Shift Aggregate Extract Networks

We introduce an architecture based on deep hierarchical decompositions to learn effective representations of large graphs. Our framework extends classic R-decompositions used in kernel methods, enabling nested "part-of-part" relations. Unlike recursive neural networks, which unroll a template on input graphs directly, we unroll a neural network template over the decomposition hierarchy, allowing us to deal with the high degree variability that typically characterize social network graphs. Deep hierarchical decompositions are also amenable to domain compression, a technique that reduces both space and time complexity by exploiting symmetries. We show empirically that our approach is competitive with current state-of-the-art graph classification methods, particularly when dealing with social network datasets

Stress-induced reduction of dorsal striatal D2 dopamine receptors prevents retention of a newly acquired adaptive coping strategy

The inability to learn an adaptive coping strategy in a novel stressful condition leads to dysfunctional stress coping, a marker of mental disturbances. This study tested the involvement of dorsal striatal dopamine receptors in the dysfunctional coping with the Forced Swim test fostered by a previous experience of reduced food availability. Adult male mice were submitted to a temporary (12 days) reduction of food availability [food-restricted (FR)] or continuously free-fed (FF). Different groups of FF and FR mice were used to evaluate: (1) dorsal striatal mRNA levels of the two isoforms of the dopamine D2 receptor (D2S, D2L). (2) Forced Swim-induced c-fos expression in the dorsal striatum; (3) acquisition and 24 h retention of passive coping with Forced Swim. Additional groups of FF mice were tested for 24 h retention of passive coping acquired during a first experience with Forced Swim immediately followed by intra-striatal infusion of vehicle or two doses of the dopamine D2/D3 receptors antagonist sulpiride or the D1/D5 receptors antagonist SCH23390. Previous restricted feeding selectively reduced mRNA levels of both D2 isoforms and abolished Forced Swim-induced c-fos expression in the left Dorsolateral Striatum and selectively prevented 24 h retention of the coping strategy acquired in a first experience of Forced Swim. Finally, temporary blockade of left Dorsolateral Striatum D2/D3 receptors immediately following the first Forced Swim experience selectively reproduced the behavioral effect of restricted feeding in FF mice. In conclusion, the present results demonstrate that mice previously exposed to a temporary reduction of food availability show low striatal D2 receptors, a known marker of addiction-associated aberrant neuroplasticity, as well as liability to relapse into maladaptive stress coping strategies. Moreover, they offer strong support to a causal relationship between reduction of D2 receptors in the left Dorsolateral Striatum and impaired consolidation of newly acquired adaptive coping

A hermite radial basis functions control volume numerical method to simulate transport problems

This thesis presents a Control Volume (CV) method for transient transport problems where the cell surface fluxes are reconstructed using local interpolation functions that besides interpolating the nodal values of the field variable, also satisfies the governing equation at some auxiliary points in the interpolation stencils. The interpolation function relies on a Hermitian Radial Basis Function (HRBF) mesh less collocation approach to find the solution of auxiliary local boundary/initial value problems, which are solved using the same time integration scheme adopted to update the global control volume solution. By the use of interpolation functions that approximate the governing equation, a form of analytical upwinding scheme is achieved without the need of using predefined interpolation stencils according to the magnitude and direction of the local advective velocity. In this way, the interpolation formula retains the desired information about the advective velocity field, allowing the use of centrally defined stencils even in the case of advective dominant problems. This new CV approach, which is referred to as the CV-HRBF method, is applied to a series of transport problems characterised by high Peclet number. This method is also more flexible than the classical CV formulations because the boundary conditions are explicitly imposed in the interpolation formula, without the need for artificial schemes (e.g. utilising dummy cells). The flexibility of the local meshless character of the CVHRBF is shown in the modelling of the saturated zone of the unconfined aquifer where a mesh adapting algorithm is needed to track the phreatic surface (moving boundary). Due to the use of a local RBF interpolation, the dynamic boundary condition can be applied in an arbitrary number of points on the phreatic surface, independently from the mesh element. The robustness of the Hermite interpolation is exploited to formulate a non-overlapping non-iterative multi-domain scheme where physical matching conditions are satisfied locally, i.e. imposing the continuity of the function and flux at the sub-domain interface

A hermite radial basis functions control volume numerical method to simulate transport problems

This thesis presents a Control Volume (CV) method for transient transport problems where the cell surface fluxes are reconstructed using local interpolation functions that besides interpolating the nodal values of the field variable, also satisfies the governing equation at some auxiliary points in the interpolation stencils. The interpolation function relies on a Hermitian Radial Basis Function (HRBF) mesh less collocation approach to find the solution of auxiliary local boundary/initial value problems, which are solved using the same time integration scheme adopted to update the global control volume solution. By the use of interpolation functions that approximate the governing equation, a form of analytical upwinding scheme is achieved without the need of using predefined interpolation stencils according to the magnitude and direction of the local advective velocity. In this way, the interpolation formula retains the desired information about the advective velocity field, allowing the use of centrally defined stencils even in the case of advective dominant problems. This new CV approach, which is referred to as the CV-HRBF method, is applied to a series of transport problems characterised by high Peclet number. This method is also more flexible than the classical CV formulations because the boundary conditions are explicitly imposed in the interpolation formula, without the need for artificial schemes (e.g. utilising dummy cells). The flexibility of the local meshless character of the CVHRBF is shown in the modelling of the saturated zone of the unconfined aquifer where a mesh adapting algorithm is needed to track the phreatic surface (moving boundary). Due to the use of a local RBF interpolation, the dynamic boundary condition can be applied in an arbitrary number of points on the phreatic surface, independently from the mesh element. The robustness of the Hermite interpolation is exploited to formulate a non-overlapping non-iterative multi-domain scheme where physical matching conditions are satisfied locally, i.e. imposing the continuity of the function and flux at the sub-domain interface

Evaluating the features of Museum Websites (The Bologna Report)

MiLE (Milano – Lugano Evaluation Method) is an innovative method for evaluating the quality and usability of hypermedia applications. This paper focuses upon the specific “module” of MiLE concerning cultural heritage applications, synthesizing the results of research carried on by a group of seven museum experts of Bologna (Italy), with the joint coordination of IBC (Institute for the Cultural Heritage of the Emilia Romagna Region) and Politecnico di Milano. The “Bologna group” is composed of different professional figures working in the museum domain: museum curators of artistic, archaeological and historical heritage; museum communication experts; Web sites of cultural institutions’ communication experts. After illustrating the general features of MiLE and the specific features for Cultural Heritage, we will briefly show a few of the results which are to be published in the “Bologna Report”

The MEPS server for identifying protein conformational epitopes

<p>Abstract</p> <p>Background</p> <p>One of the most interesting problems in molecular immunology is epitope mapping, i.e. the identification of the regions of interaction between an antigen and an antibody. The solution to this problem, even if approximate, would help in designing experiments to precisely map the residues involved in the interaction and could be instrumental both in designing peptides able to mimic the interacting surface of the antigen and in understanding where immunologically important regions are located in its three-dimensional structure. From an experimental point of view, both genetically encoded and chemically synthesised peptide libraries can be used to identify sequences recognized by a given antibody. The problem then arises of which region of a folded protein the selected peptides correspond to.</p> <p>Results</p> <p>We have developed a method able to find the surface region of a protein that can be effectively mimicked by a peptide, given the structure of the protein and the maximum number of side chains deemed to be required for recognition. The method is implemented as a publicly available server. It can also find and report all peptide sequences of a specified length that can mimic the surface of a given protein and store them in a database.</p> <p>The immediate application of the server is the mapping of antibody epitopes, however the system is sufficiently flexible for allowing other questions to be asked, for example one can compare the peptides representing the surface of two proteins known to interact with the same macromolecule to find which is the most likely interacting region.</p> <p>Conclusion</p> <p>We believe that the MEPS server, available at <url>http://www.caspur.it/meps</url>, will be a useful tool for immunologists and structural and computational biologists. We plan to use it ourselves to implement a database of "surface mimicking peptides" for all proteins of known structure and proteins that can be reliably modelled by comparative modelling.</p

MAISTAS: a tool for automatic structural evaluation of alternative splicing products

Motivation: Analysis of the human genome revealed that the amount of transcribed sequence is an order of magnitude greater than the number of predicted and well-characterized genes. A sizeable fraction of these transcripts is related to alternatively spliced forms of known protein coding genes. Inspection of the alternatively spliced transcripts identified in the pilot phase of the ENCODE project has clearly shown that often their structure might substantially differ from that of other isoforms of the same gene, and therefore that they might perform unrelated functions, or that they might even not correspond to a functional protein. Identifying these cases is obviously relevant for the functional assignment of gene products and for the interpretation of the effect of variations in the corresponding proteins

Stress-Induced Reduction of Dorsal Striatal D2 Dopamine Receptors Prevents Retention of a Newly Acquired Adaptive Coping Strategy

The inability to learn an adaptive coping strategy in a novel stressful condition leads to dysfunctional stress coping, a marker of mental disturbances. This study tested the involvement of dorsal striatal dopamine receptors in the dysfunctional coping with the Forced Swim test fostered by a previous experience of reduced food availability. Adult male mice were submitted to a temporary (12 days) reduction of food availability [food-restricted (FR)] or continuously free-fed (FF). Different groups of FF and FR mice were used to evaluate: (1) dorsal striatal mRNA levels of the two isoforms of the dopamine D2 receptor (D2S, D2L). (2) Forced Swim-induced c-fos expression in the dorsal striatum; (3) acquisition and 24 h retention of passive coping with Forced Swim. Additional groups of FF mice were tested for 24 h retention of passive coping acquired during a first experience with Forced Swim immediately followed by intra-striatal infusion of vehicle or two doses of the dopamine D2/D3 receptors antagonist sulpiride or the D1/D5 receptors antagonist SCH23390. Previous restricted feeding selectively reduced mRNA levels of both D2 isoforms and abolished Forced Swim-induced c-fos expression in the left Dorsolateral Striatum and selectively prevented 24 h retention of the coping strategy acquired in a first experience of Forced Swim. Finally, temporary blockade of left Dorsolateral Striatum D2/D3 receptors immediately following the first Forced Swim experience selectively reproduced the behavioral effect of restricted feeding in FF mice. In conclusion, the present results demonstrate that mice previously exposed to a temporary reduction of food availability show low striatal D2 receptors, a known marker of addiction-associated aberrant neuroplasticity, as well as liability to relapse into maladaptive stress coping strategies. Moreover, they offer strong support to a causal relationship between reduction of D2 receptors in the left Dorsolateral Striatum and impaired consolidation of newly acquired adaptive coping

Forward and backward digit span difficulties in children with specific learning disorder

This study examined performance in the forward and backward digit span task of the Wechsler Intelligence Scale for Children–Fourth Edition (WISC–IV) in a large group of children with specific learning disorder (SLD) as compared with a group of typically developing children matched for age and sex. Our results further support the hypothesis that the intellectual difficulties of children with SLD involve working memory in the forward digit span task to a greater extent than in the backward digit span task. The correlation of the two spans with a General Ability Index (GAI) was similar in SLD, and smaller in magnitude than in typically developing children. Despite a GAI within normal range, children with SLD had difficulty with both digit span tasks, but more so for forward span. This pattern was similar for different SLD profiles with clinical diagnoses of dyslexia and mixed disorder, but the impairments were more severe in the latter. Age differences were also investigated, demonstrating larger span impairment in older children with SLD than in younger