Prototyping a ROOT-based distributed analysis workflow for HL-LHC: the CMS use case

The challenges expected for the next era of the Large Hadron Collider (LHC), both in terms of storage and computing resources, provide LHC experiments with a strong motivation for evaluating ways of rethinking their computing models at many levels. Great efforts have been put into optimizing the computing resource utilization for the data analysis, which leads both to lower hardware requirements and faster turnaround for physics analyses. In this scenario, the Compact Muon Solenoid (CMS) collaboration is involved in several activities aimed at benchmarking different solutions for running High Energy Physics (HEP) analysis workflows. A promising solution is evolving software towards more user-friendly approaches featuring a declarative programming model and interactive workflows. The computing infrastructure should keep up with this trend by offering on the one side modern interfaces, and on the other side hiding the complexity of the underlying environment, while efficiently leveraging the already deployed grid infrastructure and scaling toward opportunistic resources like public cloud or HPC centers. This article presents the first example of using the ROOT RDataFrame technology to exploit such next-generation approaches for a production-grade CMS physics analysis. A new analysis facility is created to offer users a modern interactive web interface based on JupyterLab that can leverage HTCondor-based grid resources on different geographical sites. The physics analysis is converted from a legacy iterative approach to the modern declarative approach offered by RDataFrame and distributed over multiple computing nodes. The new scenario offers not only an overall improved programming experience, but also an order of magnitude speedup increase with respect to the previous approach

Photobiomodulation at Multiple Wavelengths Differentially Modulates Oxidative Stress In Vitro and In Vivo

Photobiomodulation (PBM) is emerging as an effective strategy for the management of multiple inflammatory conditions, including oral mucositis (OM) in cancer patients who receive chemotherapy or radiotherapy. Still, the poor understanding of the mechanisms by which the light interacts with biological tissues and the heterogeneity of light sources and protocols employed worldwide significantly limits its applicability. Reactive oxygen species (ROS) are massively generated during the early phases of OM and play a major role in the pathogenesis of inflammation in general. Here, we report the results of a clinical and experimental study, aimed at evaluating the effect of laser light at different wavelengths on oxidative stress in vivo in oncologic patients suffering from OM and in vitro in two cell types abundantly present within the inflamed oral mucosa, neutrophil polymorphonuclear (PMN) granulocytes, and keratinocytes. In addition to standard ROS detection methods, we exploited a roGFP2-Orp1 genetically encoded sensor, allowing specific, quantitative, and dynamic imaging of redox events in living cells in response to oxidative stress and PBM. We found that the various wavelengths differentially modulate ROS production. In particular, the 660\u2009nm laser light increases ROS production when applied either before or after an oxidative stimulus. In contrast, the 970\u2009nm laser light exerted a moderate antioxidant activity both in the saliva of OM patients and in both cell types. The most marked reduction in the levels of ROS was detected in cells exposed either to the 800\u2009nm laser light or to the combination of the three wavelengths. Overall, our study demonstrates that PBM exerts different effects on the redox state of both PMNs and keratinocytes depending on the used wavelength and prompts the validation of a multiwavelength protocol in the clinical settings

Implementation and use of a highly available and innovative IaaS solution: the Cloud Area Padovana

While in the business world the cloud paradigm is typically implemented purchasing resources and services from third party providers (e.g. Amazon), in the scientific environment there's usually the need of on-premises IaaS infrastructures which allow efficient usage of the hardware distributed among (and owned by) different scientific administrative domains. In addition, the requirement of open source adoption has led to the choice of products like OpenStack by many organizations. We describe a use case of the Italian National Institute for Nuclear Physics (INFN) which resulted in the implementation of a unique cloud service, called ’Cloud Area Padovana’, which encompasses resources spread over two different sites: the INFN Legnaro National Laboratories and the INFN Padova division. We describe how this IaaS has been implemented, which technologies have been adopted and how services have been configured in high-availability (HA) mode. We also discuss how identity and authorization management were implemented, adopting a widely accepted standard architecture based on SAML2 and OpenID: by leveraging the versatility of those standards the integration with authentication federations like IDEM was implemented. We also discuss some other innovative developments, such as a pluggable scheduler, implemented as an extension of the native OpenStack scheduler, which allows the allocation of resources according to a fair-share based model and which provides a persistent queuing mechanism for handling user requests that can not be immediately served. Tools, technologies, procedures used to install, configure, monitor, operate this cloud service are also discussed. Finally we present some examples that show how this IaaS infrastructure is being used

Autonomic Management of Large Clusters and Their Integration into the Grid

We present a framework for the co-ordinated, autonomic management of multiple clusters in a compute center and their integration into a Grid environment. Site autonomy and the automation of administrative tasks are prime aspects in this framework. The system behavior is continuously monitored in a steering cycle and appropriate actions are taken to resolve any problems. All presented components have been implemented in the course of the EU project DataGrid: The Lemon monitoring components, the FT fault-tolerance mechanism, the quattor system for software installation and configuration, the RMS job and resource management system, and the Gridification scheme that integrates clusters into the Grid

Anxiety and depression in keratotic oral lichen planus: a multicentric study from the SIPMO

Objectives: Oral lichen planus with exclusive keratotic reticular, papular, and/or plaque-like lesions (K-OLP) is a clinical pattern of OLP that may be associated with a complex symptomatology and psychological alteration. The aim of the study was to evaluate the prevalence of anxiety (A) and depression (D) in patients with K-OLP, analyzing the potential predictors which can affect mental health status. Methods: Three hundred K-OLP patients versus 300 healthy controls (HC) were recruited in 15 Italian universities. The Numeric Rating Scale (NRS), Total Pain Rating Index (T-PRI), and Hamilton Rating Scales for Depression and for Anxiety (HAM-D and HAM-A) were administered. Results: The K-OLP patients showed statistically higher scores in the NRS, T-PRI, HAM-D, and HAM-A compared with the HC (p-value < 0.001**). A and D were found in 158 (52.7%) and 148 (49.3%) K-OLP patients. Strong linear correlations were identified between HAM-A, HAM-D, NRS, T-PRI, and employment status and between HAM-D, HAM-A, NRS, T-PRI, employment status, and female gender. Multivariate logistic regression revealed that HAM-D and HAM-A showed the greatest increase in the R2 value for A and D in the K-OLP patients, respectively (DR2 = 55.5% p-value < 0.001**; DR2 = 56.5% p-value < 0.001**). Conclusions: The prevalence of A and D is higher in the K-OLP patients compared with the HC, also found in K-OLP subjects without pain, suggesting that the processing of pain may be in a certain way independent of the processing of mood. Clinical relevance: Mood disorders and pain assessment should be carefully performed in relation to K-OLP to obtain a complete analysis of the patients

Multicenter randomized, double-blind controlled trial to evaluate the efficacy of laser therapy for the treatment of severe oral mucositis induced by chemotherapy in children: LaMPO RCT

OBJECTIVES: To demonstrate the efficacy of laser photobiomodulation (PBM) compared to that of placebo on severe oral mucositis (OM) in pediatric oncology patients. The primary objective was the reduction of OM grade (World Health Organization [WHO] scale) 7 days after starting PBM. Secondary objectives were reduction of pain, analgesic consumption, and incidence of side effects. METHODS: One hundred and one children with WHO grade > 2 chemotherapy-induced OM were enrolled in eight Italian hospitals. Patients were randomized to either PBM or sham treatment for four consecutive days (days +1 to +4). On days +4, +7, and +11, OM grade, pain (following a 0-10 numeric pain rating scale, NRS) and need for analgesics were evaluated by an operator blinded to treatment. RESULTS: Fifty-one patients were allocated to the PBM group, and 50 were allocated to the sham group. In total, 93.7% of PBM patients and 72% of sham patients had OM grade < 3 WHO on day +7 (P = 0.01). A significant reduction of pain was registered on day +7 in the PBM versus sham group (NRS 1 [0-3] vs. 2.5 [1-5], P < 0.006). Reduced use of analgesics was reported in the PBM group, although it was not statistically significant. No significant adverse events attributable to treatment were recorded. CONCLUSIONS: PBM is a safe, feasible, and effective treatment for children affected by chemotherapy-induced OM, as it accelerates mucosal recovery and reduces pain

Inclusive Search for a Highly Boosted Higgs Boson Decaying to a Bottom Quark-Antiquark Pair

© 2018 CERN. An inclusive search for the standard model Higgs boson (H) produced with large transverse momentum (pT) and decaying to a bottom quark-antiquark pair (bb) is performed using a data set of pp collisions at s=13 TeV collected with the CMS experiment at the LHC. The data sample corresponds to an integrated luminosity of 35.9 fb-1. A highly Lorentz-boosted Higgs boson decaying to bb is reconstructed as a single, large radius jet, and it is identified using jet substructure and dedicated b tagging techniques. The method is validated with Z→bb decays. The Z→bb process is observed for the first time in the single-jet topology with a local significance of 5.1 standard deviations (5.8 expected). For a Higgs boson mass of 125 GeV, an excess of events above the expected background is observed (expected) with a local significance of 1.5 (0.7) standard deviations. The measured cross section times branching fraction for production via gluon fusion of H→bb with reconstructed pT > 450 GeV and in the pseudorapidity range -2.5 < η < 2.5 is 74±48(stat)-10+17(syst) fb, which is consistent within uncertainties with the standard model prediction