Information and treatment of unknown correlations in the combination of measurements using the BLUE method

We discuss the effect of large positive correlations in the combinations of several measurements of a single physical quantity using the Best Linear Unbiased Estimate (BLUE) method. We suggest a new approach for comparing the relative weights of the different measurements in their contributions to the combined knowledge about the unknown parameter, using the well-established concept of Fisher information. We argue, in particular, that one We discuss the effect of large positive correlations in the combinations of several measurements of a single physical quantity using the Best Linear Unbiased Estimate (BLUE) method. We suggest a new approach for comparing the relative weights of the different measurements in their contributions to the combined knowledge about the unknown parameter, using the well-established concept of Fisher information. We argue, in particular, that one contribution to information comes from the collective interplay of the measurements through their correlations and that this contribution cannot be attributed to any of the individual measurements alone. We show that negative coefficients in the BLUE weighted average invariably indicate the presence of a regime of high correlations, where the effect of further increasing some of these correlations is that of reducing the error on the combined estimate. In these regimes, we stress that assuming fully correlated systematic uncertainties is not a truly conservative choice, and that the correlations provided as input to BLUE combinations need to be assessed with extreme care instead. In situations where the precise evaluation of these correlations is impractical, or even impossible, we provide tools to help experimental physicists perform more conservative combinations

Integrating LHCb workflows on HPC resources: status and strategies

High Performance Computing (HPC) supercomputers are expected to play an increasingly important role in HEP computing in the coming years. While HPC resources are not necessarily the optimal fit for HEP workflows, computing time at HPC centers on an opportunistic basis has already been available to the LHC experiments for some time, and it is also possible that part of the pledged computing resources will be offered as CPU time allocations at HPC centers in the future. The integration of the experiment workflows to make the most efficient use of HPC resources is therefore essential. This paper describes the work that has been necessary to integrate LHCb workflows at a specific HPC site, the Marconi-A2 system at CINECA in Italy, where LHCb benefited from a joint PRACE (Partnership for Advanced Computing in Europe) allocation with the other Large Hadron Collider (LHC) experiments. This has required addressing two types of challenges: on the software application workloads, for optimising their performance on a many-core hardware architecture that differs significantly from those traditionally used in WLCG (Worldwide LHC Computing Grid), by reducing memory footprint using a multi-process approach; and in the distributed computing area, for submitting these workloads using more than one logical processor per job, which had never been done yet in LHCb.Comment: 9 pages, submitted to CHEP2019 proceedings in EPJ Web of Conference

Design and engineering of a simplified workflow execution for the MG5aMC event generator on GPUs and vector CPUs

Physics event generators are essential components of the data analysis software chain of high energy physics experiments, and important consumers of their CPU resources. Improving the software performance of these packages on modern hardware architectures, such as those deployed at HPC centers, is essential in view of the upcoming HL-LHC physics programme. In this paper, we describe an ongoing activity to reengineer the Madgraph5_aMC@NLO physics event generator, primarily to port it and allow its efficient execution on GPUs, but also to modernize it and optimize its performance on vector CPUs. We describe the motivation, engineering process and software architecture design of our developments, as well as the current challenges and future directions for this project. This paper is based on our submission to vCHEP2021 in March 2021,complemented with a few preliminary results that we presented during the conference. Further details and updated results will be given in later publications.Comment: 17 pages, 6 figures, submitted to vCHEP2021 proceedings in EPJ Web of Conferences; minor changes to address comments from the EPJWOC reviewe

DNA profiling, telomere analysis and antioxidant properties as tools for monitoring ex situ seed longevity

Background and Aims The germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across species and populations from different environments and studies related to the eco-physiological processes underlying such variations are still limited in their depth. The aim of the present work was the identification of reliable molecular markers that might help monitoring seed deterioration. Methods Dry seeds were subjected to artificial aging and collected at different time points for molecular/biochemical analyses. DNA damage was measured using the RAPD (Random Amplified Polymorphic DNA) approach while the seed antioxidant profile was obtained using both the DPPH (1,1-diphenyl, 2-picrylhydrazyl) assay and the Folin Ciocalteu reagent method. Electron Paramagnetic Resonance (EPR) provided profiles of free radicals. Quantitative RealTime-Polymerase Chain Reaction (QRT-PCR) was used to assess the expression profiles of the antioxidant genes MT2 (Type 2 Metallothionein) and SOD (Superoxide Dismutase). A modified QRT-PCR protocol was used to determine telomere length. Key Results The RAPD profiles highlighted different capacities of the two Silene species to overcome DNA damage induced by artificial aging. The antioxidant profiles of dry and rehydrated seeds revealed that the high-altitude taxon Silene acaulis was characterised by a lower antioxidant specific activity. Significant up-regulation of the MT2 and SOD genes was observed only in the rehydrated seeds of the low-altitude species. Rehydration resulted in telomere lengthening in both Silene species. Conclusions Different seed viability markers have been selected for plant species showing inherent variation of seed longevity. RAPD analysis, quantification of redox activity of non enzymatic antioxidant compounds and gene expression profiling provide deeper insights to study seed viability during storage. Telomere lengthening is a promising tool to discriminate between short- and long-lived species

Speeding up Madgraph5 aMC@NLO through CPU vectorization and GPU offloading: towards a first alpha release

The matrix element (ME) calculation in any Monte Carlo physics event generator is an ideal fit for implementing data parallelism with lockstep processing on GPUs and vector CPUs. For complex physics processes where the ME calculation is the computational bottleneck of event generation workflows, this can lead to large overall speedups by efficiently exploiting these hardware architectures, which are now largely underutilized in HEP. In this paper, we present the status of our work on the reengineering of the Madgraph5_aMC@NLO event generator at the time of the ACAT2022 conference. The progress achieved since our previous publication in the ICHEP2022 proceedings is discussed, for our implementations of the ME calculations in vectorized C++, in CUDA and in the SYCL framework, as well as in their integration into the existing MadEvent framework. The outlook towards a first alpha release of the software supporting QCD LO processes usable by the LHC experiments is also discussed.Comment: 7 pages, 4 figures, 4 tables; submitted to ACAT 2022 proceedings in IO

HEPScore: A new CPU benchmark for the WLCG

HEPScore is a new CPU benchmark created to replace the HEPSPEC06 benchmark that is currently used by the WLCG for procurement, computing resource pledges and performance studies. The development of the new benchmark, based on HEP applications or workloads, has involved many contributions from software developers, data analysts, experts of the experiments, representatives of several WLCG computing centres, as well as the WLCG HEPScore Deployment Task Force. In this contribution, we review the selection of workloads and the validation of the new HEPScore benchmark.Comment: Paper submitted to the proceedings of the Computing in HEP Conference 2023, Norfol

Post-receptor IGF1 insensitivity restricted to the MAPK pathway in a Silver-Russell syndrome patient with hypomethylation at the imprinting control region on chromosome 11

Background: Hypomethylation of the paternal imprinting center region 1 (ICR1) is the most frequent molecular cause of Silver-Russell syndrome (SRS). Clinical evidence suggests that patients with this epimutation have mild IGF1 insensitivity. Objective: To assess in vitro IGF1 action in fibroblast culture from a patient with SRS and IGF1 insensitivity. Methods: Fibroblast cultures from one patient with SRS due to ICR1 demethylation and controls were established. The SRS patient has severe growth failure, elevated IGF1 level, and poor growth rate during human recombinant GH treatment. IGF1 action was assessed by cell proliferation, AKT, and p42/44-MAPK phosphorylation. Gene expression was determined by real-time PCR. Results: Despite normal IGF1R sequence and expression, fibroblast proliferation induced by IGF1 was 50% lower in SRS fibroblasts in comparison with controls. IGF1 and insulin promoted a p42/44-MAPK activation in SRS fibroblasts 40 and 36%, respectively, lower than that in control fibroblasts. On the other hand, p42/44-MAPK activation induced by EGF stimulation was only slightly reduced (75% in SRS fibroblasts in comparison with control), suggesting a general impairment in MAPK pathway with a greater impairment of the stimulation induced by insulin and IGF1 than by EGF. A PCR array analysis disclosed a defect in MAPK pathway characterized by an increase in DUSP4 and MEF2C gene expressions in patient fibroblasts. Conclusion: A post-receptor IGF1 insensitivity was characterized in one patient with SRS and ICR1 hypomethylation. Although based on one unique severely affected patient, these results raise an intriguing mechanism to explain the postnatal growth impairment observed in SRS patients that needs confirmation in larger cohorts.Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [08/57915-2, 05/04726-0, 05/50144-2]Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) [142062/06-5, 301339/2008-9, 300938/06-3, 307951/06-5

Corticotroph tumor progression after bilateral adrenalectomy (Nelson’s syndrome):systematic review and expert consensus recommendations

Corticotroph tumor progression (CTP) leading to Nelson's syndrome (NS) is a severe and difficult-to-treat complication subsequent to bilateral adrenalectomy (BADX) for Cushing's disease. Its characteristics are not well described, and consensus recommendations for diagnosis and treatment are missing

Search for CP Violation in the Decay Z -> b (b bar) g

About three million hadronic decays of the Z collected by ALEPH in the years 1991-1994 are used to search for anomalous CP violation beyond the Standard Model in the decay Z -> b \bar{b} g. The study is performed by analyzing angular correlations between the two quarks and the gluon in three-jet events and by measuring the differential two-jet rate. No signal of CP violation is found. For the combinations of anomalous CP violating couplings, ${\hat{h}}_b = {\hat{h}}_{Ab}g_{Vb}-{\hat{h}}_{Vb}g_{Ab}$ and $h^{\ast}_b = \sqrt{\hat{h}_{Vb}^{2}+\hat{h}_{Ab}^{2}}$, limits of \hat{h}_b < 0.59$and$h^{\ast}_{b} < 3.02$ are given at 95\% CL.Comment: 8 pages, 1 postscript figure, uses here.sty, epsfig.st

Time to diagnosis in Cushing’s syndrome: A meta-analysis based on 5367 patients

The time from first symptom to diagnosis of Cushing's syndrome is considered relevant for the severity of phenotype at presentation and long-term outcome. We therefore performed a systematic literature search to investigate relevant factors associated with a short time to diagnosis. The meta-analysis of 45 studies with 5560 patients showed significant differences for adrenal Cushing’s syndrome, Cushing’s disease and the ectopic Cushing’s syndrome. We did not find difference for gender, age or time of publication