A methodology for determining amino-acid substitution matrices from set covers

We introduce a new methodology for the determination of amino-acid substitution matrices for use in the alignment of proteins. The new methodology is based on a pre-existing set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitution-matrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration

Geochronological and geochemical constraints on Late Cryogenian to Early Ediacaran magmatic rocks on the northern Tarim Craton:implications for tectonic setting and affinity with Gondwana

The Tarim Craton provides a geologic record of both the fragmentation of the Rodinian supercontinent and the subsequent assembly of Gondwana. However, the timing and interactions of these radically different tectonic processes remain contested. A critical part of this debate revolves around the Late Cryogenian-Ediacaran igneous rocks along the Craton’s northern margin, specifically, whether they record super-plume related Rodinian breakup or Gondwanan orogeny. To address this issue, we present zircon U-Pb-Hf isotopic data and whole rock geochemistry from Late Cryogenian to Early Ediacaran granitoids of the northern Tarim Craton. U-Pb zircon ages reveal three magmatic periods along the northern Tarim margin: ca. 660–640 Ma, 635–625 Ma and 620–600 Ma, associated with small scale felsic and mafic magmas. These granitoids have an A2-type affinity and are enriched in alkalines, but are depleted in Nb, Ta, Sr, P and Ti. Elemental data and generally negative εHf(t) values (−13.96 to 1.65) suggest that they were mainly derived from partial melting of enriched, subduction-modified lithospheric mantle triggered by upwelling of the asthenospheric mantle along the active continental margin of northern Tarim. We suggest that the Tarim Craton travelled as an isolated plate for much of the Late Neoproterozoic, near the outer part of Rodinia and subsequently Gondwana. During this time it was affected by localized and periodic subduction-related intrusion and eruption. However, within the samples of this study, there is no U-Pb-Hf isotopic and whole-rock geochemical evidence to support either super-plume-related rifting (i.e. Rodinian breakup) or Pan-African orogeny (i.e. Gondwanan assembly).</p

Gamma-ray Observations Under Bright Moonlight with VERITAS

Imaging atmospheric Cherenkov telescopes (IACTs) are equipped with sensitive photomultiplier tube (PMT) cameras. Exposure to high levels of background illumination degrades the efficiency of and potentially destroys these photo-detectors over time, so IACTs cannot be operated in the same configuration in the presence of bright moonlight as under dark skies. Since September 2012, observations have been carried out with the VERITAS IACTs under bright moonlight (defined as about three times the night-sky-background (NSB) of a dark extragalactic field, typically occurring when Moon illumination > 35%) in two observing modes, firstly by reducing the voltage applied to the PMTs and, secondly, with the addition of ultra-violet (UV) bandpass filters to the cameras. This has allowed observations at up to about 30 times previous NSB levels (around 80% Moon illumination), resulting in 30% more observing time between the two modes over the course of a year. These additional observations have already allowed for the detection of a flare from the 1ES 1727+502 and for an observing program targeting a measurement of the cosmic-ray positron fraction. We provide details of these new observing modes and their performance relative to the standard VERITAS observations

Combining Optical Remote Sensing, McFLI Discharge Estimation, Global Hydrologic Modeling, and Data Assimilation to Improve Daily Discharge Estimates Across an Entire Large Watershed

Remote sensing has gained attention as a novel source of primary information for estimating river discharge, and the Mass-conserved Flow Law Inversion (McFLI) approach has successfully estimated river discharge in ungauged basins solely from optical satellite data. However, McFLI currently suffers from two major drawbacks: (1) existing optical satellites lead to temporally and spatially sparse discharge estimates and (2) because of the assumptions required, McFLI cannot guarantee downstream flow continuity. Hydrological modeling has neither drawback, yet model accuracy is frequently limited by a lack of discharge observations. We therefore combine McFLI and models in a data assimilation framework applicable globally. We establish a daily “ungauged” baseline model for 28,998 reaches of the Missouri river basin forced by recently published global runoff data, which we do not calibrate. We estimate discharge via McFLI using ∼1 million width measurements made from 12,000 Landsat scenes and assimilate McFLI into the model before validating at 403 USGS gauges. Results show that assimilated discharges did not impair already accurate baseline flows and achieved median improvements of 28% normalized root mean square error, 0.50 Nash–Sutcliffe efficiency (NSE), and 0.23 Kling–Gupta efficiency where baseline performance was poor (defined as baseline negative NSE, 225/403 reaches). We ultimately improved flows at 92% of these originally poorly modeled gauges, even though Landsat images only provide McFLI discharges at 1.5% of reaches and 26% of simulated days. Our results suggest that the combination of McFLI and state-of-the-art hydrology models can improve flow estimations in ungauged basins globally

Poor nutritional status is associated with other geriatric domain impairments and adverse postoperative outcomes in onco-geriatric surgical patients – a multicentre cohort study

Background: Nutritional status (NS), though frequently affected in onco-geriatric patients, is no standard part of a geriatric assessment. The aim of this study was to analyse the association between a preoperatively impaired NS and geriatric domain impairments and adverse postoperative outcomes in onco-geriatric surgical patients. Methods: 309 patients ≥70 years undergoing surgery for solid tumours were prospectively recruited. Nine screening tools were preoperatively administered as part of a geriatric assessment. NS was based on BMI, weight loss and food intake. Odds ratio’s (OR) and 95% confidence intervals (95%CI) were estimated using logistic regression analysis. The occurrence of 30-day adverse postoperative outcomes was recorded. Results: At a median age of 76 years, 107 patients (34.6%) had an impaired NS. Decreased performance status and depression were associated with an impaired NS, when adjusted for tumour characteristics and comorbidities (ORPS>1 3.46; 95%CI 1.56-7.67. ORGDS>5 2.11; 95%CI 1.05-4.26). An impaired NS was an independent predictor for major complications (OR 3.3; 95%CI 1.6-6.8). Ten out of 11 patients who deceased had an impaired NS. Conclusion: An impaired NS is prevalent in onco-geriatric patients considered to be fit for surgery. It is associated with decreased performance status and depression. An impaired NS is a predictor for adverse postoperative outcomes. NS should be incorporated in a geriatric assessment

Origins of the Ambient Solar Wind: Implications for Space Weather

The Sun's outer atmosphere is heated to temperatures of millions of degrees, and solar plasma flows out into interplanetary space at supersonic speeds. This paper reviews our current understanding of these interrelated problems: coronal heating and the acceleration of the ambient solar wind. We also discuss where the community stands in its ability to forecast how variations in the solar wind (i.e., fast and slow wind streams) impact the Earth. Although the last few decades have seen significant progress in observations and modeling, we still do not have a complete understanding of the relevant physical processes, nor do we have a quantitatively precise census of which coronal structures contribute to specific types of solar wind. Fast streams are known to be connected to the central regions of large coronal holes. Slow streams, however, appear to come from a wide range of sources, including streamers, pseudostreamers, coronal loops, active regions, and coronal hole boundaries. Complicating our understanding even more is the fact that processes such as turbulence, stream-stream interactions, and Coulomb collisions can make it difficult to unambiguously map a parcel measured at 1 AU back down to its coronal source. We also review recent progress -- in theoretical modeling, observational data analysis, and forecasting techniques that sit at the interface between data and theory -- that gives us hope that the above problems are indeed solvable.Comment: Accepted for publication in Space Science Reviews. Special issue connected with a 2016 ISSI workshop on "The Scientific Foundations of Space Weather." 44 pages, 9 figure

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Upper limits from five years of blazar observations with the VERITAS Cherenkov telescopes

Between the beginning of its full-scale scientific operations in 2007 and 2012, the VERITAS Cherenkov telescope array observed more than 130 blazars; of these, 26 were detected as very-high-energy (VHE; E > 100 GeV) γ-ray sources. In this work, we present the analysis results of a sample of 114 undetected objects. The observations constitute a total live-time of ~570 hr. The sample includes several unidentified Fermi-Large Area Telescope (LAT) sources (located at high Galactic latitude) as well as all the sources from the second Fermi-LAT catalog that are contained within the field of view of the VERITAS observations. We have also performed optical spectroscopy measurements in order to estimate the redshift of some of these blazars that do not have spectroscopic distance estimates. We present new optical spectra from the Kast instrument on the Shane telescope at the Lick observatory for 18 blazars included in this work, which allowed for the successful measurement or constraint on the redshift of four of them. For each of the blazars included in our sample, we provide the flux upper limit in the VERITAS energy band. We also study the properties of the significance distributions and we present the result of a stacked analysis of the data set, which shows a 4σ excess

Observation of the gamma-ray binary HESS J0632+057 with the HESS, MAGIC, and VERITAS telescopes

The results of gamma-ray observations of the binary system HESS J0632 + 057 collected during 450 hr over 15 yr, between 2004 and 2019, are presented. Data taken with the atmospheric Cherenkov telescopes H.E.S.S., MAGIC, and VERITAS at energies above 350 GeV were used together with observations at X-ray energies obtained with Swift-XRT, Chandra, XMM-Newton, NuSTAR, and Suzaku. Some of these observations were accompanied by measurements of the Hα emission line. A significant detection of the modulation of the very high-energy gamma-ray fluxes with a period of 316.7 ± 4.4 days is reported, consistent with the period of 317.3 ± 0.7 days obtained with a refined analysis of X-ray data. The analysis of data from four orbital cycles with dense observational coverage reveals short-timescale variability, with flux-decay timescales of less than 20 days at very high energies. Flux variations observed over a timescale of several years indicate orbit-to-orbit variability. The analysis confirms the previously reported correlation of X-ray and gamma-ray emission from the system at very high significance, but cannot find any correlation of optical Hα parameters with fluxes at X-ray or gamma-ray energies in simultaneous observations. The key finding is that the emission of HESS J0632 + 057 in the X-ray and gamma-ray energy bands is highly variable on different timescales. The ratio of gamma-ray to X-ray flux shows the equality or even dominance of the gamma-ray energy range. This wealth of new data is interpreted taking into account the insufficient knowledge of the ephemeris of the system, and discussed in the context of results reported on other gamma-ray binary systems.C. B. Adams, W. Benbow, A. Brill, J. H. Buckley, M. Capasso, A. J. Chromey ... et al