Looking at COVID-19 from a Systems Biology Perspective

The sudden outbreak and worldwide spread of the SARS-CoV-2 pandemic pushed the scientific community to find fast solutions to cope with the health emergency. COVID-19 complexity, in terms of clinical outcomes, severity, and response to therapy suggested the use of multifactorial strategies, characteristic of the network medicine, to approach the study of the pathobiology. Proteomics and interactomics especially allow to generate datasets that, reduced and represented in the forms of networks, can be analyzed with the tools of systems biology to unveil specific pathways central to virus\u2013human host interaction. Moreover, artificial intelligence tools can be implemented for the identification of druggable targets and drug repurposing. In this review article, we provide an overview of the results obtained so far, from a systems biology perspective, in the understanding of COVID-19 pathobiology and virus\u2013host interactions, and in the development of disease classifiers and tools for drug repurposing

Ligand-Based Regulation of Dynamics and Reactivity of Hemoproteins

Hemoproteins include several heme-binding proteins with distinct structure and function. The presence of the heme group confers specific reactivity and spectroscopic properties to hemoproteins. In this review, we provide an overview of five families of hemoproteins in terms of dynamics and reactivity. First, we describe how ligands modulate cooperativity and reactivity in globins, such as myoglobin and hemoglobin. Second, we move on to another family of hemoproteins devoted to electron transport, such as cytochromes. Later, we consider heme-based reactivity in hemopexin, the main heme-scavenging protein. Then, we focus on heme-albumin, a chronosteric hemoprotein with peculiar spectroscopic and enzymatic properties. Eventually, we analyze the reactivity and dynamics of the most recently discovered family of hemoproteins, i.e., nitrobindins

The WINGS Survey: a progress report

A two-band (B and V) wide-field imaging survey of a complete, all-sky X-ray selected sample of 78 clusters in the redshift range z=0.04-0.07 is presented. The aim of this survey is to provide the astronomical community with a complete set of homogeneous, CCD-based surface photometry and morphological data of nearby cluster galaxies located within 1.5 Mpc from the cluster center. The data collection has been completed in seven observing runs at the INT and ESO-2.2m telescopes. For each cluster, photometric data of about 2500 galaxies (down to V~23) and detailed morphological information of about 600 galaxies (down to V~21) are obtained by using specially designed automatic tools. As a natural follow up of the photometric survey, we also illustrate a long term spectroscopic program we are carrying out with the WHT-WYFFOS and AAT-2dF multifiber spectrographs. Star formation rates and histories, as well as metallicity estimates will be derived for about 350 galaxies per cluster from the line indices and equivalent widths measurements, allowing us to explore the link between the spectral properties and the morphological evolution in high- to low-density environments, and across a wide range in cluster X-ray luminosities and optical properties.Comment: 12 pages, 10 eps figures, Proceedings of the SAIt Conference 200

Scaling relations of cluster elliptical galaxies at z~1.3. Distinguishing luminosity and structural evolution

[Abridged] We studied the size-surface brightness and the size-mass relations of a sample of 16 cluster elliptical galaxies in the mass range 10^{10}-2x10^{11} M_sun which were morphologically selected in the cluster RDCS J0848+4453 at z=1.27. Our aim is to assess whether they have completed their mass growth at their redshift or significant mass and/or size growth can or must take place until z=0 in order to understand whether elliptical galaxies of clusters follow the observed size evolution of passive galaxies. To compare our data with the local universe we considered the Kormendy relation derived from the early-type galaxies of a local Coma Cluster reference sample and the WINGS survey sample. The comparison with the local Kormendy relation shows that the luminosity evolution due to the aging of the stellar content already assembled at z=1.27 brings them on the local relation. Moreover, this stellar content places them on the size-mass relation of the local cluster ellipticals. These results imply that for a given mass, the stellar mass at z~1.3 is distributed within these ellipticals according to the same stellar mass profile of local ellipticals. We find that a pure size evolution, even mild, is ruled out for our galaxies since it would lead them away from both the Kormendy and the size-mass relation. If an evolution of the effective radius takes place, this must be compensated by an increase in the luminosity, hence of the stellar mass of the galaxies, to keep them on the local relations. We show that to follow the Kormendy relation, the stellar mass must increase as the effective radius. However, this mass growth is not sufficient to keep the galaxies on the size-mass relation for the same variation in effective radius. Thus, if we want to preserve the Kormendy relation, we fail to satisfy the size-mass relation and vice versa.Comment: Accepted for publication in A&A, updated to match final journal versio

First order phase transition from the vortex liquid to an amorphous solid

We present a systematic study of the topology of the vortex solid phase in superconducting Bi$_{2}$Sr$_{2}$CaCu$_{2}$O$_{8}$ samples with low doses of columnar defects. A new state of vortex matter imposed by the presence of geometrical contours associated with the random distribution of columns is found. The results show that the first order liquid-solid transition in this vortex matter does not require a structural symmetry change.Comment: 4 pages, 5 figure

Deep-sea reverse osmosis desalination for energy efficient low salinity enhanced oil recovery

The decrease in the oil discoveries fuels the development of innovative and more efficient extraction processes. It has been demonstrated that Enhanced Oil Recovery (EOR, or tertiary recovery technique) offers prospects for producing 30 to 60% of the oil originally trapped in the reservoir. Interestingly, oil extraction is significantly enhanced by the injection of low salinity water into oilfields, which is known as one of the EOR techniques. Surface Reverse Osmosis (SRO) plants have been adopted to provide the large and continuous amount of low salinity water for this EOR technique, especially in offshore sites. In this article, we outline an original solution for producing low salinity water for offshore EOR processes, and we demonstrate its energy convenience. In fact, the installation of reverse osmosis plants under the sea level (Deep-Sea Reverse Osmosis, DSRO) is found to have significant potential energy savings (up to 50%) with respect to traditional SRO ones. This convenience mainly arises from the non-ideality of reverse osmosis membranes and hydraulic machines, and it is especially evident - from both energy and technological point of view - when the permeate is kept pressurized at the outlet of the reverse osmosis elements. In perspective, DSRO may be a good alternative to improve the sustainability of low salinity EOR

3D printed lattice metal structures for enhanced heat transfer in latent heat storage systems

The low thermal conductivity of Phase Change Materials (PCMs), e.g., paraffin waxes, is one of the main drawbacks of latent heat storage, especially when fast charging and discharging cycles are required. The introduction of highly conductive fillers in the PCM matrix may be an effective solution; however, it is difficult to grant their stable and homogeneous dispersion, which therefore limits the resulting enhancement of the overall thermal conductivity. Metal 3D printing or additive manufacturing, instead, allows to manufacture complex geometries with precise patterns, therefore allowing the design of optimal paths for heat conduction within the PCM. In this work, a device-scale latent heat storage system operating at medium temperatures (similar to 90 celcius) was manufactured and characterized. Its innovative design relies on a 3D Cartesian metal lattice, fabricated via laser powder bed fusion, to achieve higher specific power densities. Numerical and experimental tests demonstrated remarkable specific power (approximately 714 +/- 17 W kg-1 and 1310 +/- 48 W kg-1 during heat charge and discharge, respectively). Moreover, the device performance remained stable over multiple charging and discharging cycles. Finally, simulation results were used to infer general design guidelines to further enhance the device performance. This work aims at promoting the use of metal additive manufacturing to design efficient and responsive thermal energy storage units for medium-sized applications, such as in the automotive sector (e.g. speed up of the engine warm up or as an auxiliary for other enhanced thermal management strategies)

Dense conjugate initialization for deterministic PSO in applications: ORTHOinit+

This paper describes a class of novel initializations in Deterministic Particle Swarm Optimization (DPSO) for approximately solving costly unconstrained global optimization problems. The initializations are based on choosing specific dense initial positions and velocities for particles. These choices tend to induce in some sense orthogonality of particles’ trajectories, in the early iterations, in order to better explore the search space. Our proposal is inspired by both a theoretical analysis on a reformulation of PSO iteration, and by possible limits of the proposals reported in Campana et al. (2010); Campana et al. (2013). We explicitly show that, in comparison with other initializations from the literature, our initializations tend to scatter PSO particles, at least in the first iterations. The latter goal is obtained by imposing that the initial choice of particles’ position/velocity satisfies specific conjugacy conditions, with respect to a matrix depending on the parameters of PSO. In particular, by an appropriate condition on particles’ velocities, our initializations also resemble and partially extend a general paradigm in the literature of exact methods for derivative-free optimization. Moreover, we propose dense initializations for DPSO, so that the final approximate global solution obtained is possibly not too sparse, which might cause troubles in some applications. Numerical results, on both Portfolio Selection and Computational Fluid Dynamics problems, validate our theory and prove the effectiveness of our proposal, which applies also in case different neighborhood topologies are adopted in DPSO