SmartTrack: Efficient Predictive Race Detection

Widely used data race detectors, including the state-of-the-art FastTrack algorithm, incur performance costs that are acceptable for regular in-house testing, but miss races detectable from the analyzed execution. Predictive analyses detect more data races in an analyzed execution than FastTrack detects, but at significantly higher performance cost. This paper presents SmartTrack, an algorithm that optimizes predictive race detection analyses, including two analyses from prior work and a new analysis introduced in this paper. SmartTrack's algorithm incorporates two main optimizations: (1) epoch and ownership optimizations from prior work, applied to predictive analysis for the first time; and (2) novel conflicting critical section optimizations introduced by this paper. Our evaluation shows that SmartTrack achieves performance competitive with FastTrack-a qualitative improvement in the state of the art for data race detection.Comment: Extended arXiv version of PLDI 2020 paper (adds Appendices A-E) #228 SmartTrack: Efficient Predictive Race Detectio

Do anemia treatments improve quality of life and physical function in patients with myelodysplastic syndromes (MDS)? A systematic review

Anemia is common in Myelodysplastic Syndromes (MDS). Different anemia treatments have been tested in clinical studies, but the full impact on patients' health-related quality of life (HRQoL) and physical function is unknown. The main aim of this review was to assess whether improvements in anemia are associated with changes in HRQoL/physical function. Twenty-six full-text publications were identified, enrolling 2211 patients: nine randomized trials (RCTs), fourteen non-randomized studies of interventions and three cross-sectional studies. Interventions included: growth factors/erythropoiesis-stimulating agents (n = 14), red cell transfusion (n = 9), erythroid maturation agents (n = 1), or a combination (n = 2). Five RCTs reported no changes in HRQoL despite erythroid response to the intervention, raising the question of whether anemia treatment alone can effectively improve HRQoL. Many studies were considered at high risk of bias for assessing HRQoL. There is a pressing need for future clinical trials to better define the nature of the relationship between anemia and HRQoL/functional outcomes

The long-term effects of invasive signal crayfish (Pacifastacus leniusculus) on instream macroinvertebrate communities

Non-native species represent a significant threat to indigenous biodiversity and ecosystem functioning worldwide. It is widely acknowledged that invasive crayfish species may be instrumental in modifying benthic invertebrate community structure, but there is limited knowledge regarding the temporal and spatial extent of these effects within lotic ecosystems. This study investigates the long term changes to benthic macroinvertebrate community composition following the invasion of signal crayfish, Pacifastacus leniusculus, into English rivers. Data from long-term monitoring sites on 7 rivers invaded by crayfish and 7 rivers where signal crayfish were absent throughout the record (control sites) were used to examine how invertebrate community composition and populations of individual taxa changed as a result of invasion. Following the detection of non-native crayfish, significant shifts in invertebrate community composition were observed at invaded sites compared to control sites. This pattern was strongest during autumn months but was also evident during spring surveys. The observed shifts in community composition following invasion were associated with reductions in the occurrence of ubiquitous Hirudinea species (Glossiphonia complanata and Erpobdella octoculata), Gastropoda (Radix spp.), Ephemeroptera (Caenis spp.), and Trichoptera (Hydropsyche spp.); although variations in specific taxa affected were evident between regions and seasons. Changes in community structure were persistent over time with no evidence of recovery, suggesting that crayfish invasions represent significant perturbations leading to permanent changes in benthic communities. The results provide fundamental knowledge regarding non-native crayfish invasions of lotic ecosystems required for the development of future management strategies

Exoplanetary Monte Carlo radiative transfer with correlated-k - I. Benchmarking transit and emission observables

G.K.H. Lee acknowledges support from the University of Oxford and CSH Bern through the Bernoulli fellowship. G.K.H Lee acknowledges funding from the European community through the ERC project EXOCONDENSE (740963). The participants of the OWL 2018 summer program are thanked for numerous discussions and encouragement on the development of the model. J. Taylor is a Penrose Scholar and would like to thank the Oxford Physics Endowment for Graduates (OXPEG) for funding this research. J-L Baudino acknowledges the support of the UK Science and Technology Facilities Council.Current observational data of exoplanets are providing increasing detail of their 3D atmospheric structures. As characterization efforts expand in scope, the need to develop consistent 3D radiative-transfer methods becomes more pertinent as the complex atmospheric properties of exoplanets are required to be modelled together consistently. We aim to compare the transmission and emission spectra results of a 3D Monte Carlo radiative transfer (MCRT) model to contemporary radiative-transfer suites. We perform several benchmarking tests of an MCRT code, Cloudy Monte Carlo Radiative Transfer (CMCRT), to transmission and emission spectra model output. We add flexibility to the model through the use of k-distribution tables as input opacities. We present a hybrid MCRT and ray tracing methodology for the calculation of transmission spectra with a multiple scattering component. CMCRT compares well to the transmission spectra benchmarks at the 10s of ppm level. Emission spectra benchmarks are consistent to within 10 per cent of the 1D models. We suggest that differences in the benchmark results are likely caused by geometric effects between plane-parallel and spherical models. In a practical application, we post-process a cloudy 3D HD 189733b GCM model and compare to available observational data. Our results suggest the core methodology and algorithms of CMCRT produce consistent results to contemporary radiative transfer suites. 3D MCRT methods are highly suitable for detailed post-processing of cloudy and non-cloudy 1D and 3D exoplanet atmosphere simulations in instances where atmospheric inhomogeneities, significant limb effects/geometry or multiple scattering components are important considerations.Publisher PDFPeer reviewe

First-year Sloan Digital Sky Survey-II (SDSS-II) Supernova Results: Hubble Diagram and Cosmological Parameters

We present measurements of the Hubble diagram for 103 Type Ia supernovae (SNe) with redshifts 0.04 < z < 0.42, discovered during the first season (Fall 2005) of the Sloan Digital Sky Survey-II (SDSS-II) Supernova Survey. These data fill in the redshift "desert" between low- and high-redshift SN Ia surveys. We combine the SDSS-II measurements with new distance estimates for published SN data from the ESSENCE survey, the Supernova Legacy Survey, the Hubble Space Telescope, and a compilation of nearby SN Ia measurements. Combining the SN Hubble diagram with measurements of Baryon Acoustic Oscillations from the SDSS Luminous Red Galaxy sample and with CMB temperature anisotropy measurements from WMAP, we estimate the cosmological parameters w and Omega_M, assuming a spatially flat cosmological model (FwCDM) with constant dark energy equation of state parameter, w. For the FwCDM model and the combined sample of 288 SNe Ia, we find w = -0.76 +- 0.07(stat) +- 0.11(syst), Omega_M = 0.306 +- 0.019(stat) +- 0.023(syst) using MLCS2k2 and w = -0.96 +- 0.06(stat) +- 0.12(syst), Omega_M = 0.265 +- 0.016(stat) +- 0.025(syst) using the SALT-II fitter. We trace the discrepancy between these results to a difference in the rest-frame UV model combined with a different luminosity correction from color variations; these differences mostly affect the distance estimates for the SNLS and HST supernovae. We present detailed discussions of systematic errors for both light-curve methods and find that they both show data-model discrepancies in rest-frame $U$-band. For the SALT-II approach, we also see strong evidence for redshift-dependence of the color-luminosity parameter (beta). Restricting the analysis to the 136 SNe Ia in the Nearby+SDSS-II samples, we find much better agreement between the two analysis methods but with larger uncertainties.Comment: Accepted for publication by ApJ

Study Protocol for the COVID-19 Pandemic Adjustment Survey (CPAS): A Longitudinal Study of Australian Parents of a Child 0–18 Years

Background: The COVID-19 pandemic presents significant risks to the mental health and wellbeing of Australian families. Employment and economic uncertainty, chronic stress, anxiety, and social isolation are likely to have negative impacts on parent mental health, couple and family relationships, as well as child health and development. Objective: This study aims to: (1) provide timely information on the mental health impacts of the emerging COVID-19 crisis in a close to representative sample of Australian parents and children (0–18 years), (2) identify adults and families most at risk of poor mental health outcomes, and (3) identify factors to target through clinical and public health intervention to reduce risk. Specifically, this study will investigate the extent to which the COVID-19 pandemic is associated with increased risk for parents’ mental health, lower well-being, loneliness, and alcohol use; parent-parent and parent-child relationships (both verbal and physical); and child and adolescent mental health problems. Methods: The study aims to recruit a close to representative sample of at least 2,000 adults aged 18 years and over living in Australia who are parents of a child 0–4 years (early childhood, N = 400), 5–12 years (primary school N = 800), and 13–18 years (secondary school, N = 800). The design will be a longitudinal cohort study using an online recruitment methodology. Participants will be invited to complete an online baseline self-report survey (20 min) followed by a series of shorter online surveys (10 min) scheduled every 2 weeks for the duration of the COVID-19 pandemic (i.e., estimated to be 14 surveys over 6 months). Results: The study will employ post stratification weights to address differences between the final sample and the national population in geographic communities across Australia. Associations will be analyzed using multilevel modeling with time-variant and time-invariant predictors of change in trajectory over the testing period. Conclusions: This study will provide timely information on the mental health impacts of the COVID-19 crisis on parents and children in Australia; identify communities, parents, families, and children most at risk of poor outcomes; and identify potential factors to address in clinical and public health interventions to reduce risk

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

Quantification of measurable residual disease using duplex sequencing in adults with acute myeloid leukemia

The presence of measurable residual disease (MRD) is strongly associated with treatment outcomes in acute myeloid leukemia (AML). Despite the correlation with clinical outcomes, MRD assessment has yet to be standardized or routinely incorporated into clinical trials and discrepancies have been observed between different techniques for MRD assessment. In 62 patients with AML, aged 18-60 years, in first complete remission after intensive induction therapy on the randomized phase III SWOG-S0106 clinical trial (clinicaltrials gov. Identifier: NCT00085709), MRD detection by centralized, high-quality multiparametric flow cytometry was compared with a 29-gene panel utilizing duplex sequencing (DS), an ultrasensitive next-generation sequencing method that generates double-stranded consensus sequences to reduce false positive errors. MRD as defined by DS was observed in 22 (35%) patients and was strongly associated with higher rates of relapse (68% vs. 13%; hazard ratio [HR] =8.8; 95% confidence interval [CI]: 3.2-24.5; P<0.001) and decreased survival (32% vs. 82%; HR=5.6; 95% CI: 2.3-13.8; P<0.001) at 5 years. DS MRD strongly outperformed multiparametric flow cytometry MRD, which was observed in ten (16%) patients and marginally associated with higher rates of relapse (50% vs. 30%; HR=2.4; 95% CI: 0.9-6.7; P=0.087) and decreased survival (40% vs. 68%; HR=2.5; 95% CI: 1.0-6.3; P=0.059) at 5 years. Furthermore, the prognostic significance of DS MRD status at the time of remission for subsequent relapse was similar on both randomized arms of the trial. These findings suggest that next-generation sequencing-based AML MRD testing is a powerful tool that could be developed for use in patient management and for early anti-leukemic treatment assessment in clinical trials

The state of the Martian climate

60°N was +2.0°C, relative to the 1981–2010 average value (Fig. 5.1). This marks a new high for the record. The average annual surface air temperature (SAT) anomaly for 2016 for land stations north of starting in 1900, and is a significant increase over the previous highest value of +1.2°C, which was observed in 2007, 2011, and 2015. Average global annual temperatures also showed record values in 2015 and 2016. Currently, the Arctic is warming at more than twice the rate of lower latitudes

Priorities for synthesis research in ecology and environmental science

ACKNOWLEDGMENTS We thank the National Science Foundation grant #1940692 for financial support for this workshop, and the National Center for Ecological Analysis and Synthesis (NCEAS) and its staff for logistical support.Peer reviewedPublisher PD