PyCUDA and PyOpenCL: A Scripting-Based Approach to GPU Run-Time Code Generation

High-performance computing has recently seen a surge of interest in heterogeneous systems, with an emphasis on modern Graphics Processing Units (GPUs). These devices offer tremendous potential for performance and efficiency in important large-scale applications of computational science. However, exploiting this potential can be challenging, as one must adapt to the specialized and rapidly evolving computing environment currently exhibited by GPUs. One way of addressing this challenge is to embrace better techniques and develop tools tailored to their needs. This article presents one simple technique, GPU run-time code generation (RTCG), along with PyCUDA and PyOpenCL, two open-source toolkits that support this technique. In introducing PyCUDA and PyOpenCL, this article proposes the combination of a dynamic, high-level scripting language with the massive performance of a GPU as a compelling two-tiered computing platform, potentially offering significant performance and productivity advantages over conventional single-tier, static systems. The concept of RTCG is simple and easily implemented using existing, robust infrastructure. Nonetheless it is powerful enough to support (and encourage) the creation of custom application-specific tools by its users. The premise of the paper is illustrated by a wide range of examples where the technique has been applied with considerable success.Comment: Submitted to Parallel Computing, Elsevie

Investigating Variation in the Prevalence of Weathering in Faunal Assemblages in the UK: A Multivariate Statistical Approach

This article presents an exploratory multivariate statistical approach to gaining a more comprehensive understanding of variation in subaerial bone weathering in a British context. Weathering is among the most common taphonomic modifications and provides a crucial line of evidence for reconstructing the taphonomic trajectories of faunal assemblages and archaeological deposits. It provides clear evidence for prolonged subaerial exposure either before deposition in a context or because of later disturbance. In combination with other taphonomic indices such as gnawing, trampling, abrasion and fracture patterns, weathering can be used to reconstruct depositional histories and to investigate the structured treatment of different body parts or taxa in deposition. However, a broad range of factors affect the prevalence and severity of weathering, and therefore patterns can rarely be interpreted at face value. Many variables such as predepositional microenvironment cannot be traced archaeologically. Other contributory factors pertaining to the structural properties of elements and taxa can be discerned and must be taken into account in interpreting weathering signatures. However, disagreement exists regarding which variables are most important in mediating weathering. In addition for zooarchaeologists to interpret modification patterns, it is necessary for elements and taxa that are most likely to be affected by weathering to be defined. This is the case as deposits that are dominated by those classes of remains are likely to exhibit greater modification than those that are not, even if depositional histories were similar. Through a combination of classification tree and ordinal regression analysis, this article identifies which archaeologically recoverable variables explain the greatest variance in weathering and which anatomical elements and taxa are most likely to be affected in archaeological deposits in the UK

Defining new therapeutics using a more immunocompetent mouse model of antibody-enhanced dengue virus infection

With over 3.5 billion people at risk and approximately 390 million human infections per year, dengue virus (DENV) disease strains health care resources worldwide. Previously, we and others established models for DENV pathogenesis in mice that completely lack subunits of the receptors (Ifnar and Ifngr) for type I and type II interferon (IFN) signaling; however, the utility of these models is limited by the pleotropic effect of these cytokines on innate and adaptive immune system development and function. Here, we demonstrate that the specific deletion of Ifnar expression on subsets of murine myeloid cells (LysM Cre(+) Ifnar(flox/flox) [denoted as Ifnar(f/f) herein]) resulted in enhanced DENV replication in vivo. The administration of subneutralizing amounts of cross-reactive anti-DENV monoclonal antibodies to LysM Cre(+) Ifnar(f/f) mice prior to infection with DENV serotype 2 or 3 resulted in antibody-dependent enhancement (ADE) of infection with many of the characteristics associated with severe DENV disease in humans, including plasma leakage, hypercytokinemia, liver injury, hemoconcentration, and thrombocytopenia. Notably, the pathogenesis of severe DENV-2 or DENV-3 infection in LysM Cre(+) Ifnar(f/f) mice was blocked by pre- or postexposure administration of a bispecific dual-affinity retargeting molecule (DART) or an optimized RIG-I receptor agonist that stimulates innate immune responses. Our findings establish a more immunocompetent animal model of ADE of infection with multiple DENV serotypes in which disease is inhibited by treatment with broad-spectrum antibody derivatives or innate immune stimulatory agents

Global variations in pubertal growth spurts in adolescents living with perinatal HIV

Objective: To describe pubertal growth spurts among adolescents living with perinatally-acquired HIV (ALWPHIV) on antiretroviral therapy (ART)./ Design: Observational data collected from 1994–2015 in the CIPHER global cohort collaboration./ Methods: ALWPHIV who initiated ART age <10 years with ≥4 height measurements age ≥8 were included. Super Imposition by Translation And Rotation (SITAR) models, with parameters representing timing and intensity of the growth spurt, were used to describe growth, separately by sex. Associations between region, ART regimen, age, height-for-age (HAZ), and BMI-for-age z-scores (BMIz) at ART initiation (baseline) and age 10 years and SITAR parameters were explored./ Results: 4,723 ALWPHIV were included: 51% from East and Southern Africa (excluding Botswana and South Africa), 17% Botswana and South Africa, 6% West and Central Africa, 11% Europe and North America, 11% Asia-Pacific, and 4% Central, South America, and Caribbean. Growth spurts were later and least intense in sub-Saharan regions. In females, older baseline age and lower BMIz at baseline were associated with later and more intense growth spurts; lower HAZ was associated with later growth spurts. In males, older baseline age and lower HAZ were associated with later and less intense growth spurts; however, associations between baseline HAZ and timing varied by age. Lower HAZ and BMIz at 10 years were associated with later and less intense growth spurts in both sexes./ Conclusions: ALWPHIV who started ART at older ages or already stunted were more likely to have delayed pubertal growth spurts. Longer-term follow-up is important to understand the impact of delayed growth.

Lightning as a space-weather hazard: UK thunderstorm activity modulated by the passage of the heliospheric current sheet

Lightning flash rates, RL, are modulated by corotating interaction regions (CIRs) and the polarity of the heliospheric magnetic field (HMF) in near-Earth space. As the HMF polarity reverses at the heliospheric current sheet (HCS), typically within a CIR, these phenomena are likely related. In this study, RL is found to be significantly enhanced at the HCS and at 27 days prior/after. The strength of the enhancement depends on the polarity of the HMF reversal at the HCS. Near-Earth solar and galactic energetic particle fluxes are also ordered by HMF polarity, though the variations qualitatively differ from RL, with the main increase occurring prior to the HCS crossing. Thus, the CIR effect on lightning is either the result of compression/amplification of the HMF (and its subsequent interaction with the terrestrial system) or that energetic particle preconditioning of the Earth system prior to the HMF polarity change is central to solar wind lightning coupling mechanism

Interstellar Turbulence II: Implications and Effects

Interstellar turbulence has implications for the dispersal and mixing of the elements, cloud chemistry, cosmic ray scattering, and radio wave propagation through the ionized medium. This review discusses the observations and theory of these effects. Metallicity fluctuations are summarized, and the theory of turbulent transport of passive tracers is reviewed. Modeling methods, turbulent concentration of dust grains, and the turbulent washout of radial abundance gradients are discussed. Interstellar chemistry is affected by turbulent transport of various species between environments with different physical properties and by turbulent heating in shocks, vortical dissipation regions, and local regions of enhanced ambipolar diffusion. Cosmic rays are scattered and accelerated in turbulent magnetic waves and shocks, and they generate turbulence on the scale of their gyroradii. Radio wave scintillation is an important diagnostic for small scale turbulence in the ionized medium, giving information about the power spectrum and amplitude of fluctuations. The theory of diffraction and refraction is reviewed, as are the main observations and scintillation regions.Comment: 46 pages, 2 figures, submitted to Annual Reviews of Astronomy and Astrophysic

Evaluation of the ACS NSQIP Surgical Risk Calculator in Elderly Patients Undergoing Hepatectomy for Hepatocellular Carcinoma

Background: The American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) surgical risk calculator (SRC) aims to help predict patient-specific risk for morbidity and mortality. The performance of the SRC among an elderly population undergoing curative-intent hepatectomy for hepatocellular carcinoma (HCC) remains unknown. Methods: Patients > 70 years of age who underwent hepatectomy for HCC between 1998 and 2017 were identified using a multi-institutional international database. To estimate the performance of SRC, 12 observed postoperative outcomes were compared with median SRC-predicted risk, and C-statistics and Brier scores were calculated. Results: Among 500 patients, median age was 75 years (IQR 72-78). Most patients (n = 324, 64.8%) underwent a minor hepatectomy, while 35.2% underwent a major hepatectomy. The observed incidence of venous thromboembolism (VTE) (3.2%) and renal failure (RF) (4.4%) exceeded the median predicted risk (VTE, 1.8%; IQR 1.5-3.1 and RF, 1.0%; IQR 0.5-2.0). In contrast, the observed incidence of 30-day readmission (7.0%) and non-home discharge (2.5%) was lower than median-predicted risk (30-day readmission, 9.4%; IQR 7.4-12.8 and non-home discharge, 5.7%; IQR 3.3-11.7). Only 57.8% and 71.2% of patients who experienced readmission (C-statistic, 0.578; 95%CI 0.468-0.688) or mortality (C-statistic, 0.712; 95%CI 0.508-0.917) were correctly identified by the model. Conclusion: Among elderly patients undergoing hepatectomy for HCC, the SRC underestimated the risk of complications such as VTE and RF, while being no better than chance in estimating the risk of readmission. The ACS SRC has limited clinical applicability in estimating perioperative risk among elderly patients being considered for hepatic resection of HCC.info:eu-repo/semantics/publishedVersio