Computing Activities at the Spanish Tier-1 and Tier-2s for the ATLAS experiment in the LHC Run 3 period and towards High Luminosity (HL-LHC)

The ATLAS Spanish Tier-1 and Tier-2s have more than 18 years of experience in the deployment and development of LHC computing components and their successful operation. The sites are actively participating in, and in some cases coordinating, R&D computing activities in the LHC Run 3 and developing the computing models needed in the HL-LHC period. In this contribution, we present details on the integration of some components, such as HPC computing resources to execute ATLAS simulation workflows; the development of new techniques to improve efficiency in a cost-effective way; and improvements in Data Organization, Management and Access through storage consolidations, the use of data caches, and improving experiment data catalogues, through contributions such as Event Index. The design and deployment of novel analysis facilities using GPUs together with CPUs and techniques like Machine Learning are also presented. ATLAS Tier-1 and Tier-2 sites in Spain, are, and will be, contributing to significant R&D in computing and evaluating different models for improving performance of computing and data storage capacity in the LHC High Luminosity era

The ATLAS EventIndex: a BigData catalogue for all ATLAS experiment events

The ATLAS EventIndex system comprises the catalogue of all events collected, processed or generated by the ATLAS experiment at the CERN LHC accelerator, and all associated software tools to collect, store and query this information. ATLAS records several billion particle interactions every year of operation, processes them for analysis and generates even larger simulated data samples; a global catalogue is needed to keep track of the location of each event record and be able to search and retrieve specific events for in-depth investigations. Each EventIndex record includes summary information on the event itself and the pointers to the files containing the full event. Most components of the EventIndex system are implemented using BigData open-source tools. This paper describes the architectural choices and their evolution in time, as well as the past, current and foreseen future implementations of all EventIndex components.Comment: 21 page

Deployment and Operation of the ATLAS EventIndex for LHC Run 3

The ATLAS Eventlndex is the global catalogue of all ATLAS real and simulated events. During the LHC long shutdown between Run 2 (20152018) and Run 3 (2022-2025) all its components were substantially revised and a new system was deployed for the start of Run 3 in Spring 2022. The new core storage system, based on HBase tables with a SQL interface provided by Phoenix, allows much faster data ingestion rates and scales much better than the old one to the data rates expected for the end of Run 3 and beyond. All user interfaces were also revised and a new command-line interface and web services were also deployed. The new system was initially populated with all existing data relative to Run 1 and Run 2 datasets, and then put online to receive Run 3 data in real time. After extensive testing, the old system, which ran in parallel to the new one for a few months, was finally switched off in October 2022. This paper describes the new system, the move of all existing data from the old to the new storage schemas and the operational experience gathered so far

Fat Oxidation, Fitness and Skeletal Muscle Expression of Oxidative/Lipid Metabolism Genes in South Asians: Implications for Insulin Resistance?

<p><b>Background:</b> South Asians are more insulin resistant than Europeans, which cannot be fully explained by differences in adiposity. We investigated whether differences in oxidative capacity and capacity for fatty acid utilisation in South Asians might contribute, using a range of whole-body and skeletal muscle measures.</p> <p><b>Methodology/Principal Findings:</b> Twenty men of South Asian ethnic origin and 20 age and BMI-matched men of white European descent underwent exercise and metabolic testing and provided a muscle biopsy to determine expression of oxidative and lipid metabolism genes and of insulin signalling proteins. In analyses adjusted for age, BMI, fat mass and physical activity, South Asians, compared to Europeans, exhibited; reduced insulin sensitivity by 26% (p = 0.010); lower VO2max (40.6±6.6 vs 52.4±5.7 ml.kg−1.min−1, p = 0.001); and reduced fat oxidation during submaximal exercise at the same relative (3.77±2.02 vs 6.55±2.60 mg.kg−1.min−1 at 55% VO2max, p = 0.013), and absolute (3.46±2.20 vs 6.00±1.93 mg.kg−1.min−1 at 25 ml O2.kg−1.min−1, p = 0.021), exercise intensities. South Asians exhibited significantly higher skeletal muscle gene expression of CPT1A and FASN and significantly lower skeletal muscle protein expression of PI3K and PKB Ser473 phosphorylation. Fat oxidation during submaximal exercise and VO2max both correlated significantly with insulin sensitivity index and PKB Ser473 phosphorylation, with VO2max or fat oxidation during exercise explaining 10–13% of the variance in insulin sensitivity index, independent of age, body composition and physical activity.</p> <p><b>Conclusions/Significance:</b> These data indicate that reduced oxidative capacity and capacity for fatty acid utilisation at the whole body level are key features of the insulin resistant phenotype observed in South Asians, but that this is not the consequence of reduced skeletal muscle expression of oxidative and lipid metabolism genes.</p&gt

A natural mutation in Pisum sativum L. (pea) alters starch assembly and improves glucose homeostasis in humans

Elevated postprandial glucose (PPG) is a significant risk factor for non-communicable diseases globally. Currently, there is a limited understanding of how starch structures within a carbohydrate-rich food matrix interact with the gut luminal environment to control PPG. Here, we use pea seeds (Pisum sativum) and pea flour, derived from two near-identical pea genotypes (BC1/19RR and BC1/19rr) differing primarily in the type of starch accumulated, to explore the contribution of starch structure, food matrix and intestinal environment to PPG. Using stable isotope 13C-labelled pea seeds, coupled with synchronous gastric, duodenal and plasma sampling in vivo, we demonstrate that maintenance of cell structure and changes in starch morphology are closely related to lower glucose availability in the small intestine, resulting in acutely lower PPG and promotion of changes in the gut bacterial composition associated with long-term metabolic health improvements

Forty years of carabid beetle research in Europe - from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation

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Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements