Inference of gene-phenotype associations via protein-protein interaction and orthology

published_or_final_versio

Per la corretta attribuzione del "Romanzo delle donne contemporanee in Italia" (1863)

The use of free energy simulation techniques in the study of protein stability is critically evaluated. Results from two simulations of the thermostability mutation Asn218 to Ser218 in Subtilisin are presented. It is shown that components of the free energy change can be highly sensitive to the computational details of the simulation leading to the conclusion that free energy calculations cannot currently be used to reliably predict protein stability. The different factors that undermine the reliability are discussed

Evolution of superconductivity in K2-xFe4+ySe5: Spectroscopic studies of X-ray absorption and emission.

This study investigates the evolution of superconductivity in K2-xFe4+ySe5 using temperature-dependent X-ray absorption and resonant inelastic X-ray scattering techniques. Magnetization measurements show that polycrystalline superconducting (SC) K1.9Fe4.2Se5 has a critical temperature (T c) of ∼31 K with a varying superconducting volume fraction, which strongly depends on its synthesis temperature. An increase in Fe-structural/vacancy disorder in SC samples with more Fe atoms occupying vacant 4d sites is found to be closely related to the decrease in the spin magnetic moment of Fe. Moreover, the nearest-neighbor Fe-Se bond length in SC samples exceeds that in the non-SC (NS) sample, K2Fe4Se5, which indicates a weaker hybridization between the Fe 3d and Se 4p states in SC samples. These results clearly demonstrate the correlations among the local electronic and atomic structures and the magnetic properties of K2-xFe4+ySe5 superconductors, providing deeper insight into the electron pairing mechanisms of superconductivity

Possibilities for CO2 emission reduction using biomass in European integrated steel plants

Iron and steel plants producing steel via the blast furnace-basic oxygen furnace (BF-BOF) route constitute among the largest single point CO2 emitters within the European Union (EU). As the iron ore reduction process in the blast furnace is fully dependent on carbon mainly supplied by coal and coke, bioenergy is the only renewable that presents a possibility for their partial substitution. Using the BeWhere model, this work optimised the mobilization and use of biomass resources within the EU in order to identify the opportunities that bioenergy can bring to the 30 operating BF-BOF plants. The results demonstrate competition for the available biomass resources within existing industries and economically unappealing prices of the bio-based fuels. A carbon dioxide price of 60 € t−1 is required to substitute 20% of the CO2 emissions from the fossil fuels use, while a price of 140 € t−1 is needed to reach the maximum potential of 42%. The possibility to use organic wastes to produce hydrochar would not enhance the maximum emission reduction potential, but it would broaden the available feedstock during the low levels of substitution. The scope for bioenergy integration is different for each plant and so consideration of its deployment should be treated individually. Therefore, the EU-ETS (Emission Trading System) may not be the best policy tool for bioenergy as an emission reduction strategy for the iron and steel industry, as it does not differentiate between the opportunities across the different steel plants and creates additional costs for the already struggling European steel industry

Template-free synthesis of Nd0.1Bi0.9FeO3 nanotubes with large inner diameter and wasp-waisted hysteresis loop

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Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Resistive switching and threshold switching behaviors in La 0.1Bi 0.9Fe 1-xCo xO 3 ceramics

The effects of cobalt doping on the electrical conductivity of La 0.1Bi 0.9Fe 1-xCo xO 3 (LBFCO, x=0, 0.01, 0.03) ceramics were investigated. It is found that the leakage current increases with cobalt dopant concentration in LBFCO. On the application of bias voltage LBFCO ceramics with cobalt doping exhibits resistive switching effects at room temperature and threshold switching effects at elevated temperatures (50°C and 80°C). X-ray photoelectron spectroscopy of LBFCO ceramics show that cobalt dopant is bivalent as an acceptor, which induces an enhancement of oxygen vacancy concentration in LBFCO ceramics. Possible mechanisms for both resistive switching and threshold switching effects are discussed on the basis of the interplay of bound ferroelectric charges and mobile charged defects. © 2012 American Institute of Physics.published_or_final_versio

Effects of hydrogen bond and solvent polarity on the C=O strectching of bis(2-thienyl)ketone in solution

The optimized structural parameters, the absorption and the resonance Raman spectra have been investigated for the bis(2-thienyl)ketone in gas phase, in cyclohexane, methanol, and acetonitrile solvents by means of time dependent density functional theory calculations, the solvent electronic polarization effect on the solvation shift is examined and in well accordance with the calculation. The effect of increasing the polarity of the solvent is well represented by the polarizable continuum model, both for the absorption spectra and resonance Raman intensities. The Raman spectra of the C=O stretching mode, which is sensitive to the intermolecular interaction for bis(2-thienyl)ketone dissolved in solvents, were systematically studied. It was found that the hydrogen bond effect plays an important role in reducing the carbonyl stretching wavenumbers. The results of Raman shifts were interpreted through the dilution effect, solvation effects, and hydrogen bond-forming effects. Furthermore, the excitation profiles of several important Raman bands of bis(2-thienyl)ketone molecule in different solvents have been critically analyzed. The solvent effects on structural and symmetry properties of the molecule in S2 electronic state as well as the short-time photo relaxation dynamics have been discussed.published_or_final_versio

Cyclodextrin-PEI-Tat Polymer as a Vector for Plasmid DNA Delivery to Placenta Mesenchymal Stem Cells

This study aims to modify a cyclodextrin-PEI-based polymer, PEI-β-CyD, with the TAT peptide for plasmid DNA delivery to placenta mesenchymal stem cells (PMSCs). By using the disulfide exchange between the SPDP-activated PEI-β-CyD and TAT peptide, the TAT-PEI-β-CyD polymer was fabricated and the success of this was confirmed by the presence of characteristic peaks for PEI (at δ 2.8-3.2 ppm), CyD (at δ 5.2, 3.8-4.0 and 3.4-3. 6 ppm) and TAT (at δ 1.6-1.9 and 6.8-7.2 ppm) in the 1H NMR spectrum of TAT-PEI-β-CyD. The polymer-plasmid-DNA polyplex could condense DNA at an N/P ratio of 7.0-8.0, and form nanoparticles with the size of 150.6±5.6 nm at its optimal N/P ratio (20/1). By examining the transfection efficiency and cytotoxicity of TAT-PEI-β-CyD, conjugation of the TAT peptide onto PEI-β-CyD was demonstrated to improve the transfection efficiency of PEI-β-CyD in PMSCs after 48 and 96 hours of post-transfection incubation. The viability of PEI-β-CyD-treated PMSCs was shown to be over 80% after 5 h of treatment and 24 h of post-treatment incubation. In summary, this study showed that the TAT-PEI-β-CyD polymer as a vector for plasmid DNA delivery to PMSCs and other cells warrants further investigations. © 2011 The Author(s).published_or_final_versionSpringer Open Choice, 21 Feb 201

Amelioration of bleomycin-induced lung fibrosis in hamsters by dietary supplementation with taurine and niacin: biochemical mechanisms.

Interstitial pulmonary fibrosis induced by intratracheal instillation of bleomycin (BL) involves an excess production of reactive oxygen species, unavailability of adequate levels of NAD and ATP to repair the injured pulmonary epithelium, and an overexuberant lung collagen reactivity followed by deposition of highly cross-linked mature collagen fibrils resistant to enzymatic degradation. In the present study, we have demonstrated that dietary supplementation with taurine and niacin offered almost complete protection against the lung fibrosis in a multidose BL hamster model. The mechanisms for the protective effect of taurine and niacin are multifaceted. These include the ability of taurine to scavenge HOCl and stabilize the biomembrane; niacin's ability to replenish the BL-induced depletion of NAD and ATP; and the combined effect of taurine and niacin to suppress all aspects of BL-induced increases in the lung collagen reactivity, a hallmark of interstitial pulmonary fibrosis. It was concluded from the data presented at this Conference that the combined treatment with taurine and niacin, which offers a multipronged approach, will have great therapeutic potential in the intervention of the development of chemically induced interstitial lung fibrosis in animals and humans