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.     

Control problems for energy harvester model and interpolation in Hardy space

Three control problems for the system of two coupled differential equations governing the dynamics of an energy harvesting model are studied. The system consists of the equation of an Euler–Bernoulli beam model and the equation representing the Kirchhoff's electric circuit law. Both equations contain coupling terms representing the inverse and direct piezoelectric effects. The system is reformulated as a single evolution equation in the state space of 3-component functions. The control is introduced as a separable forcing term $\text{◂⋅▸}\mathbf{g}(x)f(t)$ on the right-hand side of the operator equation. The first control problem deals with an explicit construction of $f(t)$ that steers an initial state to zero on a time interval [0, T]. The second control problem deals with the construction of $f(t)$ such that the voltage output is equal to some given function $\mathbf{v}(t)$ (with $\mathbf{g}(x)$ being given as well). The third control problem deals with an explicit construction of both the force profile, $\mathbf{g}(x)$, and the control, $f(t)$, which generate the desired voltage output $\mathbf{v}(t)$. Interpolation theory in the Hardy space of analytic functions is used in the solution of the second and third problems.     

A comparison between X-ray absorption spectroscopy and Bremsstrahlung Isochromat Spectroscopy: The empty states of Pd−Al alloys and Pd2Si

We present X-ray absorption spectra (XAS) obtained with synchrotron radiaton at the PdL _2,3 edges of Pd–Al alloys and Bremsstrahlung Isochromat Spectra (BIS) at 1,486.7 eV of Pd–Al alloys and of Pd₂Si. The XAS and BIS results for the alloys are very similar indicating that the effect of the core potential (e.g. many-body, electronhole excitation) is negligible. The BIS results on Pd₂Si show differences with respect to Pd–Al due to the more localized bonds. The comparison between XAS and BIS data in Pd₂Si is still an open problem and might indicate a more subtle role of the core-hole potential.     

Photon-stimulated desorption of methanol on Si(111)7 × 7 and Si(100)2 × 1 at the C 1s and O 1s thresholds

Photostimulated desorption experiments have been performed on deuterated methanol adsorbed on Si(111)7 × 7 and Si(100)2 × 1 at the C 1s and O 1s thresholds. D⁺ and the masses of the series CD⁺_x are produced in the photofragmentation process in both energy ranges. A comparison has been made with the photofragmentation spectra of methanol in the gas phase and two different desorption mechanisms have been hypothesized for the desorption of D⁺ and higher masses from the silicon surfaces at the C 1s threshold.     

Electronic structure of 4H-pyrido[1,2-a]pyrimidin-4-ones

The characteristic features of ir and uv spectra of 43 4H-pyrido[1,2-a]pyrimidin-4-one derivatives with electron donor or acceptor groups in position 3, and positions 6, 7, 8, or 9, respectively, have been systematically studied. On the basis of the spectra some conclusions have been drawn for the molecular structure. The negative solvent effect of the lowest-energy π → π* transition is investigated by the PPP method.     

Basis property of eigenfunctions of nonselfadjoint operator pencils generated by the equation of nonhomogeneous damped string

We consider a class of nonselfadjoint quadratic operator pencils generated by the equation, which governs the vibrations of a string with nonconstant bounded density subject to viscous damping with a nonconstant damping coefficient. These pencils depend on a complex parameterh, which enters the boundary conditions. Depending on the values ofh, the eigenvalues of the above pencils may describe the resonances in the scattering of elastic waves on an infinite string or the eingenmodes of a finite string. We obtain the 7asymptotic representations for these eigenvalues. Assuming that the proper multiplicity of each eigenvalue is equal to one, we prove that the eigenfunctions of these pencils form Riesz bases in the weightedL ²-space, whose weight function is exactly the density of the string. The general case of multiple eigenvalues will be treated in another paper, based on the results of the present work.     

Electronic structure of CaSi and CaSi2

The electronic properties of calcium silicides (CaSi and CaSi₂) are investigated through a joint experimental and theoretical study using Bremsstrahlung Isochromat spectroscopy (BIS) and self-consistent calculation of the electronic states by the Linear Muffin-Tin Orbitals (LMTO) method in the Atomic Sphere Approximation (ASA). The peculiar crystal structure of CaSi₂ with two inequivalent Si atoms is responsible for a well defined BIS feature. We found that the calculated high energy DOS features are consistently lower in energy compared to the BIS spectra. Inclusion of the cross-sections of different states into the calculations improves the agreement between the experimental spectra and the calculated curve. We also show that considerable covalent character is present in the bond of calcium silicides.