Packed Memory Arrays – Rewired

The physical memory layout of a tree-based index structure deteriorates over time as it sustains more updates; such that sequential scans on the physical level become non-sequential, and therefore slower. Packed Memory Arrays (PMAs) prevent this by managing all data in a sequential sparse array. PMAs have been studied mostly theoretically but suffer from practical problems, as we show in this paper. We study and fix these problems, resulting in an improved data structure: the Rewired Memory Array (RMA). We compare RMA with the main previous PMA implementations as well as state-of-the-art tree index structures and show on a wide variety of data and query distributions that RMA can reach competitive update and point lookup performance, while always providing superior scan performance – close to dense column scans

Extending SQL for computing shortest paths

Reachability and shortest paths are among two of the most common queries realized on graphs. While graph frameworks and property graph databases provide an extensive and convenient built-in support for these operations, it is still both clunky and inefficient to perform on standard SQL DBMSs. In this paper, we present an extension to the standard SQL language to compute both reachability predicates and many-to-many shortest path queries. We first describe a methodology to represent a directed graph starting from virtual table expressions. Second, we introduce a new type of operator to compute shortest

Precision luminosity measurements at LHCb

Measuring cross-sections at the LHC requires the luminosity to be determined accurately at each centre-of-mass energy $\sqrt{s}$. In this paper results are reported from the luminosity calibrations carried out at the LHC interaction point 8 with the LHCb detector for $\sqrt{s}$ = 2.76, 7 and 8 TeV (proton-proton collisions) and for $\sqrt{s_{NN}}$ = 5 TeV (proton-lead collisions). Both the "van der Meer scan" and "beam-gas imaging" luminosity calibration methods were employed. It is observed that the beam density profile cannot always be described by a function that is factorizable in the two transverse coordinates. The introduction of a two-dimensional description of the beams improves significantly the consistency of the results. For proton-proton interactions at $\sqrt{s}$ = 8 TeV a relative precision of the luminosity calibration of 1.47% is obtained using van der Meer scans and 1.43% using beam-gas imaging, resulting in a combined precision of 1.12%. Applying the calibration to the full data set determines the luminosity with a precision of 1.16%. This represents the most precise luminosity measurement achieved so far at a bunched-beam hadron collider.Comment: 100 pages, 57 figure

Measurement of the semileptonic CPCP asymmetry in B0−B‾0B^0-\overline{B}{}^0 mixing

The semileptonic $CP$ asymmetry in $B^0-\overline{B}{}^0$ mixing, $a_{\rm sl}^d$, is measured in proton-proton collision data, corresponding to an integrated luminosity of 3.0 fb$^{-1}$, recorded by the LHCb experiment. Semileptonic $B^0$ decays are reconstructed in the inclusive final states $D^-\mu^+$ and $D^{*-}\mu^+$, where the $D^-$ meson decays into the $K^+\pi^-\pi^-$ final state, and the $D^{*-}$ meson into the $\overline{D}{}^0(\rightarrow K^+\pi^-)\pi^-$ final state. The asymmetry between the numbers of $D^{(*)-}\mu^+$ and $D^{(*)+}\mu^-$ decays is measured as a function of the decay time of the $B^0$ mesons. The $CP$ asymmetry is measured to be $a_{\rm sl}^d = (-0.02 \pm 0.19 \pm 0.30)\%$, where the first uncertainty is statistical and the second systematic. This is the most precise measurement of $a_{\rm sl}^d$ to date and is consistent with the prediction from the Standard Model.Comment: 10 pages, 2 figure

Study of η − η′ mixing from measurement of B (s) 0 → J/ψη(′) decay rates

A study of B and B0 s meson decays into J/ψη and J/ψη0 final states is performed using a data set of proton-proton collisions at centre-of-mass energies of 7 and 8 TeV, collected by the LCHb experiment and corresponding to 3.0 fb−1 of integrated luminosity. The decay B0 → J/ψη0 is observed for the first time. The following ratios of branching fractions are measured: B(B0 → J/ψη0 ) B(B0 s → J/ψη0) = (2.28 ± 0.65 (stat) ± 0.10 (syst) ± 0.13 (fs/fd)) × 10−2 , B(B0 → J/ψη) B(B0 s → J/ψη) = (1.85 ± 0.61 (stat) ± 0.09 (syst) ± 0.11 (fs/fd)) × 10−2 , where the third uncertainty is related to the present knowledge of fs/fd, the ratio between the probabilities for a b quark to form a B0 s or a B0 meson. The branching fraction ratios are used to determine the parameters of η−η 0 meson mixing. In addition, the first evidence for the decay B0 s → ψ(2S)η 0 is reported, and the relative branching fraction is measured, B(B0 s → ψ(2S)η 0 ) B(B0 s → J/ψη0) = (38.7 ± 9.0 (stat) ± 1.3 (syst) ± 0.9(B)) × 10−2 , where the third uncertainty is due to the limited knowledge of the branching fractions of J/ψ and ψ(2S) mesons

Measurement of the inelastic pp cross-section at a centre-of-mass energy of √s = 7 TeV

The cross-section for inelastic proton-proton collisions, with at least one prompt long-lived charged particle of transverse momentum pT > 0.2GeV/c in the pseudorapidity range 2.0 > η > 4.5, is measured by the LHCb experiment at a centre-ofmass energy of √ s = 7 TeV. The cross-section in this kinematic range is determined to be σ acc inel = 55.0 ± 2.4 mb with an experimental uncertainty that is dominated by systematic contributions. Extrapolation to the full phase space, using Pythia 6, yields σinel = 66.9 ± 2.9 ± 4.4 mb, where the first uncertainty is experimental and the second is due to the extrapolation

Mortality and pulmonary complications in patients undergoing surgery with perioperative sars-cov-2 infection: An international cohort study

Background The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (740%) had emergency surgery and 280 (248%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (261%) patients. 30-day mortality was 238% (268 of 1128). Pulmonary complications occurred in 577 (512%) of 1128 patients; 30-day mortality in these patients was 380% (219 of 577), accounting for 817% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 175 [95% CI 128-240], p<00001), age 70 years or older versus younger than 70 years (230 [165-322], p<00001), American Society of Anesthesiologists grades 3-5 versus grades 1-2 (235 [157-353], p<00001), malignant versus benign or obstetric diagnosis (155 [101-239], p=0046), emergency versus elective surgery (167 [106-263], p=0026), and major versus minor surgery (152 [101-231], p=0047). Interpretation Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Global, regional, and national incidence and mortality for HIV, tuberculosis, and malaria during 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

BACKGROUND: The Millennium Declaration in 2000 brought special global attention to HIV, tuberculosis, and malaria through the formulation of Millennium Development Goal (MDG) 6. The Global Burden of Disease 2013 study provides a consistent and comprehensive approach to disease estimation for between 1990 and 2013, and an opportunity to assess whether accelerated progress has occured since the Millennium Declaration. METHODS: To estimate incidence and mortality for HIV, we used the UNAIDS Spectrum model appropriately modified based on a systematic review of available studies of mortality with and without antiretroviral therapy (ART). For concentrated epidemics, we calibrated Spectrum models to fit vital registration data corrected for misclassification of HIV deaths. In generalised epidemics, we minimised a loss function to select epidemic curves most consistent with prevalence data and demographic data for all-cause mortality. We analysed counterfactual scenarios for HIV to assess years of life saved through prevention of mother-to-child transmission (PMTCT) and ART. For tuberculosis, we analysed vital registration and verbal autopsy data to estimate mortality using cause of death ensemble modelling. We analysed data for corrected case-notifications, expert opinions on the case-detection rate, prevalence surveys, and estimated cause-specific mortality using Bayesian meta-regression to generate consistent trends in all parameters. We analysed malaria mortality and incidence using an updated cause of death database, a systematic analysis of verbal autopsy validation studies for malaria, and recent studies (2010-13) of incidence, drug resistance, and coverage of insecticide-treated bednets. FINDINGS: Globally in 2013, there were 1·8 million new HIV infections (95% uncertainty interval 1·7 million to 2·1 million), 29·2 million prevalent HIV cases (28·1 to 31·7), and 1·3 million HIV deaths (1·3 to 1·5). At the peak of the epidemic in 2005, HIV caused 1·7 million deaths (1·6 million to 1·9 million). Concentrated epidemics in Latin America and eastern Europe are substantially smaller than previously estimated. Through interventions including PMTCT and ART, 19·1 million life-years (16·6 million to 21·5 million) have been saved, 70·3% (65·4 to 76·1) in developing countries. From 2000 to 2011, the ratio of development assistance for health for HIV to years of life saved through intervention was US$4498 in developing countries. Including in HIV-positive individuals, all-form tuberculosis incidence was 7·5 million (7·4 million to 7·7 million), prevalence was 11·9 million (11·6 million to 12·2 million), and number of deaths was 1·4 million (1·3 million to 1·5 million) in 2013. In the same year and in only individuals who were HIV-negative, all-form tuberculosis incidence was 7·1 million (6·9 million to 7·3 million), prevalence was 11·2 million (10·8 million to 11·6 million), and number of deaths was 1·3 million (1·2 million to 1·4 million). Annualised rates of change (ARC) for incidence, prevalence, and death became negative after 2000. Tuberculosis in HIV-negative individuals disproportionately occurs in men and boys (versus women and girls); 64·0% of cases (63·6 to 64·3) and 64·7% of deaths (60·8 to 70·3). Globally, malaria cases and deaths grew rapidly from 1990 reaching a peak of 232 million cases (143 million to 387 million) in 2003 and 1·2 million deaths (1·1 million to 1·4 million) in 2004. Since 2004, child deaths from malaria in sub-Saharan Africa have decreased by 31·5% (15·7 to 44·1). Outside of Africa, malaria mortality has been steadily decreasing since 1990. INTERPRETATION: Our estimates of the number of people living with HIV are 18·7% smaller than UNAIDS's estimates in 2012. The number of people living with malaria is larger than estimated by WHO. The number of people living with HIV, tuberculosis, or malaria have all decreased since 2000. At the global level, upward trends for malaria and HIV deaths have been reversed and declines in tuberculosis deaths have accelerated. 101 countries (74 of which are developing) still have increasing HIV incidence. Substantial progress since the Millennium Declaration is an encouraging sign of the effect of global action. FUNDING: Bill & Melinda Gates Foundation

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States

Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks