An Extensive Assessment of Network Embedding in PPI Network Alignment

Network alignment is a fundamental task in network analysis. In the biological field, where the protein–protein interaction (PPI) is represented as a graph, network alignment allowed the discovery of underlying biological knowledge such as conserved evolutionary pathways and functionally conserved proteins throughout different species. A recent trend in network science concerns network embedding, i.e., the modelling of nodes in a network as a low-dimensional feature vector. In this survey, we present an overview of current PPI network embedding alignment methods, a comparison among them, and a comparison to classical PPI network alignment algorithms. The results of this comparison highlight that: (i) only five network embeddings for network alignment algorithms have been applied in the biological context, whereas the literature presents several classical network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms perform network embedding through matrix factorization-based techniques; (iv) three out of five algorithms leverage external biological resources, while the remaining two are designed for domain agnostic network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.     

Differential tissue expression of a calpastatin isoform in Xenopus embryos

This study is aimed at demonstrating the role played by a calpastatin isoform (Xcalp3) in Xenopus embryos. A specific monoclonal antibody (mAb) was raised against a glutathione S-transferase (GST)-Xcalp3 fusion protein and characterized by immunoblotting and confocal fluorescence microscopy on stage 20-36 embryos. Under these conditions, calpastatin reactivity is associated with a major 110kDa protein fraction and preferentially expressed by notochord and somitic cells. In notochord cells, anti-calpastatin reactive sites were initially restricted to the luminal space of the vacuoles and later became diffused throughout the cytoplasm. In contrast, anti-calpastatin reactive sites in somitic cells were initially diffused throughout the cytoplasm and became restricted to a few intracellular granules in the later developmental stages. At the ultrastructural level, notochord cells appeared as flattened discs containing several vacuoles and numerous electron-dense granules. During transition from stages 26 to 32, electron-dense granules were gradually reduced in number as vacuoles enlarged in size and losed their calpastatin reactivity. Electron-dense granules were also present in myoblast cells and their number gradually reduced during development. To determine whether these observations bear any causal relationship to the calpain/calpastatin system, a number of Xenopus embryos were examined both ultrastructurally and histochemically following exposure to a specific calpain inhibitor (CI3). Under these conditions, Xenopus embryos exhibited an altered right-left symmetry and an abnormal axial shortening. In CI3-treated stage 32 embryos, notochord cells had a reduced vacuolar extension and exhibited at the same time an increase in granular content. The overall morphology of the somites was also distorted and myoblasts were altered both in shape and granular content. Based on these findings, it is concluded that the calpain/calpastatin may play an important role in the control of notochord elongation and somite differentiation during Xenopus embryogenesis.     

Initial state effects on J/ψ production at RHIC energy: from d+Au to Au+Au

We present a calculation of the cold nuclear matter effect on inclusive production of J/ψ in d+A and A+A collisions in the framework of the gluon saturation/CGC approach. Our model is based on the observation that the leading production mechanism involves odd number of inelastic interactions with the nuclei. Our numerical calculations are in good agreement with the experimental data in the case of d+Au collisions. However, in Au+Au collisions the cold nuclear matter effect is not suffcient to describe the data.     

The evaporation–condensation problem for a binary mixture of rarefied gases

Continuum Mechanics and Thermodynamics - Half space problems of evaporation and condensation for a binary mixture of inert gases are investigated when the dynamics is governed by a system of...     

On the Essential Features of Metastability: Tunnelling Time and Critical Configurations

We consider Metropolis Markov chains with finite state space and transition probabilities of the form $$P(\eta ,\eta ')=q(\eta ,\eta ')e^{- \beta [H(\eta ') - H(\eta)]_+}$$ for given energy function H and symmetric Markov kernel q. We propose a simple approach to determine the asymptotic behavior, for large β, of the first hitting time to the ground state starting from a particular class of local minima for H called metastable states. We separate the asymptotic behavior of the transition time from the determination of the tube of typical paths realizing the transition. This approach turns out to be useful when the determination of the tube of typical paths is too difficult, as for instance in the case of conservative dynamics. We analyze the structure of the saddles introducing the notion of “essentiality” and describing essential saddles in terms of “gates.” As an example we discuss the case of the 2D Ising Model in the degenerate case of integer ${\tfrac{{2j}}{h}}$ .     

Representing products of manifolds by edge-coloured graphs: the boundary case

In this paper we generalize the construction - introduced by Gagliardi and Grasselli in the closed case - of a coloured-graph representing the product of two manifolds, starting by two coloured graphs representing the manifolds themselves, to the boundary case. In particular we study the genus of the graph product of low dimensional manifold ( resp. n-spheres ) with m-disks. Received September 28, 1998; in final form January 5, 2000 / Published online October 11, 2000