Matrix-free GPU implementation of a preconditioned conjugate gradient solver for anisotropic elliptic PDEs

Many problems in geophysical and atmospheric modelling require the fast solution of elliptic partial differential equations (PDEs) in "flat" three dimensional geometries. In particular, an anisotropic elliptic PDE for the pressure correction has to be solved at every time step in the dynamical core of many numerical weather prediction models, and equations of a very similar structure arise in global ocean models, subsurface flow simulations and gas and oil reservoir modelling. The elliptic solve is often the bottleneck of the forecast, and an algorithmically optimal method has to be used and implemented efficiently. Graphics Processing Units have been shown to be highly efficient for a wide range of applications in scientific computing, and recently iterative solvers have been parallelised on these architectures. We describe the GPU implementation and optimisation of a Preconditioned Conjugate Gradient (PCG) algorithm for the solution of a three dimensional anisotropic elliptic PDE for the pressure correction in NWP. Our implementation exploits the strong vertical anisotropy of the elliptic operator in the construction of a suitable preconditioner. As the algorithm is memory bound, performance can be improved significantly by reducing the amount of global memory access. We achieve this by using a matrix-free implementation which does not require explicit storage of the matrix and instead recalculates the local stencil. Global memory access can also be reduced by rewriting the algorithm using loop fusion and we show that this further reduces the runtime on the GPU. We demonstrate the performance of our matrix-free GPU code by comparing it to a sequential CPU implementation and to a matrix-explicit GPU code which uses existing libraries. The absolute performance of the algorithm for different problem sizes is quantified in terms of floating point throughput and global memory bandwidth.Comment: 18 pages, 7 figure

Assessing global-scale organic matter reactivity patterns in marine sediments using a lognormal reactive continuum model

Organic matter (OM) degradation in marine sediments is largely controlled by its reactivity and profoundly affects the global carbon cycle. Yet, there is currently no general framework that can constrain OM reactivity on a global scale. In this study, we propose a reactive continuum model based on a lognormal distribution (l-RCM), where OM reactivity is fully described by parameters μ (the mean reactivity of the initial OM bulk mixture) and σ (the variance of OM components around the mean reactivity). We use the l-RCM to inversely determine μ and σ at 123 sites across the global ocean. The results show that the apparent OM reactivity (〈k〉=μ⋅exp⁡(σ2/2)) decreases with decreasing sedimentation rate (ω) and that OM reactivity is more than 3 orders of magnitude higher in shelf than in abyssal regions. Despite the general global trends, higher than expected OM reactivity is observed in certain ocean regions characterized by great water depth or pronounced oxygen minimum zones, such as the eastern–western coastal equatorial Pacific and the Arabian Sea, emphasizing the complex control of the depositional environment (e.g., OM flux, oxygen content in the water column) on benthic OM reactivity. Notably, the l-RCM can also highlight the variability in OM reactivity in these regions. Based on inverse modeling results in our dataset, we establish the significant statistical relationships between 〈k〉 and ω and further map the global OM reactivity distribution. The novelty of this study lies in its unifying view but also in contributing a new framework that allows predicting OM reactivity in data-poor areas based on readily available (or more easily obtainable) information. Such a framework is currently lacking and limits our abilities to constrain OM reactivity in global biogeochemical or Earth system models

The role of anaerobic methane oxidation on the carbonate authigenesis in sediments of the subtropical Beibu Gulf, South China Sea: A reactive–transport modelling approach

The formation and burial of authigenic carbonate in marine sediment significantly affect the sedimentary carbon cycle and its isotopic mass balance in geological history. Anaerobic oxidation of methane (AOM) is the primary driver of authigenic carbonate precipitation within the sulfate-methane transition zone (SMTZ). Quantitative estimations of the role of AOM on the authigenic carbonate precipitation and its carbon isotope under non-steady-state processes (e.g., changes in methane fluxes at the bottom sediment, sedimentation rates or organic fluxes in the surface sediment), however, are still limited. In this study, we use geochemical data from porewater (e.g., the concentration of sulfate, calcium, magnesium, strontium, dissolved inorganic carbon, total alkalinity) and solid sediment (e.g., organic matter content, and carbonate content) in different depositional environments of the subtropical Beibu Gulf, South China Sea, combined with a diagenetic reactive-transport modelling approach, to estimate the mineralogy of authigenic carbonate, the relationship between AOM and authigenic carbonate precipitation, and the impact of AOM rate on carbon isotope of sediment carbonate (δ13CCar). The results show that high-Mg carbonates (high-Mg calcite and dolomite) are the main type of authigenic carbonate (∼80%) formed in the methane-bearing sediments, leading to higher porewater Sr2+/Ca2+ (>0.02) and Mg2+/Ca2+ (>20) within the SMTZ. Our modelling analysis highlights that the non-steady-state induced by increased methane flux from the underlying sediments can significantly accelerate the authigenic carbonates formation within the SMTZ. Using parametric sensitivity analysis, we observed that even a 1% increase in the authigenic carbonate fraction of sediment carbonates results in significant changes in δ13CCar within the SMTZ (from −1‰ to −2‰), mainly due to lighter carbon isotopes produced by more intensive AOM processes. Noteworthily, the terrestrial-to-marine transition was identified by the sediment and porewater geochemical profiles at site SO-8. Although lower authigenic carbonate precipitation occurs in terrestrial sedimentary environments, the proportion of authigenic carbonate in terrestrial environments (11%) is much higher than that in marine environments (1%), resulting in carbon isotopes of carbonate in terrestrial sediments becoming more negative (−5‰)

Periodontal health: A national cross‐sectional study of knowledge, attitudes and practices for the public oral health strategy in China

Aim To assess the status of periodontal health knowledge, attitudes and practices (KAP) among Chinese adults. Materials and Methods A cross‐sectional study was conducted in a nationally representative sample of adults (N = 50,991) aged 20 years or older from ten provinces, autonomous regions, and municipalities. Percentages of Chinese adults with correct periodontal knowledge, positive periodontal attitudes, and practices were estimated. Multiple logistic regression analyses were used to examine the related factors. Results Less than 20% of Chinese adults were knowledgeable about periodontal disease. Very few (2.6%) of Chinese adults use dental floss ≥once a day and undergo scaling ≥once a year and visit a dentist (6.4%) in the case of gingival bleeding. Periodontal health KAP was associated with gender, age, body mass index, marital status, place of residence, education level, income, smoking status, and history of periodontal disease. Conclusions Periodontal health KAP are generally poor among the Chinese adult population. Community‐based health strategies to improve periodontal health KAP need to be implemented. Increasing knowledge of periodontal disease, the cultivation of correct practices in response to gingival bleeding, and the development of good habits concerning the use of dental floss and regular scaling should be public oral health priorities

The Effect of Mobility on the Spread of COVID-19 in Light of Regional Differences in the European Union

The COVID-19 pandemic has spread rapidly all over the world, affecting many countries to varying degrees. In this study, an in-depth analysis of the factors influencing the spread of COVID-19 is offered mainly through big data in the European Union (EU) context. In doing so, the data of the first wave of the pandemic are assessed. Afterward, we evaluate the impacts of the COVID-19 spread in specific countries and regions. Based on the existing literature, mobility is recognized as a significant direct factor affecting disease transmission. The same applies to the case of COVID-19. However, compared with the analysis of mobility itself, this paper explores more profound reasons that affect mobility, ranging from policy and economy to geographical and transportation factors. Specifically, this paper studies nine EU countries based on their population density and the degree of impact of the epidemic in the first six months (February to July 2020) of the pandemic. Our study aims to illustrate how policies, economies, and geographical locations (including transportation factors) directly or indirectly affect the spread of the novel coronavirus by applying the SEIR model to analyze all selected countries’ big data. The key findings of this research are: (1) the timeliness of relevant policies and the effectiveness of government implementation indirectly limit the spread of the epidemic by reducing population mobility; (2) a better medical level would contribute to detect, isolate, and treat patients, and help control the epidemic; and (3) the large land borders and developed transportation between countries exacerbate the spread of the COVID-19. The paper contributes to ongoing research on COVID-19 by addressing the above points

Associations between urinary paraben levels and obesity of 10-year-old children

BackgroundParabens, a widely used class of preservatives, are suspected to be potential obesogens as emerging endocrine disrupting chemicals with reproductive and developmental toxicity. ObjectiveTo analyze five urinary parabens (PBs) and estimate the associations of exposure to PBs with adiposity measures in 10-year-old school-age children. MethodsA total of 471 school-age children aged 10 years from the Sheyang Mini Birth Cohort were enrolled in this study. A questionnaire survey was conducted to collect socio-demographic information, physical activity, and dietary intake. Weight, height, and waist circumference of children were measured, and age- and sex-adjusted body mass index (BMI-Z score) was calculated. Spot urine samples were collected during the follow-up visits. Urinary concentrations of five PBs including methyl-paraben (MeP), ethyl-paraben (EtP), propyl-paraben (PrP), butyl-paraben (BuP), and benzyl-paraben (BzP) were detected by gas chromatography-tandem mass spectrometry (GC-MS/MS). Generalized linear models (GLMs) and Bayesian kernel machine regression (BKMR) models were applied to estimate associations of individual/overall urinary PBs concentrations with BMI Z-score and waist circumference. ResultsThe positive rates of selected five urinary PBs were in the range from 78.98% to 98.94%. The urinary PBs concentrations (geometric mean) were in the range of 0.31-5.43 μg·L−1. The children's BMI Z-score and waist circumference (mean ± standard deviation) were (0.56±1.40) and (67.62±10.07) cm respectively. The GLMs results showed that the urinary BzP concentration was negatively associated with waist circumference (b=−0.08, 95%CI: −0.14, −0.02; P=0.01). In sex-stratified analysis, the urinary concentration of BzP was negatively associated with BMI-Z score (b=−0.59, 95%CI: −0.88, −0.30; P<0.001) and waist circumference (b=−0.80, 95%CI: −1.23, −0.37; P<0.001) in boys, but not in girls. The BKMR results also found significant negative correlations of urinary BzP concentrations with BMI-Z score and waist circumference, which were consistent with the GLM results. ConclusionThe selected 10-year-old children are extensively exposed to PBs in the study area. Furthermore, childhood PBs exposure may have potential impacts on childhood adiposity measures with sex-specific effects

Living Bacterial Sacrificial Porogens to Engineer Decellularized Porous Scaffolds

Decellularization and cellularization of organs have emerged as disruptive methods in tissue engineering and regenerative medicine. Porous hydrogel scaffolds have widespread applications in tissue engineering, regenerative medicine and drug discovery as viable tissue mimics. However, the existing hydrogel fabrication techniques suffer from limited control over pore interconnectivity, density and size, which leads to inefficient nutrient and oxygen transport to cells embedded in the scaffolds. Here, we demonstrated an innovative approach to develop a new platform for tissue engineered constructs using live bacteria as sacrificial porogens. E.coli were patterned and cultured in an interconnected three-dimensional (3D) hydrogel network. The growing bacteria created interconnected micropores and microchannels. Then, the scafold was decellularized, and bacteria were eliminated from the scaffold through lysing and washing steps. This 3D porous network method combined with bioprinting has the potential to be broadly applicable and compatible with tissue specific applications allowing seeding of stem cells and other cell types

Qwen Technical Report

Large language models (LLMs) have revolutionized the field of artificial intelligence, enabling natural language processing tasks that were previously thought to be exclusive to humans. In this work, we introduce Qwen, the first installment of our large language model series. Qwen is a comprehensive language model series that encompasses distinct models with varying parameter counts. It includes Qwen, the base pretrained language models, and Qwen-Chat, the chat models finetuned with human alignment techniques. The base language models consistently demonstrate superior performance across a multitude of downstream tasks, and the chat models, particularly those trained using Reinforcement Learning from Human Feedback (RLHF), are highly competitive. The chat models possess advanced tool-use and planning capabilities for creating agent applications, showcasing impressive performance even when compared to bigger models on complex tasks like utilizing a code interpreter. Furthermore, we have developed coding-specialized models, Code-Qwen and Code-Qwen-Chat, as well as mathematics-focused models, Math-Qwen-Chat, which are built upon base language models. These models demonstrate significantly improved performance in comparison with open-source models, and slightly fall behind the proprietary models.Comment: 59 pages, 5 figure

Report from Working Group 3: Beyond the standard model physics at the HL-LHC and HE-LHC

This is the third out of five chapters of the final report [1] of the Workshop on Physics at HL-LHC, and perspectives on HE-LHC [2]. It is devoted to the study of the potential, in the search for Beyond the Standard Model (BSM) physics, of the High Luminosity (HL) phase of the LHC, defined as $3$ ab$^{-1}$ of data taken at a centre-of-mass energy of 14 TeV, and of a possible future upgrade, the High Energy (HE) LHC, defined as $15$ ab$^{-1}$ of data at a centre-of-mass energy of 27 TeV. We consider a large variety of new physics models, both in a simplified model fashion and in a more model-dependent one. A long list of contributions from the theory and experimental (ATLAS, CMS, LHCb) communities have been collected and merged together to give a complete, wide, and consistent view of future prospects for BSM physics at the considered colliders. On top of the usual standard candles, such as supersymmetric simplified models and resonances, considered for the evaluation of future collider potentials, this report contains results on dark matter and dark sectors, long lived particles, leptoquarks, sterile neutrinos, axion-like particles, heavy scalars, vector-like quarks, and more. Particular attention is placed, especially in the study of the HL-LHC prospects, to the detector upgrades, the assessment of the future systematic uncertainties, and new experimental techniques. The general conclusion is that the HL-LHC, on top of allowing to extend the present LHC mass and coupling reach by $20-50\%$ on most new physics scenarios, will also be able to constrain, and potentially discover, new physics that is presently unconstrained. Moreover, compared to the HL-LHC, the reach in most observables will, generally more than double at the HE-LHC, which may represent a good candidate future facility for a final test of TeV-scale new physics