Competition of the connectivity with the local and the global order in polymer melts and crystals

The competition between the connectivity and the local or global order in model fully-flexible chain molecules is investigated by molecular-dynamics simulations. States with both missing (melts) and high (crystal) global order are considered. Local order is characterized within the first coordination shell (FCS) of a tagged monomer and found to be lower than in atomic systems in both melt and crystal. The role played by the bonds linking the tagged monomer to FCS monomers (radial bonds), and the bonds linking two FCS monomers (shell bonds) is investigated. The detailed analysis in terms of Steinhardt's orientation order parameters Q_l (l = 2 - 10) reveals that increasing the number of shell bonds decreases the FCS order in both melt and crystal. Differently, the FCS arrangements organize the radial bonds. Even if the molecular chains are fully flexible, the distribution of the angle formed by adjacent radial bonds exhibits sharp contributions at the characteristic angles {\theta} = 70{\deg}, 122{\deg}, 180{\deg}. The fractions of adjacent radial bonds with {\theta} = 122{\deg}, 180{\deg} are enhanced by the global order of the crystal, whereas the fraction with 70{\deg} < {\theta} < 110{\deg} is nearly unaffected by the crystallization. Kink defects, i.e. large lateral displacements of the chains, are evidenced in the crystalline state.Comment: J. Chem. Phys. in pres

The surface accessibility of α-bungarotoxin monitored by a novel paramagnetic probe

The surface accessibility of {alpha}-bungarotoxin has been investigated by using Gd2L7, a newly designed paramagnetic NMR probe. Signal attenuations induced by Gd2L7 on {alpha}-bungarotoxin C{alpha}H peaks of 1H-13C HSQC spectra have been analyzed and compared with the ones previously obtained in the presence of GdDTPA-BMA. In spite of the different molecular size and shape, for the two probes a common pathway of approach to the {alpha}-bungarotoxin surface can be observed with an equally enhanced access of both GdDTPA-BMA and Gd2L7 towards the protein surface side where the binding site is located. Molecular dynamics simulations suggest that protein backbone flexibility and surface hydration contribute to the observed preferential approach of both gadolinium complexes specifically to the part of the {alpha}-bungarotoxin surface which is involved in the interaction with its physiological target, the nicotinic acetylcholine receptor

Effects of systemic glucocorticosteroids on peripheral neutrophil functions in asthmatic subjects: an ex vivo study

In 21 asthmatic subjects, several functions of isolated peripheral neutrophils (chemokinesis and chemotaxis toward 10% E. coli; superoxide anion generation after PMA; leukotriene B4 (LTB4) release from whole blood and isolated neutrophtls, before and after different stimuli) were evaluated during an acute exacerbation of asthma, and after 14 – 54 days of treatment with systemic glucocorticosteroids (GCS). During acute exacerbation, superoxide anion generation was higher in asthmatics than in eleven normal subjects (39.2 ± 14.1 vs. 25.2 ± 7.3 nmol, p < 0.05); there was a significant correlation between FEV1 (% of predicted) and neutrophil chemotaxis (r = −0.52, p = 0.04). After treatment, there was no significant change in all neutrophil functions, except for a decrease in neutrophil chemotaxis in subjects who showed an FEV1 increase > 20% after GCS treatment (from 131 ± 18 to 117 ± 21 μm, p = 0.005). Chemokinesis sicantly decreased in all subjects, and the changes significantly correlated with an arbitrary score of the total administered dose of GCS (r = 0.57, p < 0.05). These data suggest that neutrophil activation plays a minor role in asthma, and that treatment with GCS is not able to modify most functions of peripheral neutrophils in asthmatic subjects; chemotaxis seems to be related only to the severity of the asthma and it could reflect the improvement of the disease

LIGHTNESS: a function-virtualizable software defined data center network with all-optical circuit/packet switching

©2016 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Modern high-performance data centers are responsible for delivering a huge variety of cloud applications to the end-users, which are increasingly pushing the limits of the currently deployed computing and network infrastructure. All-optical dynamic data center network (DCN) architectures are strong candidates to overcome those adversities, especially when they are combined with an intelligent software defined control plane. In this paper, we report the first harmonious integration of an optical flexible hardware framework operated by an agile software and virtualization platform. The LIGHTNESS deeply programmable all-optical circuit and packet switched data plane is able to perform unicast/multicast switch-over on-demand, while the powerful software defined networking (SDN) control plane enables the virtualization of computing and network resources creating a virtual data center and virtual network functions (VNF) on top of the data plane. We experimentally demonstrate realistic intra DCN with deterministic latencies for both unicast and multicast, showcasing monitoring, and database migration scenarios each of which is enabled by an associated network function virtualization element. Results demonstrate a fully functional complete unification of an advanced optical data plane with an SDN control plane, promising more efficient management of the next-generation data center compute and network resources.Peer ReviewedPostprint (author's final draft

Study of the MgB2 grain size role in ex-situ multifilamentary wires with thin filaments

The MgB2 superconductor has already demonstrated its applicative potential, in particular for DC applications such as MRI magnets, thanks to the low costs of the raw materials and to its simple production process. However further efforts have still to be made in order to broaden its employment also towards the AC applications such as SFCL, motors, transformers. The main issues are related to the reduction of the AC losses. Some of these can be faced by obtaining multifilamentary conductors with a large number of very fine filaments and, in this context, the powders granulometry can play a crucial role. We have prepared MgB2 starting powders with different granulometries and by the ex-situ P.I.T method we have realized multifilamentary wires with a number of filaments up to 361 and an average size of each filament lowered down to 30 microns. In particular we have studied the relationship between grain and filament size in terms of transport properties and show that the optimization of this ratio is possible in order to obtain suitable conductors for AC industrial applications

An oribatid mite (Arachnida: Acari) from the Oxford Clay (Jurassic: Upper Callovian) of South Cave Station Quarry, Yorkshire, UK

A single specimen of a new species of oribatid mite belonging to the genus Jureremus Krivolutsky, in Krivolutsky and Krassilov 1977, previously described from the Upper Jurassic of the Russian Far East, is described as J. phippsi sp. nov. The mite is preserved by iron pyrite replacement, and was recovered by sieving from the Oxford Clay Formation (Jurassic: Upper Callovian) of South Cave, Yorkshire. It is the first record of a pre-Pleistocene mite, and the second species record of the family Cymbaeremaeidae, from the British Isles; also, it is only the third record of Acari from the Jurassic Period. The presence of a terrestrial mite in a sedimentary sequence of open marine origin is noteworthy, and suggestions for its mode of transport to the site of deposition are discussed

VID22 counteracts G-quadruplex-induced genome instability

Genome instability is a condition characterized by the accumulation of genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways affecting endogenous DNA damage and genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, reported to be involved in DNA double-strand break repair. vid22Δ cells exhibit increased levels of endogenous DNA damage, chronic DNA damage response activation and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. Vid22 binds to and protects DNA at G4-containing regions both in vitro and in vivo. Loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. Moreover, the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism

VID22 counteracts G-quadruplex-induced genome instability

Genome instability is a condition characterized by the accumulation of genetic alterations and is a hallmark of cancer cells. To uncover new genes and cellular pathways affecting endogenous DNA damage and genome integrity, we exploited a Synthetic Genetic Array (SGA)-based screen in yeast. Among the positive genes, we identified VID22, reported to be involved in DNA double-strand break repair. vid22Δ cells exhibit increased levels of endogenous DNA damage, chronic DNA damage response activation and accumulate DNA aberrations in sequences displaying high probabilities of forming G-quadruplexes (G4-DNA). If not resolved, these DNA secondary structures can block the progression of both DNA and RNA polymerases and correlate with chromosome fragile sites. Vid22 binds to and protects DNA at G4-containing regions both in vitro and in vivo. Loss of VID22 causes an increase in gross chromosomal rearrangement (GCR) events dependent on G-quadruplex forming sequences. Moreover, the absence of Vid22 causes defects in the correct maintenance of G4-DNA rich elements, such as telomeres and mtDNA, and hypersensitivity to the G4-stabilizing ligand TMPyP4. We thus propose that Vid22 is directly involved in genome integrity maintenance as a novel regulator of G4 metabolism.Associazione Italiana per la Ricerca sul Cancro (AIRC) [15631, 21806 to M.M.F.]; MIUR [PRIN 2015-2015SJLMB9; PRIN 2017-2017KSZZJW to M.M.F.]; Telethon [GGP15227 to M.M.F.]; F.L. was supported by the University of Milano: ‘‘Piano di Sviluppo dell’Ateneo per la Ricerca. Linea B: Supporto per i Giovani Ricercatori’’; M.C.B. was supported by Fondazione Veronesi; Research at the laboratory of A.A. was funded by the Spanish Ministry of Economy and Competitiveness [BFU2016-75058-P]; B.G.G. was funded by the Spanish Association Against Cancer; MIUR [PRIN2017-2017Z55KC to T.B.]; M.C., D.S.H. are supported by MIUR [PRIN 2017] and CNRbiomics [PIR01_00017]; H2020 Projects ELIXIR-EXCELERATE, EOSC-Life, EOSC-Pillar and Elixir-IIB; G.W.B. was supported by the Canadian Institutes of Health Research[FDN-159913]. Funding for open access charge: Associazione Italiana per la Ricerca sul Cancro (AIRC) [21806]

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

Partial Least Squares-Discriminant Analysis (PLS-DA) is a PLS regression method with a special binary ‘dummy’ y-variable and it is commonly used for classification purposes and biomarker selection in metabolomics studies. Several statistical approaches are currently in use to validate outcomes of PLS-DA analyses e.g. double cross validation procedures or permutation testing. However, there is a great inconsistency in the optimization and the assessment of performance of PLS-DA models due to many different diagnostic statistics currently employed in metabolomics data analyses. In this paper, properties of four diagnostic statistics of PLS-DA, namely the number of misclassifications (NMC), the Area Under the Receiver Operating Characteristic (AUROC), Q2 and Discriminant Q2 (DQ2) are discussed. All four diagnostic statistics are used in the optimization and the performance assessment of PLS-DA models of three different-size metabolomics data sets obtained with two different types of analytical platforms and with different levels of known differences between two groups: control and case groups. Statistical significance of obtained PLS-DA models was evaluated with permutation testing. PLS-DA models obtained with NMC and AUROC are more powerful in detecting very small differences between groups than models obtained with Q2 and Discriminant Q2 (DQ2). Reproducibility of obtained PLS-DA models outcomes, models complexity and permutation test distributions are also investigated to explain this phenomenon. DQ2 and Q2 (in contrary to NMC and AUROC) prefer PLS-DA models with lower complexity and require higher number of permutation tests and submodels to accurately estimate statistical significance of the model performance. NMC and AUROC seem more efficient and more reliable diagnostic statistics and should be recommended in two group discrimination metabolomic studies