Mapping of RNA- temperature-sensitive mutants of Sindbis virus: assignment of complementation groups A, B, and G to nonstructural proteins

Four complementation groups of temperature-sensitive (ts) mutants of Sindbis virus that fail to make RNA at the nonpermissive temperature are known, and we have previously shown that group F mutants have defects in nsP4. Here we map representatives of groups A, B, and G. Restriction fragments from a full-length clone of Sindbis virus, Toto1101, were replaced with the corresponding fragments from the various mutants. These hybrid plasmids were transcribed in vitro by SP6 RNA polymerase to produce infectious RNA transcripts, and the virus recovered was tested for temperature sensitivity. After each lesion was mapped to a specific region, cDNA clones of both mutants and revertants were sequenced in order to determine the precise nucleotide change responsible for each mutation. Synthesis of viral RNA and complementation by rescued mutants were also examined in order to study the phenotype of each mutation in a uniform genetic background. The single mutant of group B, ts11, had a defect in nsP1 (Ala-348 to Thr). All of the group A and group G mutants examined had lesions in nsP2 (Ala-517 to Thr in ts17, Cys-304 to Tyr in ts21, and Gly-736 to Ser in ts24 for three group A mutants, and Phe-509 to Leu in ts18 and Asp-522 to Asn in ts7 for two group G mutants). In addition, ts7 had a change in nsP3 (Phe-312 to Ser) which also rendered the virus temperature sensitive and RNA-. Thus, changes in any of the four nonstructural proteins can lead to failure to synthesize RNA at a nonpermissive temperature, indicating that all four are involved in RNA synthesis. From the results presented here and from previous results, several of the activities of the nonstructural proteins can be deduced. It appears that nsP1 may be involved in the initiation of minus-strand RNA synthesis. nsP2 appears to be involved in the initiation of 26S RNA synthesis, and in addition it appears to be a protease that cleaves the nonstructural polyprotein precursors. It may also be involved in shutoff of minus-strand RNA synthesis. nsP4 appears to function as the viral polymerase or elongation factor. The functions of nsP3 are as yet unresolved

Sindbis virus ts103 has a mutation in glycoprotein E2 that leads to defective assembly of virions

Sindbis virus mutant ts103 is aberrant in the assembly of virus particles. During virus budding, proper nucleocapsid-glycoprotein interactions fail to occur such that particles containing many nucleocapsids are formed, and the final yield of virus is low. We have determined that a mutation in the external domain of glycoprotein E2, Ala-344-->Val, is the change that leads to this phenotype. Mapping was done by making recombinant viruses between ts103 and a parental strain of the virus, using a full-length cDNA clone of Sindbis virus from which infectious RNA can be transcribed, together with sequence analysis of the region of the genome shown in this way to contain the ts103 lesion. A partial revertant of ts103, called ts103R, was also mapped and sequenced and found to be a second-site revertant in which a change in glycoprotein E1 from lysine to methionine at position 227 partially suppresses the phenotypic effects of the change at E2 position 344. An analysis of revertants from ts103 mutants in which the Ala-->Val change had been transferred into a defined background showed that pseudorevertants were more likely to arise than were true revertants and that the ts103 change itself reverted very infrequently. The assembly defect in ts103 appeared to result from weakened interactions between the virus membrane glycoproteins or between these glycoproteins and the nucleocapsid during budding. Both the E2 mutation leading to the defect in virus assembly and the suppressor mutation in glycoprotein E1 are in the domains external to the lipid bilayer and thus in domains that cannot interact directly with the nucleocapsid. This suggests that in ts103, either the E1-E2 heterodimers or the trimeric spikes (consisting of three E1-E2 heterodimers) are unstable or have an aberrant configuration, and thus do not interact properly with the nucleocapsid, or cannot assembly correctly to form the proper icosahedral array on the surface of the virus

Wavelength Dependent PSFs and their impact on Weak Lensing Measurements

We measure and model the wavelength dependence of the PSF in the Hyper Suprime-Cam (HSC) Subaru Strategic Program (SSP) survey. We find that PSF chromaticity is present in that redder stars appear smaller than bluer stars in the $g, r,$ and $i$-bands at the 1-2 per cent level and in the $z$ and $y$-bands at the 0.1-0.2 per cent level. From the color dependence of the PSF, we fit a model between the monochromatic PSF trace radius, $R$, and wavelength of the form $R(\lambda)\propto \lambda^{b}$. We find values of $b$ between -0.2 and -0.5, depending on the epoch and filter. This is consistent with the expectations of a turbulent atmosphere with an outer scale length of $\sim 10-100$ m, indicating that the atmosphere is dominating the chromaticity. We find evidence in the best seeing data that the optical system and detector also contribute some wavelength dependence. Meyers and Burchat (2015) showed that $b$ must be measured to an accuracy of $\sim 0.02$ not to dominate the systematic error budget of the Large Synoptic Survey Telescope (LSST) weak lensing (WL) survey. Using simple image simulations, we find that $b$ can be inferred with this accuracy in the $r$ and $i$-bands for all positions in the LSST field of view, assuming a stellar density of 1 star arcmin$^{-2}$ and that the optical PSF can be accurately modeled. Therefore, it is possible to correct for most, if not all, of the bias that the wavelength-dependent PSF will introduce into an LSST-like WL survey.Comment: 14 pages, 10 figures. Submitted to MNRAS. Comments welcom

High resolution Ge/Li/ spectrometer reduces rate-dependent distortions at high counting rates

Modified spectrometer system with a low-noise preamplifier reduces rate-dependent distortions at high counting rates, 25,000 counts per second. Pole-zero cancellation minimizes pulse undershoots due to multiple time constants, baseline restoration improves resolution and prevents spectral shifts

Magnetic Quench Antenna for MQXF Quadrupoles

High-field MQXF-series quadrupoles are presently under development by LARP and CERN for the upcoming LHC luminosity upgrade. Quench training and protection studies on MQXF prototypes require a capability to accurately localize quenches and measure their propagation velocity in the magnet coils. The voltage tap technique commonly used for such purposes is not a convenient option for the 4.2-m-long MQXF-A prototype, nor can it be implemented in the production model. We have developed and tested a modular inductive magnetic antenna for quench localization. The base element of our quench antenna is a round-shaped printed circuit board containing two orthogonal pairs of flat coils integrated with low-noise preamplifiers. The elements are aligned axially and spaced equidistantly in 8-element sections using a supporting rod structure. The sections are installed in the warm bore of the magnet, and can be stacked together to adapt for the magnet length. We discuss the design, operational characteristics and preliminary qualification of the antenna. Axial quench localization capability with an accuracy of better than 2 cm has been validated during training test campaign of the MQXF-S1 quadrupole

Development of an mHealth platform for HIV Care: gathering user perspectives through co-design workshops and interviews

Background: Despite advances in testing and treatment, HIV incidence rates within European countries are at best stable or else increasing. mHealth technology has been advocated to increase quality and cost-effectiveness of health services while dealing with growing patient numbers. However, studies suggested that mHealth apps are rarely adopted and often considered to be of low quality by users. Only a few studies (conducted in the United States) have involved people living with HIV (PLWH) in the design of mHealth. Objective: The goal of this study was to facilitate a co-design process among PLWH and clinicians across 5 clinical sites in the European Union to inform the development of an mHealth platform to be integrated into clinical care pathways. We aimed to (1) elicit experiences of living with HIV and of working in HIV care, (2) identify mHealth functionalities that are considered useful for HIV care, and (3) identify potential benefits as well as concerns about mHealth. Methods: Between January and June 2016, 14 co-design workshops and 22 semistructured interviews were conducted, involving 97 PLWH and 63 clinicians. Data were analyzed thematically and iteratively, drawing on grounded theory techniques. Results: Findings were established into 3 thematic clusters: (1) approaching the mHealth platform, (2) imagining the mHealth platform, and (3) anticipating the mHealth platform’s implications. Co-design participants approached the mHealth platform with pre-existing concerns arising from their experiences of receiving or providing care. PLWH particularly addressed issues of stigma and questioned how mHealth could enable them to manage their HIV. Clinicians problematized the compatibility of mHealth with existing information technology systems and questioned which patients should be targeted by mHealth. Imagining the potential of mHealth for HIV care, co-design participants suggested medical functionalities (accessing test results, managing medicines and appointments, and digital communication channels), social functionalities (peer support network, international travel, etc), and general features (security and privacy, credibility, language, etc). Co-design participants also anticipated potential implications of mHealth for self-management and the provision of care. Conclusions: Our approach to co-design enabled us to facilitate early engagement in the mHealth platform, enabling patient and clinician feedback to become embedded in the development process at a preprototype phase. Although the technologies in question were not yet present, understanding how users approach, imagine, and anticipate technology formed an important source of knowledge and proved highly significant within the technology design and development process

Plasma Edge Kinetic-MHD Modeling in Tokamaks Using Kepler Workflow for Code Coupling, Data Management and Visualization

A new predictive computer simulation tool targeting the development of the H-mode pedestal at the plasma edge in tokamaks and the triggering and dynamics of edge localized modes (ELMs) is presented in this report. This tool brings together, in a coordinated and effective manner, several first-principles physics simulation codes, stability analysis packages, and data processing and visualization tools. A Kepler workflow is used in order to carry out an edge plasma simulation that loosely couples the kinetic code, XGC0, with an ideal MHD linear stability analysis code, ELITE, and an extended MHD initial value code such as M3D or NIMROD. XGC0 includes the neoclassical ion-electron-neutral dynamics needed to simulate pedestal growth near the separatrix. The Kepler workflow processes the XGC0 simulation results into simple images that can be selected and displayed via the Dashboard, a monitoring tool implemented in AJAX allowing the scientist to track computational resources, examine running and archived jobs, and view key physics data, all within a standard Web browser. The XGC0 simulation is monitored for the conditions needed to trigger an ELM crash by periodically assessing the edge plasma pressure and current density profiles using the ELITE code. If an ELM crash is triggered, the Kepler workflow launches the M3D code on a moderate-size Opteron cluster to simulate the nonlinear ELM crash and to compute the relaxation of plasma profiles after the crash. This process is monitored through periodic outputs of plasma fluid quantities that are automatically visualized with AVS/Express and may be displayed on the Dashboard. Finally, the Kepler workflow archives all data outputs and processed images using HPSS, as well as provenance information about the software and hardware used to create the simulation. The complete process of preparing, executing and monitoring a coupled-code simulation of the edge pressure pedestal buildup and the ELM cycle using the Kepler scientific workflow system is described in this paper