High-Confidence Placement of Fragments into Electron Density Using Anomalous Diffraction—A Case Study Using Hits Targeting SARS-CoV-2 Non-Structural Protein 1

The identification of multiple simultaneous orientations of small molecule inhibitors binding to a protein target is a common challenge. It has recently been reported that the conformational heterogeneity of ligands is widely underreported in the Protein Data Bank, which is likely to impede optimal exploitation to improve affinity of these ligands. Significantly less is even known about multiple binding orientations for fragments (<300 Da), although this information would be essential for subsequent fragment optimisation using growing, linking or merging and rational structure-based design. Here, we use recently reported fragment hits for the SARS-CoV-2 non-structural protein 1 (nsp1) N-terminal domain to propose a general procedure for unambiguously identifying binding orientations of 2-dimensional fragments containing either sulphur or chloro substituents within the wavelength range of most tunable beamlines. By measuring datasets at two energies, using a tunable beamline operating in vacuum and optimised for data collection at very low X-ray energies, we show that the anomalous signal can be used to identify multiple orientations in small fragments containing sulphur and/or chloro substituents or to verify recently reported conformations. Although in this specific case we identified the positions of sulphur and chlorine in fragments bound to their protein target, we are confident that this work can be further expanded to additional atoms or ions which often occur in fragments. Finally, our improvements in the understanding of binding orientations will also serve to improve the rational optimisation of SARS-CoV-2 nsp1 fragment hit

Production of four-quark states with double heavy quarks at LHC

We study the hadronic production of four-quark states with double heavy quarks and double light antiquarks at LHC. The production mechanism is that a color anti-triplet diquark cluster consisting of double heavy quarks is formed first from the produced double heavy quark-antiquark pairs via $gg$ fusion hard process, followed by the fragmentation of the diquark cluster into a four-quark (tetraquark) state. Predictions for the production cross sections and their differential distributions are presented. Our results show that it is quite promising to discover these tetraquark states in LHC experiments both for large number events and for their unique signatures in detectors.Comment: 17 pages,8 figure

Association of MRI T1 relaxation time with neuropsychological test performance in manganese- exposed welders

This study examines the results of neuropsychological testing of 26 active welders and 17 similar controls and their relationship to welders' shortened MRI T1 relaxation time, indicative of increased brain manganese (Mn) accumulation. Welders were exposed to Mn for an average duration of 12.25 years to average levels of Mn in air of 0.11±0.05mg/m3. Welders scored significantly worse than controls on Fruit Naming and the Parallel Lines test of graphomotor tremor. Welders had shorter MRI T1 relaxation times than controls in the globus pallidus, substantia nigra, caudate nucleus, and the anterior prefrontal lobe. 63% of the variation in MRI T1 relaxation times was accounted for by exposure group. In welders, lower relaxation times in the caudate nucleus and substantia nigra were associated with lower neuropsychological test performance on tests of verbal fluency (Fruit Naming), verbal learning, memory, and perseveration (WHO-UCLA AVLT). Results indicate that verbal function may be one of the first cognitive domains affected by brain Mn deposition in welders as reflected by MRI T1 relaxation times

Scaling Study of Pure Gauge Lattice QCD by Monte Carlo Renormalization Group Method

The scaling behavior of pure gauge SU(3) in the region $\beta=5.85 - 7.60$ is examined by a Monte Carlo Renormalization Group analysis. The coupling shifts induced by factor 2 blocking are measured both on 32$^4$ and 16$^4$ lattices with high statistics. A systematic deviation from naive 2-loop scaling is clearly seen. The mean field and effective coupling constant schemes explain part, but not all of the deviation. It can be accounted for by a suitable change of coupling constant, including a correction term ${\cal O}(g^7)$ in the 2-loop lattice $\beta$-function. Based on this improvement, $\sqrt{\sigma}/\Lambda_{\overline {MS}}^{n_f=0}$ is estimated to be $2.2(\pm 0.1)$ from the analysis of the string tension $\sigma$.Comment: 4 pages of A4 format including 7-postscript figure

Event-based prospective memory performance in autism spectrum disorder

The purpose of the present study was to investigate event-based prospective memory performance in individuals with autism spectrum disorder and to explore possible relations between laboratory-based prospective memory performance and everyday performance. Nineteen children and adolescents with autism spectrum disorder and 19 matched neurotypical controls participated. The laboratory-based prospective memory test was embedded in a visuo-spatial working memory test and required participants to remember to respond to a cue-event. Everyday planning performance was assessed with proxy ratings. Although parents of the autism group rated their children’s everyday performance as significantly poorer than controls’ parents, no group differences were found in event-based prospective memory. Nevertheless, individual differences in laboratory-based and everyday performances were related. Clinical implications of these findings are discussed

Theoretical and Phenomenological Constraints on Form Factors for Radiative and Semi-Leptonic B-Meson Decays

We study transition form factors for radiative and rare semi-leptonic B-meson decays into light pseudoscalar or vector mesons, combining theoretical constraints and phenomenological information from Lattice QCD, light-cone sum rules, and dispersive bounds. We pay particular attention to form factor parameterisations which are based on the so-called series expansion, and study the related systematic uncertainties on a quantitative level. In this context, we also provide the NLO corrections to the correlation function between two flavour-changing tensor currents, which enters the unitarity constraints for the coefficients in the series expansion.Comment: 52 pages; v2: normalization error in (29ff.) corrected, conclusion about relevance of unitarity bounds modified; form factor fits unaffected; references added; v3: discussion on truncation of series expansion added, matches version to be published in JHEP; v4: corrected typos in Tables 5 and

Planet Hunters. VIII. Characterization of 41 Long-Period Exoplanet Candidates from Kepler Archival Data

The census of exoplanets is incomplete for orbital distances larger than 1 AU. Here, we present 41 long-period planet candidates in 38 systems identified by Planet Hunters based on Kepler archival data (Q0-Q17). Among them, 17 exhibit only one transit, 14 have two visible transits and 10 have more than three visible transits. For planet candidates with only one visible transit, we estimate their orbital periods based on transit duration and host star properties. The majority of the planet candidates in this work (75%) have orbital periods that correspond to distances of 1-3 AU from their host stars. We conduct follow-up imaging and spectroscopic observations to validate and characterize planet host stars. In total, we obtain adaptive optics images for 33 stars to search for possible blending sources. Six stars have stellar companions within 4". We obtain high-resolution spectra for 6 stars to determine their physical properties. Stellar properties for other stars are obtained from the NASA Exoplanet Archive and the Kepler Stellar Catalog by Huber et al. (2014). We validate 7 planet candidates that have planet confidence over 0.997 (3-{\sigma} level). These validated planets include 3 single-transit planets (KIC-3558849b, KIC-5951458b, and KIC-8540376c), 3 planets with double transits (KIC-8540376b, KIC-9663113b, and KIC-10525077b), and 1 planet with 4 transits (KIC-5437945b). This work provides assessment regarding the existence of planets at wide separations and the associated false positive rate for transiting observation (17%-33%). More than half of the long-period planets with at least three transits in this paper exhibit transit timing variations up to 41 hours, which suggest additional components that dynamically interact with the transiting planet candidates. The nature of these components can be determined by follow-up radial velocity and transit observations.Comment: Published on ApJ, 815, 127 Notations of validated planets are changed in accordance with naming convention of NASA Exoplanet Archiv

Tight-binding parameters from the full-potential linear muffin-tin orbital method: A feasibility study on NiAl

We have examined a method of direct extraction of accurate tight-binding parameters from an ab-initio band-structure calculation. The linear muffin-tin potential method, in its full-potential implementation, has been used to provide the hamiltonian and overlap matrix elements in the momentum space. These matrix elements are Fourier transformed to real space to produce the tight-binding parameters. The feasibility of this method has been tested on the intermetallic alloy NiAl, using spd orbitals for each atom. The parameters generated for this alloy have been used as input to a real-space calculation of the local density of states using the recursion method.Comment: 12 pages, RevTex, 5 figure

A route to systematic error in forecasts of Rossby waves

Recent work has shown that both the amplitude of upper-level Rossby waves and the tropopause sharpness decrease with forecast lead time for several days in some operational weather forecast systems. In this contribution, the evolution of error growth in a case study of this forecast error type is diagnosed through analysis of operational forecasts and hindcast simulations. Potential vorticity (PV) on the 320-K isentropic surface is used to diagnose Rossby waves. The Rossby-wave forecast error in the operational ECMWF high-resolution forecast is shown to be associated with errors in the forecast of a warm conveyor belt (WCB) through trajectory analysis and an error metric for WCB outflows. The WCB forecast error is characterised by an overestimation of WCB amplitude, a location of the WCB outflow regions that is too far to the southeast, and a resulting underestimation of the magnitude of the negative PV anomaly in the outflow. Essentially the same forecast error development also occurred in all members of the ECMWF Ensemble Prediction System and the Met Office MOGREPS-15 suggesting that in this case model error made an important contribution to the development of forecast error in addition to initial condition error. Exploiting this forecast error robustness, a comparison was performed between the realised flow evolution, proxied by a sequence of short-range simulations, and a contemporaneous forecast. Both the proxy to the realised flow and the contemporaneous forecast a were produced with the Met Office Unified Model enhanced with tracers of diabatic processes modifying potential temperature and PV. Clear differences were found in the way potential temperature and PV are modified in the WCB between proxy and forecast. These results demonstrate that differences in potential temperature and PV modification in the WCB can be responsible for forecast errors in Rossby waves

Heavy-light Mesons and Baryons with b quarks

We present lattice results for the spectrum of mesons containing one heavy quark and of baryons containing one or two heavy quarks. The calculation is done in the quenched approximation using the NRQCD formalism for the heavy quark. We analyze the dependence of the mass splittings on both the heavy and the light quark masses. Meson P-state fine structure and baryon hyperfine splittings are resolved for the first time. We fix the b quark mass using both M_B and M_{\Lambda_b}, and our best estimate is m_b^\MSbar(m_b^\MSbar) = 4.35(10)({}^{-3}_{+2})(10) GeV. The spectrum, obtained by interpolation to m_b, is compared with the experimental data.Comment: 34 pages, LaTeX, 13 postscript figures, version as publish in Phys. Rev.