EFFICIENT PROPAGATION OF ARCHETYPE JC POLYOMAVIRUS IN COS-7 CELLS: EVALUATION OF REARRANGEMENTS WITHIN NCCR STRUCTURAL ORGANIZATION DURING TRANSFECTION.

John Cunningham virus (JCPyV) is an ubiqui-tous human pathogen that causes disease in immunocom-promised patients. The JCPyV genome is composed of an early region and a late region, which are physically sepa-rated by the non-coding control region (NCCR). The DNA sequence of the NCCR distinguishes two forms of JCPyV, the designated archetype and the prototype, which resulted from a rearrangement of the archetype sequence. To date, the cell culture systems for propagating JCPyV archetype have been very limited in their availability and robust-ness. Prior to this study, it was demonstrated that JCPyV archetype DNA replicates in COS-7 simian kidney cells expressing SV40 TAg and COS-7 cells expressing HIV-1 Tat. Based on these observations, the present study was conducted to reproduce an in vitro model in COS-7 cells transfected with the JCPyV archetype strain in order to study JCPyV DNA replication and analyze NCCR rear-rangements during the viral life cycle. The efficiency of JCPyV replication was evaluated by quantitative PCR (Q-PCR) and by hemagglutination (HA) assay after trans-fection. In parallel, sequence analysis of JCPyV NCCR was performed. JCPyV efficiently replicated in kidney-derived COS-7 cells, as demonstrated by a progressive increase in viral load and virion particle production after transfection. The archetypal structure of NCCR was maintained during the viral cycle, but two characteristic point mutations were detected 28 days after transfection. This model is a useful tool for analyzing NCCR rearrangements during in vitroreplication in cells that are sites of viral persistence, such as tubular epithelial cells of the kidne

H2, HD, and D2 in the small cage of structure II clathrate hydrate: vibrational frequency shifts from fully coupled quantum six-dimensional calculations of the vibration-translation-rotation eigenstates

We report the first fully coupled quantum six-dimensional (6D) bound-state calculations of the vibration-translation-rotation eigenstates of a flexible H2, HD, and D2 molecule confined inside the small cage of the structure II clathrate hydrate embedded in larger hydrate domains with up to 76 H2O molecules, treated as rigid. Our calculations use a pairwise-additive 6D intermolecular potential energy surface for H2 in the hydrate domain, based on an ab initio 6D H2–H2O pair potential for flexible H2 and rigid H2O. They extend to the first excited (v = 1) vibrational state of H2, along with two isotopologues, providing a direct computation of vibrational frequency shifts. We show that obtaining a converged v = 1 vibrational state of the caged molecule does not require converging the very large number of intermolecular translation-rotation states belonging to the v = 0 manifold up to the energy of the intramolecular stretch fundamental (≈4100 cm−1 for H2). Only a relatively modest-size basis for the intermolecular degrees of freedom is needed to accurately describe the vibrational averaging over the delocalized wave function of the quantum ground state of the system. For the caged H2, our computed fundamental translational excitations, rotational j = 0 → 1 transitions, and frequency shifts of the stretch fundamental are in excellent agreement with recent quantum 5D (rigid H2) results [A. Powers et al., J. Chem. Phys. 148, 144304 (2018)]. Our computed frequency shift of −43 cm−1 for H2 is only 14% away from the experimental value at 20 K

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates

© 2018 Author(s). We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H 2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculat ions of the coupled translation-rotation eigenstates are performed for H 2 in the v=0 and v=1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H 2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H 2 inside a hydrate domain is assumed to be pairwise additive. The H 2 -H 2 O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H 2 , v=0 or v=1, is derived from the high-quality ab initio full-dimensional (9D) PES of the H 2 -H 2 O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H 2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H 2 change very little with the domain size, unlike the H 2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H 2 O molecules in the first three complete hydration shells around H 2

A novel background reduction strategy for high level triggers and processing in gamma-ray Cherenkov detectors

Gamma ray astronomy is now at the leading edge for studies related both to fundamental physics and astrophysics. The sensitivity of gamma detectors is limited by the huge amount of background, constituted by hadronic cosmic rays (typically two to three orders of magnitude more than the signal) and by the accidental background in the detectors. By using the information on the temporal evolution of the Cherenkov light, the background can be reduced. We will present here the results obtained within the MAGIC experiment using a new technique for the reduction of the background. Particle showers produced by gamma rays show a different temporal distribution with respect to showers produced by hadrons; the background due to accidental counts shows no dependence on time. Such novel strategy can increase the sensitivity of present instruments.Comment: 4 pages, 3 figures, Proc. of the 9th Int. Syposium "Frontiers of Fundamental and Computational Physics" (FFP9), (AIP, Melville, New York, 2008, in press

Design and construction of new central and forward muon counters for CDF II

New scintillation counters have been designed and constructed for the CDF upgrade in order to complete the muon coverage of the central CDF detector, and to extend this coverage to larger pseudorapidity. A novel light collection technique using wavelength shifting fibers, together with high quality polystyrene-based scintillator resulted in compact counters with good and stable light collection efficiency over lengths extending up to 320 cm. Their design and construction is described and results of their initial performance are reported.Comment: 20 pages, 15 figure

A simulation tool for MRPC telescopes of the EEE project

The Extreme Energy Events (EEE) Project is mainly devoted to the study of the secondary cosmic ray radiation by using muon tracker telescopes made of three Multigap Resistive Plate Chambers (MRPC) each. The experiment consists of a telescope network mainly distributed across Italy, hosted in different building structures pertaining to high schools, universities and research centers. Therefore, the possibility to take into account the effects of these structures on collected data is important for the large physics programme of the project. A simulation tool, based on GEANT4 and using GEMC framework, has been implemented to take into account the muon interaction with EEE telescopes and to estimate the effects on data of the structures surrounding the experimental apparata.A dedicated event generator producing realistic muon distributions, detailed geometry and microscopic behavior of MRPCs have been included to produce experimental-like data. The comparison between simulated and experimental data, and the estimation of detector resolutions is here presented and discussed

Long-term outcomes of acute severe ulcerative colitis in the rescue therapy era: A multicentre cohort study

BACKGROUND: The long‐term course of ulcerative colitis after a severe attack is poorly understood. Second‐line rescue therapy with cyclosporine or infliximab is effective for reducing short‐term colectomy but the impact in the long‐term is controversial. OBJECTIVE: The purpose of this study was to evaluate the long‐term course of acute severe ulcerative colitis patients who avoid early colectomy either because of response to steroids or rescue therapy. METHODS: This was a multicentre retrospective cohort study of adult patients with acute severe ulcerative colitis admitted to Italian inflammatory bowel disease referral centres from 2005 to 2017. All patients received intravenous steroids, and those who did not respond received either rescue therapy or colectomy. For patients who avoided early colectomy (within 3 months from the index attack), we recorded the date of colectomy, last follow‐up visit or death. The primary end‐point was long‐term colectomy rate in patients avoiding early colectomy. RESULTS: From the included 372 patients with acute severe ulcerative colitis, 337 (90.6%) avoided early colectomy. From those, 60.5% were responsive to steroids and 39.5% to the rescue therapy. Median follow‐up was 44 months (interquartile range, 21–85). Colectomy‐free survival probability was 93.5%, 81.5% and 79.4% at 1, 3 and 5 years, respectively. Colectomy risk was higher among rescue therapy users than in steroid‐responders (log‐rank test, p = 0.02). At multivariate analysis response to steroids was independently associated with a lower risk of long‐term colectomy (adjusted odds ratio = 0.5; 95% confidence interval, 0.2–0.8), while previous exposure to antitumour necrosis factor‐α agents was associated with an increased risk (adjusted odds ratio = 3.0; 95% confidence interval, 1.5–5.7). Approximately 50% of patients required additional therapy or new hospitalisation within 5 years due to a recurrent flare. Death occurred in three patients (0.9%). CONCLUSIONS: Patients with acute severe ulcerative colitis avoiding early colectomy are at risk of long‐term colectomy, especially if previously exposed to antitumour necrosis factor‐α agents or if rescue therapy during the acute attack was required because of steroid refractoriness

New Eco-gas mixtures for the Extreme Energy Events MRPCs: results and plans

The Extreme Energy Events observatory is an extended muon telescope array, covering more than 10 degrees both in latitude and longitude. Its 59 muon telescopes are equipped with tracking detectors based on Multigap Resistive Plate Chamber technology with time resolution of the order of a few hundred picoseconds. The recent restrictions on greenhouse gases demand studies for new gas mixtures in compliance with the relative requirements. Tetrafluoropropene is one of the candidates for tetrafluoroethane substitution, since it is characterized by a Global Warming Power around 300 times lower than the gas mixtures used up to now. Several mixtures have been tested, measuring efficiency curves, charge distributions, streamer fractions and time resolutions. Results are presented for the whole set of mixtures and operating conditions, %. A set of tests on a real EEE telescope, with cosmic muons, are being performed at the CERN-01 EEE telescope. The tests are focusing on identifying a mixture with good performance at the low rates typical of an EEE telescope.Comment: 8 pages, 6 figures, proceedings for the "XIV Workshop on Resistive Plate Chambers and Related Detectors" (19-23 February 2018), Puerto Vallarta, Jalisco State, Mexic