriminate them from inaccurate solutions. It is of paramount importance, therefore, to use rapidly obtained experimental data to validate the computational results.
Development of a Novel Bioinformatics Tool for In Silico Validation of Protein Interactions
Nicola Barbarini,Luca Simonelli,Alberto Azzalin,Sergio Comincini,Riccardo Bellazzi
Journal of Biomedicine and Biotechnology , 2010, DOI: 10.1155/2010/670125
Abstract: Protein interactions are crucial in most biological processes. Several in silico methods have been recently developed to predict them. This paper describes a bioinformatics method that combines sequence similarity and structural information to support experimental studies on protein interactions. Given a target protein, the approach selects the most likely interactors among the candidates revealed by experimental techniques, but not yet in vivo validated. The sequence and the structural information of the in vivo confirmed proteins and complexes are exploited to evaluate the candidate interactors. Finally, a score is calculated to suggest the most likely interactors of the target protein. As an example, we searched for GRB2 interactors. We ranked a set of 46 candidate interactors by the presented method. These candidates were then reduced to 21, through a score threshold chosen by means of a cross-validation strategy. Among them, the isoform 1 of MAPK14 was in silico confirmed as a GRB2 interactor. Finally, given a set of already confirmed interactors of GRB2, the accuracy and the precision of the approach were 75% and 86%, respectively. In conclusion, the proposed method can be conveniently exploited to select the proteins to be experimentally investigated within a set of potential interactors.
Rational Engineering of a Human Anti-Dengue Antibody through Experimentally Validated Computational Docking
Luca Simonelli, Mattia Pedotti, Martina Beltramello, Elsa Livoti, Luigi Calzolai, Federica Sallusto, Antonio Lanzavecchia, Luca Varani
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0055561
Abstract: Antibodies play an increasing pivotal role in both basic research and the biopharmaceutical sector, therefore technology for characterizing and improving their properties through rational engineering is desirable. This is a difficult task thought to require high-resolution x-ray structures, which are not always available. We, instead, use a combination of solution NMR epitope mapping and computational docking to investigate the structure of a human antibody in complex with the four Dengue virus serotypes. Analysis of the resulting models allows us to design several antibody mutants altering its properties in a predictable manner, changing its binding selectivity and ultimately improving its ability to neutralize the virus by up to 40 fold. The successful rational design of antibody mutants is a testament to the accuracy achievable by combining experimental NMR epitope mapping with computational docking and to the possibility of applying it to study antibody/pathogen interactions.
Validation of a Statistical Forecast Model for Zonda Wind in West Argentina Based on the Vertical Atmospheric Structure  [PDF]
Federico A. Norte, Silvia Simonelli
Atmospheric and Climate Sciences (ACS) , 2016, DOI: 10.4236/acs.2016.61004
Abstract: Zonda is a strong, warm, very dry wind associated with adiabatic compression upon descending the eastern slopes of the Andes Cordillera in western-central Argentina. This research seeks, first, to validate the skill of a statistical forecast of zonda based on the behavior of the vertical structure of the atmosphere and, second, to describe the climatology of the vertical profile leeward of the Andes. The forecast was built for May-August 1974/1983, and was verified against a series of cases recorded in the Mendoza Aero and San Juan Aero weather stations for May-August 2005/2014. It made use of the Stepwise Discriminant Analysis (SDA) and rawinsonde data from Mendoza Aero as predictors, with the following input variables: surface pressure, temperature, dew point, and the zonal and meridional components of the wind on surface and of the fixed levels up to 200 hPa. The variables selected as predictors by the SDA were: surface pressure, dew point depression at 850 hPa, meridional wind component at 850 hPa, and zonal wind component at 400 hPa. Climatology of the vertical profile of the atmosphere leeward of the Andes was built from daily rawinsonde data from Mendoza Aero for May-August 1974/1983. Zonda markedly influences the atmospheric structure leeward of the Andes in western-central Argentina. Its maximum impact occurs at 850 to 800 hPa, with significant heating and decrease of humidity. Validation of the prediction program considered deterministic and probabilistic forecasts. Contingency tables show that probability of zonda occurrence in the plains is generally overestimated, and false alarm cases are far more frequent than surprise events. The main contribution of this paper is precisely the validation of the prediction model, which ensures forecasters one more tool to improve zonda forecasting; this, in turn, will aid decision-makers when taking steps to ameliorate zonda wind impact.
Black-Scholes Fuzzy Numbers as Indexes of Performance
M. R. Simonelli
Applied Computational Intelligence and Soft Computing , 2010, DOI: 10.1155/2010/607214
Abstract: We use the set of propositions of some previous papers to define a fuzzy version of the Black-Scholes value where the risk free instantaneous interest intensity, the volatility and the initial stock price are fuzzy numbers whose parameters are built with statistical financial data. With our Black-Scholes fuzzy numbers we define indexes of performance varing in time. As an example, with data of the Italian Stock Exchange on MIB30, we see that in 2004 and 2006 our indexes are negative, that is, they are indexes of the refuse to invest and this refuse increased. So, on November 11, 2006 we could forecast that the market will become with more risk: the risk of loss will increase. Now, on January 25, 2010, we know that this forecast has happened. Obviously, the parameters of our Black-Scholes fuzzy numbers can be valued also with incomplete, possibilistic data. With respect to the probabilistic one, our fuzzy method is more simple and immediate to have a forecast on the financial market. 1. Introduction In this paper, we use the fuzzy theory of Zadeh [1], the set of propositions used in some previous papers of us [2–4] and statistical data, to have a fuzzy version of the Black-Scholes (B-S) value for a European call option, where the istantaneous intensity of the risk-free interest, the standard deviation of the instantaneous intensity of return from the underlying security (volatility), and the initial stock price are fuzzy numbers built with statistical financial data. Obviously, a similar method can be used if one has incomplete possibilistic data. With a theorem we deduce that our B-S fuzzy sets are fuzzy numbers. Then we give a statistical example: with the data of the Italian MIB 30, that is, with its time series, we build a B-S fuzzy number which for every belief degree gives a B-S value. With the support of our B-S fuzzy numbers we define indexes of the performance of the market varing in time. In particular, in 2004 and 2006 we see that these indexes are negative, that is, they are indexes of the refuse to invest. So, comparing our indexes of 2004 and 2006, on November 11, 2006 we could forecast for future loss in the gamble on the increase of the MIB30. The forecast happened. This paper is organized as follows. In Section 2 we set the preliminaries and give the theorems which link the Zadeh's extension principle to the construction of fuzzy numbers with cut-functions in accordance with the theorems in [2, 3, 5] and Zadeh's identity; inSection 3we define three fuzzy numbers which we deduce by probabilistic densities to use for our applications; in
Cambios recientes en la migración y en la inserción laboral en Tijuana, entre 1990 y 2000
Carlos Ernesto Simonelli
Papeles de población , 2002,
Abstract: El autor analiza los cambios que se presentaron en la migración hacia Tijuana, Baja California, y en la inserción laboral, durante la última década del siglo XX, y, a la vez, los relaciona con las transformaciones más destacadas del periodo de acuerdo con aspectos demográficos, económicos, productivos y laborales en dicha ciudad.
Deregulated Electricity Market and Auctions: The Italian Case  [PDF]
Luca Grilli
iBusiness (IB) , 2010, DOI: 10.4236/ib.2010.23030
Abstract: The Electricity Market (in Europe) undergoes a period of transformations never seen before. The competitive model suggested by the European Commission is based on a gradual increase in the classes of consumers able to choice, freely, their providers. In general, liberalization, deregulation, competition result in a spur to development and low prices for consumers. The Electricity Market isn’t likely to follow such a rule. Electricity Markets are best described and analyzed as first-price multi-unit procurement iterated auctions. In this paper we present an analysis of the Italian case in order to show the effects of deregulation on final prices for users.
Positional release techniques as a diagnostic-therapeutic approach in physiotherapy  [PDF]
Luca Collebrusco
Open Journal of Therapy and Rehabilitation (OJTR) , 2014, DOI: 10.4236/ojtr.2014.21004
Abstract: Manual Therapy is a rehabilitative approach based on the use of therapeutic procedures that includes several techniques, but this paper focuses on what is known as Positional Release (PR), a therapeutic model that includes a series of manoeuvres that are mainly used for the treatment of soft tissue. A deeper understanding of this type of therapeutic approach, especially its well known and widespread variant, Strain-Counterstrain, could, through controlled trials and systematic reviews, confirm its effectiveness, definitively explain the neurophysiological mechanism, and therefore make Positional Release another indispensable option in the professional expertise of the physiotherapist.
An Integrated Rehabilitation Model: An Ideal Framework for Limiting Health Care Costs  [PDF]
Luca Collebrusco
Open Journal of Therapy and Rehabilitation (OJTR) , 2015, DOI: 10.4236/ojtr.2015.31002
Abstract: The financial crisis has caused a severe limitation of resources for the public health service and rehabilitation. The proposal of integrated diagnosis and treatment in rehabilitation, involving the introduction of new therapeutic models alongside orthodox models, could lead to a reduction in health care costs through better patient compliance. In rehabilitative assistance in health care, the limiting of financial resources can be simplified, given its multifaceted nature and the need to integrate clinical experience with research. In addition, the phases of rehabilitative recovery do not focus on organ damage, but improved participation and the reduction of disability. For this reason, we have considered incorporating narrative based medicine (NBM) and Psycho-Neuro-Immuno-Endocrinology (PNEI) in the rehabilitation process through an empathetic approach, taking evidence based medicine (EBM) into account, thus creating a “framework” of reference. Managing patients through this “framework” would be a move towards an integrated model of care that could lead to a reduction in health care costs, given the aging population and the rise in patients with chronic pain. The decision to modify health care in rehabilitative assistance through a new “framework” will require time, organizational capacity and experimentation, but may represent the appropriate response for an improved quality of life for patients and a better allocation of resources.
New Risks and the Reframing of Local Welfare as Social Investment: The Case of the FORJAD Program in Switzerland  [PDF]
Luca Martignani
Open Journal of Political Science (OJPS) , 2016, DOI: 10.4236/ojps.2016.61002
Abstract: FORJAD (Formation Professionelle pour le Jeunes Adults en Difficulté) was a program of social policy implemented in Switzerland since 2006. Its specific aim is to sustain the professional training of young unemployed adults (18 - 25) in order to allow them to become autonomous from the social assistance and to (re)entry into the labour market. This paper deals with specific dimensions of this program, with particular reference to its complex and plural governance and to the cultural framework of the Social Investment Welfare State (SIWS). This paradigm tries to connect the logics of activation and training with the necessity to realize a better quality of welfare services and to invest in personal capabilities of welfare recipients. In this framework, FORJAD seems to represent a social innovation realized to contrast at a local level the young unemployment as an example of emergent new social risks.
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