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Landslide Susceptibility Assessment Using Conditional Analysis and Rare Events Logistics Regression: A Case-Study in the Antrodoco Area (Rieti, Italy)  [PDF]
Vittorio Chiessi, Simona Toti, Valerio Vitale
Journal of Geoscience and Environment Protection (GEP) , 2016, DOI: 10.4236/gep.2016.412001
Abstract: This paper discusses some methodological aspects for the production of susceptibility maps of slope instability developed within the CARG Project (Geological Cartography of Italy at 1:50,000 scale). It describes an example of a susceptibility map in the presence of low susceptibility, using database having zero or negligible cost, with the aim to test some methodologies that can be easily reproducible to get a first estimate of the landslide susceptibility on a wide area. Two statistical approaches have been applied: the non-parametric conditional analysis and the logistic analysis for rare events. The predictive ability obtained from the two methodologies, was evaluated by the success-prediction curves for the conditional analysis, and by the Receiver Operating Characteristic curve (ROC), for the logistic model. The landslide susceptibility maps have been classified into four classes using both the Natural Breaks algorithm and the method proposed by Chung and Fabbri (2003). The paper considers the influence of these two classification methods on the quality of final results.
Stochastic Dynamics of the Multi-State Voter Model over a Network based on Interacting Cliques and Zealot Candidates
Filippo Palombi,Simona Toti
Physics , 2013, DOI: 10.1007/s10955-014-1003-1
Abstract: The stochastic dynamics of the multi-state voter model is investigated on a class of complex networks made of non-overlapping cliques, each hosting a political candidate and interacting with the others via Erd\H{o}s-R\'enyi links. Numerical simulations of the model are interpreted in terms of an ad-hoc mean field theory, specifically tuned to resolve the inter/intra-clique interactions. Under a proper definition of the thermodynamic limit (with the average degree of the agents kept fixed while increasing the network size), the model is found to display the empirical scaling discovered by Fortunato and Castellano (Phys Rev Lett 99(13):138701, 2007), while the vote distribution resembles roughly that observed in Brazilian elections.
Use of Dirichlet Distributions and Orthogonal Projection Techniques for the Fluctuation Analysis of Steady-State Multivariate Birth-Death Systems
Filippo Palombi,Simona Toti
Physics , 2014, DOI: 10.1142/S0129183115501399
Abstract: Approximate weak solutions of the Fokker-Planck equation can represent a useful tool to analyze the equilibrium fluctuations of birth-death systems, as they provide a quantitative knowledge lying in between numerical simulations and exact analytic arguments. In the present paper, we adapt the general mathematical formalism known as the Ritz-Galerkin method for partial differential equations to the Fokker-Planck equation with time-independent polynomial drift and diffusion coefficients on the simplex. Then, we show how the method works in two examples, namely the binary and multi-state voter models with zealots.
A perturbative approach to the reconstruction of the eigenvalue spectrum of a normal covariance matrix from a spherically truncated counterpart
Filippo Palombi,Simona Toti
Statistics , 2012,
Abstract: In this paper we propose a perturbative method for the reconstruction of the covariance matrix of a multinormal distribution, under the assumption that the only available information amounts to the covariance matrix of a spherically truncated counterpart of the same distribution. We expand the relevant equations up to the fourth perturbative order and discuss the analytic properties of the first few perturbative terms. We finally compare the proposed approach with an exact iterative algorithm (presented in ref. [1]) in the hypothesis that the spherically truncated covariance matrix is estimated from samples of various sizes.
A note on the variance of the square components of a normal multivariate within a Euclidean ball
Filippo Palombi,Simona Toti
Statistics , 2012, DOI: 10.1016/j.jmva.2013.08.011
Abstract: We present arguments in favour of the inequalities $var(X_n^2|X \in B_v(\rho)) \le 2\lambda_n E[X_n^2|X \in B_v(\rho)]$, where $X \sim N_v(0,\Lambda)$ is a normal vector in $v\ge 1$ dimensions, with zero mean and covariance matrix $\Lambda = \diag(\lambda)$, and $B_v(\rho)$ is a centered $v$-dimensional Euclidean ball of square radius $\rho$. Such relations lie at the heart of an iterative algorithm, proposed in ref. [1] to perform a reconstruction of $\Lambda$ from the covariance matrix of $X$ conditioned to $B_v(\rho)$. In the regime of strong truncation, i.e. for $\rho \lesssim \lambda_n$, the above inequality is easily proved, whereas it becomes harder for $\rho \gg \lambda_n$. Here, we expand both sides in a function series controlled by powers of $\lambda_n/\rho$ and show that the coefficient functions of the series fulfill the inequality order by order if $\rho$ is sufficiently large. The intermediate region remains at present an open challenge.
Numerical reconstruction of the covariance matrix of a spherically truncated multinormal distribution
Filippo Palombi,Simona Toti,Romina Filippini
Statistics , 2012,
Abstract: In this paper we relate the matrix $S_B$ of the second moments of a spherically truncated normal multivariate to its full covariance matrix $\Sigma$ and present an algorithm to invert the relation and reconstruct $\Sigma$ from $S_B$. While the eigenvectors of $\Sigma$ are left invariant by the truncation, its eigenvalues are non-uniformly damped. We show that the eigenvalues of $\Sigma$ can be reconstructed from their truncated counterparts via a fixed point iteration, whose convergence we prove analytically. The procedure requires the computation of multidimensional Gaussian integrals over a Euclidean ball, for which we extend a numerical technique, originally proposed by Ruben in 1962, based on a series expansion in chi-square distributions. In order to study the feasibility of our approach, we examine the convergence rate of some iterative schemes on suitably chosen ensembles of Wishart matrices. We finally discuss the practical difficulties arising in sample space and outline a regularization of the problem based on perturbation theory.
A Novel Computational Method Identifies Intra- and Inter-Species Recombination Events in Staphylococcus aureus and Streptococcus pneumoniae
Lisa Sanguinetti,Simona Toti,Valerio Reguzzi,Fabio Bagnoli,Claudio Donati
PLOS Computational Biology , 2012, DOI: 10.1371/journal.pcbi.1002668
Abstract: Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.
Evaluation of latent links between irritable bowel syndrome and sleep quality
Massimo Bellini,Angelo Gemignani,Dario Gambaccini,Simona Toti
World Journal of Gastroenterology , 2011, DOI: 10.3748/wjg.v17.i46.5089
Abstract: AIM: To examine the links between quality of sleep and the severity of intestinal symptoms in irritable bowel syndrome (IBS). METHODS: One hundred and forty-two outpatients (110 female, 32 male) who met the Rome III criteria for IBS with no psychiatric comorbidity were consecutively enrolled in this study. Data on age, body mass index (BMI), and a set of life-habit variables were recorded, and IBS symptoms and sleep quality were evaluated using the questionnaires IBS Symptom Severity Score (IBS-SSS) and Pittsburgh Sleep Quality Index (PSQI). The association between severity of IBS and sleep disturbances was evaluated by comparing the global IBS-SSS and PSQI score (Pearson’s correlation and Fisher’s exact test) and then analyzing the individual items of the IBS-SSS and PSQI questionnaires by a unitary bowel-sleep model based on item response theory (IRT). RESULTS: IBS-SSS ranged from mild to severe (120-470). The global PSQI score ranged from 1 to 17 (median 5), and 60 patients were found to be poor sleepers (PSQI > 5). The correlation between the global IBS-SSS and PSQI score indicated a weak association (r = 0.2 and 95% CI: -0.03 to 0.35, P < 0.05), which becomes stronger using our unitary model. Indeed, the IBS and sleep disturbances severities, estimated as latent variables, resulted significantly high intra-subject correlation (posterior mean of r = 0.45 and 95% CI: 0.17 to 0.70, P < 0.05). Moreover, the correlations between patient features (age, sex, BMI, daily coffee and alcohol intake) and IBS and sleep disturbances were also analyzed through our unitary model. Age was a significant regressor, with patients ≤ 50 years old showing more severe bowel disturbances (posterior mean = -0.38, P < 0.05) and less severe sleep disturbances (posterior mean = 0.49, P < 0.05) than older patients. Higher daily coffee intake was correlated with a lower severity of bowel disturbances (posterior mean = -0.31, P < 0.05). Sex (female) and daily alcohol intake (modest) were correlated with less severe sleep disturbances. CONCLUSION: The unitary bowel-sleep model based on IRT revealed a strong positive correlation between the severity of IBS symptoms and sleep disturbances.
Gene expression profile and genomic alterations in colonic tumours induced by 1,2-dimethylhydrazine (DMH) in rats
Angelo Femia, Cristina Luceri, Simona Toti, Augusto Giannini, Piero Dolara, Giovanna Caderni
BMC Cancer , 2010, DOI: 10.1186/1471-2407-10-194
Abstract: For gene expression analysis, 9 tumours (TUM) and their paired normal mucosa (NM) were hybridized on 4 × 44K Whole rat arrays (Agilent) and selected genes were validated by semi-quantitative RT-PCR. Functional analysis on microarray data was performed by GenMAPP/MappFinder analysis. Array-comparative genomic hybridization (a-CGH) was performed on 10 paired TUM-NM samples hybridized on Rat genome arrays 2 × 105K (Agilent) and the results were analyzed by CGH Analytics (Agilent).Microarray gene expression analysis showed that Defcr4, Igfbp5, Mmp7, Nos2, S100A8 and S100A9 were among the most up-regulated genes in tumours (Fold Change (FC) compared with NM: 183, 48, 39, 38, 36 and 32, respectively), while Slc26a3, Mptx, Retlna and Muc2 were strongly down-regulated (FC: -500; -376, -167, -79, respectively). Functional analysis showed that pathways controlling cell cycle, protein synthesis, matrix metalloproteinases, TNFα/NFkB, and inflammatory responses were up-regulated in tumours, while Krebs cycle, the electron transport chain, and fatty acid beta oxidation were down-regulated. a-CGH analysis showed that four TUM out of ten had one or two chromosomal aberrations. Importantly, one sample showed a deletion on chromosome 18 including Apc.The results showed complex gene expression alterations in adenocarcinomas encompassing many altered pathways. While a-CGH analysis showed a low degree of genomic imbalance, it is interesting to note that one of the alterations concerned Apc, a key gene in colorectal carcinogenesis. The fact that many of the molecular alterations described in this study are documented in human colon tumours confirms the relevance of DMH-induced cancers as a powerful tool for the study of colon carcinogenesis and chemoprevention.Colorectal cancer is one of the most common neoplastic diseases in the Western World [1], developing through a multistage process which involves the accumulation of genetic and epigenetic alterations. Experimental models mimicking
Elementi di interfaccia per l’analisi di strutture murarie
Elio Sacco,Jessica Toti
Frattura ed Integrità Strutturale , 2009,
Abstract: Il presente articolo riguarda la modellazione del comportamento meccanico di elementi in muratura intesi come sistemi eterogenei composti da malta, blocchi ed interfacce di connessione. La strategiacomputazionale che viene adottata consiste nel modellare separatamente i blocchi, i letti di malta ed le interfacce responsabili di fenomeni di decoesione malta-blocco; a tale scopo, si propone uno speciale modello di interfaccia che combina il danneggiamento con l’attrito. Si sviluppa una procedura numerica, basata sull’algoritmo backward di Eulero, per risolvere il problema evolutivo; per il passo temporale si utilizza invece la tecnica predictor-corrector a controllo di spostamenti. Si effettuano alcune applicazioni numeriche con lo scopodi verificare la capacità del modello e dell’algoritmo proposto nel riprodurre la risposta non lineare della muratura dovuta a fenomeni di degrado localizzati. Infine, si conduce lo studio della modellazione di un arco murario, confrontando i risultati numerici con quelli sperimentali; si dimostra la abilità del modello proposto nel simulare il comportamento globale della struttura ad arco in termini di carico ultimo e di meccanismo di collasso.
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