A natural-norm Successive Constraint Method for inf-sup lower bounds

We present a new approach for the construction of lower bounds for the inf-sup stability constants required in a posteriori error analysis of reduced basis approximations to affinely parametrized partial differential equations. We combine the “linearized” inf-sup statement of the natural-norm approach with the approximation procedure of the Successive Constraint Method (SCM): the former (natural-norm) provides an economical parameter expansion and local concavity in parameter—a small(er) optimization problem which enjoys intrinsic lower bound properties; the latter (SCM) provides a systematic optimization framework—a Linear Program (LP) relaxation which readily incorporates continuity and stability constraints. The natural-norm SCM requires a parameter domain decomposition: we propose a greedy algorithm for selection of the SCM control points as well as adaptive construction of the optimal subdomains. The efficacy of the natural-norm SCM is illustrated through numerical results for two types of non-coercive problems: the Helmholtz equation (for acoustics, elasticity, and electromagnetics), and the convection–diffusion equation.United States. Air Force Office of Scientific Research (Grant No. FA 9550-07-1-0425

Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase

Poly(ADP-ribosyl)ation is a reversible post-translational protein modification involved in the regulation of a number of cellular processes including DNA repair, chromatin structure, mitosis, transcription, checkpoint activation, apoptosis and asexual development. The reversion of poly(ADP-ribosyl)ation is catalysed by poly(ADP-ribose) (PAR) glycohydrolase (PARG), which specifically targets the unique PAR (1''-2') ribose-ribose bonds. Here we report the structure and mechanism of the first canonical PARG from the protozoan Tetrahymena thermophila. In addition, we reveal the structure of T. thermophila PARG in a complex with a novel rhodanine-containing mammalian PARG inhibitor RBPI-3. Our data demonstrate that the protozoan PARG represents a good model for human PARG and is therefore likely to prove useful in guiding structure-based discovery of new classes of PARG inhibitors

Reduced Basis Approximation and a Posteriori Error Estimation for the Parametrized Unsteady Boussinesq Equations

In this paper we present reduced basis (RB) approximations and associated rigorous a posteriori error bounds for the parametrized unsteady Boussinesq equations. The essential ingredients are Galerkin projection onto a low-dimensional space associated with a smooth parametric manifold — to provide dimension reduction; an efficient proper orthogonal decomposition–Greedy sampling method for identification of optimal and numerically stable approximations — to yield rapid convergence; accurate (online) calculation of the solution-dependent stability factor by the successive constraint method — to quantify the growth of perturbations/residuals in time; rigorous a posteriori bounds for the errors in the RB approximation and associated outputs — to provide certainty in our predictions; and an offline–online computational decomposition strategy for our RB approximation and associated error bound — to minimize marginal cost and hence achieve high performance in the real-time and many-query contexts. The method is applied to a transient natural convection problem in a two-dimensional "complex" enclosure — a square with a small rectangle cutout — parametrized by Grashof number and orientation with respect to gravity. Numerical results indicate that the RB approximation converges rapidly and that furthermore the (inexpensive) rigorous a posteriori error bounds remain practicable for parameter domains and final times of physical interest.United States. Air Force Office of Scientific Research (Grant FA9550-07-1-0425)United States. Department of Defense. Office of the Secretary of Defense (United States. Air Force Office of Scientific Research Grant FA9550-09-1-0613

A novel technique for quantifying changes in vascular density, endothelial cell proliferation and protein expression in response to modulators of angiogenesis using the chick chorioallantoic membrane (CAM) assay

Reliable quantitative evaluation of molecular pathways is critical for both drug discovery and treatment monitoring. We have modified the CAM assay to quantitatively measure vascular density, endothelial proliferation, and changes in protein expression in response to anti-angiogenic and pro-angiogenic agents. This improved CAM assay can correlate changes in vascular density with changes seen on a molecular level. We expect that these described modifications will result in a single in vivo assay system, which will improve the ability to investigate molecular mechanisms underlying the angiogenic response

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Unraveling the temperature dependence of the yield strength in single-crystal tungsten using atomistically-informed crystal plasticity calculations

We use a physically-based crystal plasticity model to predict the yield strength of body-centered cubic (bcc) tungsten single crystals subjected to uniaxial loading. Our model captures the thermally-activated character of screw dislocation motion and full non-Schmid effects, both of which are known to play a critical role in bcc plasticity. The model uses atomistic calculations as the sole source of constitutive information, with no parameter fitting of any kind to experimental data. Our results are in excellent agreement with experimental measurements of the yield stress as a function of temperature for a number of loading orientations. The validated methodology is then employed to calculate the temperature and strain-rate dependence of the yield strength for 231 crystallographic orientations within the standard stereographic triangle. We extract the strain-rate sensitivity of W crystals at different temperatures, and finish with the calculation of yield surfaces under biaxial loading conditions that can be used to define effective yield criteria for engineering design models

Responsible, safe, and effective prescription of opioids for chronic non-cancer pain: American society of interventional pain physicians (ASIPP) guidelines

Background: Opioid use, abuse, and adverse consequences, including death, have escalated at an alarming rate since the 1990s. In an attempt to control opioid abuse, numerous regulations and guidelines for responsible opioid prescribing have been developed by various organizations. However, the US opioid epidemic is continuing and drug dose deaths tripled during 1999 to 2015. Recent data show a continuing increase in deaths due to natural and semisynthetic opioids, a decline in methadone deaths, and an explosive increase in the rates of deaths involving other opioids, specifically heroin and illicit synthetic fentanyl. Contrary to scientific evidence of efficacy and negative recommendations, a significant proportion of physicians and patients (92%) believe that opioids reduce pain and a smaller proportion (57%) report better quality of life. In preparation of the current guidelines, we have focused on the means to reduce the abuse and diversion of opioids without jeopardizing access for those patients suffering from non-cancer pain who have an appropriate medical indication for opioid use. Objectives: To provide guidance for the prescription of opioids for the management of chronic non-cancer pain, to develop a consistent philosophy among the many diverse groups with an interest in opioid use as to how appropriately prescribe opioids, to improve the treatment of chronic non-cancer pain and to reduce the likelihood of drug abuse and diversion. These guidelines are intended to provide a systematic and standardized approach to this complex and difficult arena of practice, while recognizing that every clinical situation is unique. Methods: The methodology utilized included the development of objectives and key questions. The methodology also utilized trustworthy standards, appropriate disclosures of conflicts of interest, as well as a panel of experts from various specialties and groups. The literature pertaining to opioid use, abuse, effectiveness, and adverse consequences was reviewed, with a best evidence synthesis of the available literature, and utilized grading for recommendation as described by the Agency for Healthcare Research and Quality (AHRQ)

Taxonomy of prokaryotic viruses : 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Peer reviewe

CD8 coreceptor-mediated focusing can reorder the agonist hierarchy of peptide ligands recognized via the T cell receptor

CD8+ T cells are inherently cross-reactive and recognize numerous peptide antigens in the context of a given major histocompatibility complex class I (MHCI) molecule via the clonotypically expressed T cell receptor (TCR). The lineally expressed coreceptor CD8 interacts coordinately with MHCI at a distinct and largely invariant site to slow the TCR/peptide-MHCI (pMHCI) dissociation rate and enhance antigen sensitivity. However, this biological effect is not necessarily uniform, and theoretical models suggest that antigen sensitivity can be modulated in a differential manner by CD8. We used two intrinsically controlled systems to determine how the relationship between the TCR/pMHCI interaction and the pMHCI/CD8 interaction affects the functional sensitivity of antigen recognition. Our data show that modulation of the pMHCI/CD8 interaction can reorder the agonist hierarchy of peptide ligands across a spectrum of affinities for the TCR