Modulation instability and conservation of energy:toward a new model

L'articolo analizza la propagazione in regime nonlineare di un segnale ottico CW in presenza di una "piccola" perturbazione. In letteratura sono presenti lavori che specificano i parametri fisici che regolano l'interazione tra il segnale CW e la perturbazione ma non si hanno indicazioni relative ai limiti di applicabilità dei modelli proposti. Obiettivo principale di questo lavoro è rappresentato dalla definizione dei parametri che "attivano" l'instabilità di modulazione e regolano il regime di propagazione nonlineare. A tal fine, il regime di propagazione nonlineare è analizzato vincolandolo al principio di conservazione dell'energia

Evaluation of potential miRNA sponge effects of SARS genomes in human

: To date the coronavirus family is composed of seven different viruses which were commonly known as cold viruses until the appearance of the severe acute respiratory coronavirus (SARS-CoV) in 2002, the middle east respiratory syndrome coronavirus (MERS) in 2012 and the severe acute respiratory coronavirus 2 (SARS-CoV-2) which caused the COVID-19 global pandemic in 2019. Using bioinformatic approaches we tested the potential interactions of human miRNAs, expressed in pulmonary epithelial cells, with the available coronavirus genomes. Putative miRNA binding sites were then compared between pathogenic and non pathogenic virus groups. The pathogenic group shares 6 miRNA binding sites that can be potentially involved in the sequestration of miRNAs already known to be associated with deep vein thrombosis. We then analysed ∼100k SARS-CoV-2 variant genomes for their potential interaction with human miRNAs and this study highlighted a group of 97 miRNA binding sites which is present in all the analysed genomes. Among these, we identified 6 miRNA binding sites specific for SARS-CoV-2 and the other two pathogenic viruses whose down-regulation has been seen associated with deep vein thrombosis and cardiovascular diseases. Interestingly, one of these miRNAs, namely miR-20a-5p, whose expression decreases with advancing age, is involved in cytokine signaling, cell differentiation and/or proliferation. We hypothesize that depletion of poorly expressed miRNA could be related with disease severity

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures

Phosfinder is a web server for the identification of phosphate binding sites in protein structures. Phosfinder uses a structural comparison algorithm to scan a query structure against a set of known 3D phosphate binding motifs. Whenever a structural similarity between the query protein and a phosphate binding motif is detected, the phosphate bound by the known motif is added to the protein structure thus representing a putative phosphate binding site. Predicted binding sites are then evaluated according to (i) their position with respect to the query protein solvent-excluded surface and (ii) the conservation of the binding residues in the protein family. The server accepts as input either the PDB code of the protein to be analyzed or a user-submitted structure in PDB format. All the search parameters are user modifiable. Phosfinder outputs a list of predicted binding sites with detailed information about their structural similarity with known phosphate binding motifs, and the conservation of the residues involved. A graphical applet allows the user to visualize the predicted binding sites on the query protein structure. The results on a set of 52 apo/holo structure pairs show that the performance of our method is largely unaffected by ligand-induced conformational changes. Phosfinder is available at http://phosfinder.bio.uniroma2.it

Thermal-mechanical behaviour of the hierarchical structure of human dental tissue

Human dental tissues are fascinating nano-structured hierarchical materials that combine organic and mineral phases in an intricate and ingenious way to obtain remarkable combinations of mechanical strength, thermal endurance, wear resistance and chemical stability. Attempts to imitate and emulate this performance have been made since time immemorial, in order to provide replacement (e.g. in dental prosthodontics) or to develop artificial materials with similar characteristics (e.g. light armour). The key objectives of the present project are to understand the structure-property relationships that underlie the integrity of natural materials, human dental tissues in particular, and the multi-scale architecture of mineralized tissues and its evolution under thermal treatment and mechanical loading. The final objective is to derive ideas for designing and manufacturing novel artificial materials serving biomimetic purposes. The objectives are achieved using the combination of a range of characterization techniques, with particular attention paid to the synchrotron X-ray scattering (Small- and Wide-Angle X-ray Scattering, SAXS and WAXS) and imaging techniques (Micro Computed Tomography), as well as microscopy techniques such as Environmental Scanning Electron Microscopy (ESEM), Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). Mechanical properties were characterized by nanoindentation and photoelasticity; and thermal analysis was carried out via thermogravimetric analysis (TGA). Experimental observations were critically examined and matched by advanced numerical simulation of the tissue under thermal-mechanical loading. SAXS and WAXS provided the initial basis for elucidating the structure-property relationships in human dentine and enamel through in situ experimentation. Four principal types of experiment were used to examine the thermal and mechanical behaviour of the hierarchical structure of human dental tissue and contributed to the Chapters of this thesis: (i) In situ elastic strain evolution under loading within the hydroxyapatite (HAp) in both dentine and enamel. An improved multi-scale Eshelby inclusion model was proposed taking into account the two-level hierarchical structure, and was validated against the experimental strain evaluation data. The achieved agreement indicates that the multi-scale model accurately reflects the structural arrangement of human dental tissue and its response to applied forces. (ii) The morphology of the dentine-enamel junction (DEJ) was examined by a range of techniques, including X-ray imaging and diffraction. The transition of mechanical properties across the DEJ was evaluated by the high resolution mapping and in situ compression measurement, followed by a brief description of the thermal behaviour of DEJ. The results show that DEJ is a narrow band of material with graded structure and mechanical properties, rather than a discrete interface. (iii) Further investigation regarding the thermo-mechanical structure-property relationships in human dental tissues was carried out by nanoindentation mapping of the nano-mechanical properties in ex situ thermally treated dental tissues. (iv) In order to understand the details of the thermal behaviour, in situ heat treatment was carried out on both human dental tissues and synthetic HAp crystallites. For the first time the in situ ultrastructural alteration of natural and synthetic HAp crystallites was captured in these experiments. The results presented in this thesis contribute to the fundamental understanding of the structure-property integrity mechanisms of natural materials, human dental tissues in particular. These results were reported in several first author publications in peer-reviewed journals, conference proceedings, and a book chapter.</p

Automated macular segmentation with spectral domain optical coherence tomography in the fellow eyes of patients with unilateral retinal vein occlusion.

PURPOSE: To assess the change in the macular layers in the fellow eyes of unilateral retinal vein occlusion (RVO) patients and to evaluate whether certain layers are more affected based on RVO type. METHODS: This retrospective study included 87 fellow eyes of patients with unilateral RVO (26 central, 61 branch) and 105 eyes of 105 subjects without RVO. Spectral domain optical coherence tomography was used for automatized retinal segmentation. The thicknesses of retinal nerve fiber layer (RNFL), ganglion cells, inner plexiform, inner nuclear, outer plexiform, outer nuclear, photoreceptor layers, overall inner retinal layers and retinal pigment epithelium (RPE) were documented. RESULTS: Inner plexiform layer was thinner in inferior sector in RVO group compared with the control group (p = 0.047). The subgroup analysis showed that the retina was thinner in RVO group compared with the controls without systemic diseases in some sectors of the following layers: inferior retina, RNFL, ganglion cell layer, inner plexiform layer, inner retinal layers and RPE (p < 0.05). Retinal thickness was decreased in the fellow eyes of branch RVO group compared to that in the central RVO group in the some sectors (p < 0.05). CONCLUSIONS: The fellow eyes of unilateral RVO patients did not show major structural differences compared with the controls; however, they revealed significant sectoral thinning in many retinal layers when compared with the eyes of healthy subjects without systemic diseases. Central macula was thinner in the fellow eyes of patients with branch RVO compared to that in central RVO

Optical packet network with limited-range wavelength conversion: a novel formalization of the optimal scheduling problem

We consider synchronous optical packet networks formed by switches equipped with a complete-set of limited-range wavelength converters. On these networks, we dealt with scheduling algorithm that maximizes the switch throughput. So far, previous literature works have formalized this scheduling problem as the finding of a maximum bipartite matching (MBM) in a convex graph. The MBM formalization has collected several follow-ups, mainly focused on measuring switch-level performance. We revise the MBM formalization by measuring network-level performance. Surprisingly, we find out that when optical switches are cascaded, MBM formalization has two not negligible lacks: i) a useless degradation of optical signal quality; ii) a tendency in shifting optical packets toward lower wavelengths, thus increasing the occurrence of wavelength contention. To solve these issues, we propose a novel formalization of the scheduling problem as the finding of a maximum bipartite matching with minimum edges weights (MW-MBM). We show that MW-MBM outperforms MBM in terms of both network throughput and optical signal to noise ratio. Performance evaluation is carried out by means of NS2 simulator that we extend to toughly model optical components (e.g., SOA FWM wavelength converter). The simulator is provided as open-source

Estudo Comparativo entre Densidade Básica e Penetração do Pilodyn em Espécies/Procedências de Pinus Centro-Americanos em três locais dos Cerrados.

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