Rapid System to Detect Variants of SARS-CoV-2 in Nasopharyngeal Swabs

Currently, the reference method for identifying the presence of variants of SARS-CoV-2 is whole genome sequencing. Although it is less expensive than in the past, it is still time-consuming, and interpreting the results is difficult, requiring staff with specific skills who are not always available in diagnostic laboratories. The test presented in this study aimed to detect, using traditional real-time PCR, the presence of the main variants described for the spike protein of the SARS-CoV-2 genome. The primers and probes were designed to detect the main deletions that characterize the different variants. The amplification targets were deletions in the S gene: 25-27, 69-70, 241-243, and 157-158. In the ORF1a gene, the deletion 3675-3677 was chosen. Some of these mutations can be considered specific variants, while others can be identified by the simultaneous presence of one or more deletions. We avoided using point mutations in order to improve the speed of the test. Our test can help clinical and medical microbiologists quickly recognize the presence of variants in biological samples (particularly nasopharyngeal swabs). The test can also be used to identify variants of the virus that could potentially be more diffusive as well as not responsive to the vaccine

Model and parameter dependence of heavy quark energy loss in a hot and dense medium

Within the framework of the Langevin equation, we study the energy loss of heavy quark due to quasi-elastic multiple scatterings in a quark-gluon plasma created by relativistic heavy-ion collisions. We investigate how the initial configuration of the quark-gluon plasma as well as its properties affect the final state spectra and elliptic flow of D meson and non-photonic electron. We find that both the geometric anisotropy of the initial quark-gluon plasma and the flow profiles of the hydrodynamic medium play important roles in the heavy quark energy loss process and the development of elliptic flow. The relative contribution from charm and bottom quarks is found to affect the transverse momentum dependence of the quenching and flow patterns of heavy flavor decay electron; such influence depends on the interaction strength between heavy quark and the medium.Comment: 16 pages, 7 figure

D(-)lentiginosine-induced apoptosis involves the intrinsic pathway and is p53-independent

We have recently found that D(-)lentiginosine, a synthetic iminosugar exerting glucosidase inhibitory activity, but not its natural enantiomer lentiginosine, is endowed with an unexpected, pro-apoptotic activity. Here, we investigated mechanisms involved in apoptosis induced by D(-)lentiginosine in MOLT-3, HT-29 and SH-SY5Y tumour cell lines. The results showed that D(-)lentiginosine increased caspase 9 expression at 18 h in all the cell lines from 1.5-3.1 folds. Cytochrome c in the cytoplasm was found to be increased from 2.3-2.6 folds in treated cells with respect to control cells. These effects were accompanied by a remarkable collapse of the mitochondrial membrane potential and by the downregulation of anti-apoptotic genes, as well as the upregulation of pro-apoptotic genes of the Bcl-2 family. U937Bcl-2 transfectants, highly expressing Bcl-2, were reluctant to undergo apoptosis even following treatment with 500 μM D(-)lentiginosine, whereas apoptosis by D(-)lentiginosine was induced also in U937 cells, naturally deficient in P53. Thus, our study establishes that the enantiomer of a natural iminosugar is endowed with a possible anti-tumorigenic effect that might be ascribed not only to their capacity to inhibit glycosidases but also to other unknown mechanisms. These data encourage further investigation on similar compounds to make them an interesting platform for the generation of new anticancer drugs

Inhibition of IκBα phosphorylation potentiates regulated cell death induced by azidothymidine in HTLV-1 infected cells

Adult T cell leukemia/lymphoma (ATL) can be susceptible, at least transiently, to treatments with azidothymidine (AZT) plus IFNα and/or arsenic trioxide. However, the real role of AZT in this effect is still unclear. In fact, while reverse transcriptase (RT) inhibition could explain reduction of clonal expansion and of renewal of HTLV-1 infected cells during ATL progression, this effect alone seems insufficient to justify the evident and prompt decrease of the pro-viral load in treated patients. We have previously demonstrated that AZT is endowed with an intrinsic pro-apoptotic potential towards both peripheral blood mononuclear cells from healthy donors or some tumor cell lines, but this cytotoxic potential cannot be fully achieved unless IκBα phosphorylation is inhibited. Since the constitutive activation of NF-kappa B (NF-κB) appears a common biological basis of HTLV-1-infected cells, a pharmacological inhibition of IκBα phosphorylation seems a potential strategy for treating and preventing HTLV-1 related pathologies. In this study, we have demonstrated that a combination treatment with the IκBα phosphorylation inhibitor Bay 11-7085 and AZT induced increased levels of regulated cell death (RCD) by apoptosis compared to the single treatments in HTLV-1 infected cells of different origin. Importantly, levels of RCD were considerably higher in infected cells in comparison with the uninfected ones. Inhibition of NF-κB activation following the combined treatment was confirmed by analysis of both gel-shift and functional activity of the NF-κB complex proteins, p65/p52. Moreover, a transcriptional analysis revealed that the addition of Bay 11-7085 to AZT treatment in HTLV-1-infected cells modified their transcriptional profile, by inducing the upregulation of some pro-apoptotic genes together with the downregulation of some anti-apoptotic genes. Our data suggest that addition of adequate concentrations of IκBα phosphorylation inhibitor to therapeutic regimens including AZT could be a promising strategy in ATL

Charge dependent azimuthal correlations in Pb--Pb collisions at sNN=2.76\sqrt{s_{NN}} = 2.76 TeV

Separation of charges along the extreme magnetic field created in non-central relativistic heavy--ion collisions is predicted to be a signature of local parity violation in strong interactions. We report on results for charge dependent two particle azimuthal correlations with respect to the reaction plane for Pb--Pb collisions at $\sqrt{s_{NN}} = 2.76$ TeV recorded in 2010 with ALICE at the LHC. The results are compared with measurements at RHIC energies and against currently available model predictions for LHC. Systematic studies of possible background effects including comparison with conventional (parity-even) correlations simulated with Monte Carlo event generators of heavy--ion collisions are also presented.Comment: Published in the proceedings of "Quark Matter 2011", Annecy-Franc

Restoration of peripheral blood natural killer and B cell levels in patients affected by rheumatoid and psoriatic arthritis during etanercept treatment

Etanercept (ETN) is an anti-tumour necrosis factor (TNF)-α agent used in rheumatoid arthritis (RA) and psoriatic arthritis (PsA). Few studies focused on the effects of anti-TNF-α on peripheral blood cells. We aimed to evaluate peripheral blood cells in RA and PsA patients during ETN treatment and to explore their relationships with disease activity. RA (n = 82) and PsA (n = 32) patients who started ETN were included into the study and evaluated prospectively before the beginning of ETN therapy and after 14, 22, 54 and 102 weeks. Patients were studied in terms of disease activity score on 28 joints (DAS28), clinical response and laboratory findings. Natural killer (NK) cells, B cells and T cells were characterized by immunophenotyping. Both the RA and the PsA patients showed reduced NK and B cell count before ETN treatment compared with controls. A negative correlation was demonstrated between DAS28 and B cell count in RA patients at baseline. Sustained significant increase of NK and B cells up to normal levels was observed in RA and PsA patients along ETN treatment. Increase of NK cell count was associated with a good-moderate clinical response to ETN in both RA and PsA patients. During ETN treatment peripheral blood NK and B cells levels were restored in RA and PsA patients. Correlations between NK and B cells with disease activity were observed, suggesting that those effects could be mediated by ETN treatment.Etanercept (ETN) is an anti-tumour necrosis factor (TNF)-α agent used in rheumatoid arthritis (RA) and psoriatic arthritis (PsA). Few studies focused on the effects of anti-TNF-α on peripheral blood cells. We aimed to evaluate peripheral blood cells in RA and PsA patients during ETN treatment and to explore their relationships with disease activity. RA (n = 82) and PsA (n = 32) patients who started ETN were included into the study and evaluated prospectively before the beginning of ETN therapy and after 14, 22, 54 and 102 weeks. Patients were studied in terms of disease activity score on 28 joints (DAS28), clinical response and laboratory findings. Natural killer (NK) cells, B cells and T cells were characterized by immunophenotyping. Both the RA and the PsA patients showed reduced NK and B cell count before ETN treatment compared with controls. A negative correlation was demonstrated between DAS28 and B cell count in RA patients at baseline. Sustained significant increase of NK and B cells up to normal levels was observed in RA and PsA patients along ETN treatment. Increase of NK cell count was associated with a good-moderate clinical response to ETN in both RA and PsA patients. During ETN treatment peripheral blood NK and B cells levels were restored in RA and PsA patients. Correlations between NK and B cells with disease activity were observed, suggesting that those effects could be mediated by ETN treatment

First measurement of Ξc0\Xi_{\rm c}^0 production in pp collisions at s\mathbf{\sqrt{s}} = 7 TeV

The production of the charm-strange baryon $\Xi_{\rm c}^0$ is measured for the first time at the LHC via its semileptonic decay into e$^+\Xi^-\nu_{\rm e}$ in pp collisions at $\sqrt{s}=7$ TeV with the ALICE detector. The transverse momentum ($p_{\rm T}$) differential cross section multiplied by the branching ratio is presented in the interval 1 $<$ $p_{\rm T}$ $<$ 8 GeV/$c$ at mid-rapidity, $|y|$ $<$ 0.5. The transverse momentum dependence of the $\Xi_{\rm c}^0$ baryon production relative to the D$^0$ meson production is compared to predictions of event generators with various tunes of the hadronisation mechanism, which are found to underestimate the measured cross-section ratio.Comment: 22 pages, 6 captioned figures, 1 table, authors from page 17, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/412

Gas Analysis and Monitoring Systems for the RPC Detector of CMS at LHC

The Resistive Plate Chambers (RPC) detector of the CMS experiment at the LHC proton collider (CERN, Switzerland) will employ an online gas analysis and monitoring system of the freon-based gas mixture used. We give an overview of the CMS RPC gas system, describe the project parameters and first results on gas-chromatograph analysis. Finally, we report on preliminary results for a set of monitor RPC.Comment: 9 pages, 8 figures. Presented by Stefano Bianco (Laboratori Nazionali di Frascati dell'INFN) at the IEEE NSS, San Diego (USA), October 200

Measurement of the production of charm jets tagged with D0^{0} mesons in pp collisions at s\sqrt{s}= 7 TeV

The production of charm jets in proton-proton collisions at a center-of-mass energy of $\sqrt{s}=7$ TeV was measured with the ALICE detector at the CERN Large Hadron Collider. The measurement is based on a data sample corresponding to a total integrated luminosity of $6.23$ ${\rm nb}^{-1}$, collected using a minimum-bias trigger. Charm jets are identified by the presence of a D$^0$ meson among their constituents. The D$^0$ mesons are reconstructed from their hadronic decay D$^0\rightarrow$K$^{-}\pi^{+}$. The D$^0$-meson tagged jets are reconstructed using tracks of charged particles (track-based jets) with the anti-$k_{\mathrm{T}}$ algorithm in the jet transverse momentum range $5<p_{\rm{T,jet}}^{\mathrm{ch}}<30$ ${\rm GeV/}c$ and pseudorapidity $|\eta_{\rm jet}|<0.5$. The fraction of charged jets containing a D$^0$-meson increases with $p_{\rm{T,jet}}^{\rm{ch}}$ from $0.042 \pm 0.004\, \mathrm{(stat)} \pm 0.006\, \mathrm{(syst)}$ to $0.080 \pm 0.009\, \rm{(stat)} \pm 0.008\, \rm{(syst)}$. The distribution of D$^0$-meson tagged jets as a function of the jet momentum fraction carried by the D$^0$ meson in the direction of the jet axis ($z_{||}^{\mathrm{ch}}$) is reported for two ranges of jet transverse momenta, $5<p_{\rm{T,jet}}^{\rm{ch}}<15$ ${\rm GeV/}c$ and $15<p_{\rm{T,jet}}^{\rm{ch}}<30$ ${\rm GeV/}c$ in the intervals $0.2<z_{||}^{\rm{ch}}<1.0$ and $0.4<z_{||}^{\rm{ch}}<1.0$, respectively. The data are compared with results from Monte Carlo event generators (PYTHIA 6, PYTHIA 8 and Herwig 7) and with a Next-to-Leading-Order perturbative Quantum Chromodynamics calculation, obtained with the POWHEG method and interfaced with PYTHIA 6 for the generation of the parton shower, fragmentation, hadronisation and underlying event.Comment: 29 pages, 8 captioned figures, 3 tables, authors from page 24, published version, figures at http://alice-publications.web.cern.ch/node/525