This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the ...demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications.
DODAS stands for Dynamic On Demand Analysis Service and is a Platform as a Service toolkit built around several EOSC-hub services designed to instantiate and configure on-demand container-based ...clusters over public or private Cloud resources. It automates the whole workflow from service provisioning to the configuration and setup of software applications. Therefore, such a solution allows using "any cloud provider", with almost zero effort. In this paper, we demonstrate how DODAS can be adopted as a deployment manager to set up and manage the compute resources and services required to develop an AI solution for smart data caching. The smart caching layer may reduce the operational cost and increase flexibility with respect to regular centrally managed storage of the current CMS computing model. The cache space should be dynamically populated with the most requested data. In addition, clustering such caching systems will allow to operate them as a Content Delivery System between data providers and end-users. Moreover, a geographically distributed caching layer will be functional also to a data-lake based model, where many satellite computing centers might appear and disappear dynamically. In this context, our strategy is to develop a flexible and automated AI environment for smart management of the content of such clustered cache system. In this contribution, we will describe the identified computational phases required for the AI environment implementation, as well as the related DODAS integration. Therefore we will start with the overview of the architecture for the pre-processing step, based on Spark, which has the role to prepare data for a Machine Learning technique. A focus will be given on the automation implemented through DODAS. Then, we will show how to train an AI-based smart cache and how we implemented a training facility managed through DODAS. Finally, we provide an overview of the inference system, based on the CMS-TensorFlow as a Service and also deployed as a DODAS service.
The pathogenesis of vasculitis associated with anti-neutrophil cytoplasmic antibodies is not established. The anti-neutrophil cytoplasmic antibody autoanigens proteinase 3 (PR3) and elastase induce ...detachment and cytolysis of endothelial cells in vitro. We investigated whether PR3 and elastase trigger endothelial cell apoptosis. Primary bovine pulmonary artery endothelial cells were treated with either PR3, elastase, or myeloperoxidase (MPO) and apoptosis assessed by four different methods. By the cell death detection enzyme-linked immunosorbent assay, DNA fragmentation increased to 208 +/- 84% or 153 +/- 27% of control with 1 micrograms/ml PR3 or elastase at 24 hours. By ultraviolet light microscopy, the percentage of apoptotic cells significantly increased (P < 0.05) with 5 or 10 micrograms/ml PR3 and 25 or 50 micrograms/ml elastase at 6, 12, or 24 hours. Values at the 24-hour time point are 15.3 +/- 6.4% or 25.8 +/- 6.6% for 5 or 10 micrograms/ml PR3 and 13.9 +/- 3.6% or 20.7 +/- 1.8% for 25 or 50 micrograms/ml elastase compared with 2.2 +/- 1.2% for control. Similarly, with flow cytometry, 5 or 10 micrograms/ml PR3 and 25 or 50 micrograms/ml elastase for 6, 12, or 24 hours demonstrated increasing apoptosis in a dose- and time-dependent manner with the highest values achieved at 24 hours (23.4 +/- 4.0% and 35.6% for 5 and 10 micrograms/ml PR3 and 31.8 +/- 4.0% and 47.8% for 25 and 50 micrograms/ml elastase compared with 7.9 +/- 2.2% in control). Typical DNA laddering was apparent from 6 to 24 hours at 5 or 10 micrograms/ml PR3 and 25 or 50 micrograms/ml elastase. Myeloperoxidase did not induce cell apoptosis. Release of PR3 and elastase by activated neutrophils during acute inflammation, including anti-neutrophil cytoplasmic antibody-associated vasculitis, may result in vascular damage by endothelial cell apoptosis.
Micro Pattern Gas Detectors (MPGD) are the new frontier in gas trackers. Among this kind of devices, the Gas Electron Multiplier (GEM) chambers are widely used. The experimental signals acquired with ...the detector must obviously be reconstructed and analysed. In this contribution, a new offline software to perform reconstruction, alignment and analysis on the data collected with APV-25 and TIGER ASICs will be presented. GRAAL (Gem Reconstruction And Analysis Library) is able to measure the performance of a MPGD detector with a strip segmented anode (presently). The code is divided in three parts: reconstruction, where the hits are digitized and clusterized; tracking, where a procedure fits the points from the tracking system and uses that information to align the chamber with rotations and shifts; analysis, where the performance is evaluated (e.g. efficiency, spatial resolution,etc.). The user must set the geometry of the setup and then the program returns automatically the analysis results, taking care of different conditions of gas mixture, electric field, magnetic field, geometries, strip orientation, dead strip, misalignment and many others.
The experiment BESIII, running at the accelerator BEPCII in Beijing (P.R.C.), is going to be updated with the replacement of the Inner Drift Chamber with a Cylindrical triple-GEM Inner Tracker ...(CGEM-IT). In the R&D stage, two standalone C++ codes were implemented: GTS (Garfield-based Triple-GEM Simulator), for digitization and tuning of simulated data to the experimental ones, and GRAAL (GEM Reconstruction And Analysis Library), for the reconstruction and analysis of the experimental events collected in testbeams. GTS simulates the triple-GEM response to the particle passage, treating each stage separately: ionization, GEM properties, gas mixture, magnetic field and finally the induction of the signal on the anode. The necessary information was extracted by GARFIELD++ simulations, parametrized and used as input in GTS. This speeds up the simulation, since GTS performs only samplings instead of the full digitization chain. The simulated events were reconstructed with the same procedure used for experimental data and tuning factors were evaluated to obtain a satisfactory match. GRAAL is used in the analysis of the testbeam experimental data. It provides several levels of reconstruction: from the cluster formation, gathering contiguous firing strips, to the spatial position and the signal time reconstruciton. Two algorithms are used: the charge centroid and the micro-TPC, which exploit the charge deposition on the strips and the time information. Also a merging of the two algorithms is available to efficiently weight the two outcomes and obtain the best estimate of the spatial coordinate. Moreover, GRAAL performs tracking and alignment. Both codes are going to be made available also for other MPGDs simulation and reconstruction.
Triple-GEM detectors are a well known technology in high energy physics. In order to have a complete understanding of their behavior, in parallel with on beam testing, a Monte Carlo code has to be ...developed to simulate their response to the passage of particles. The software must take into account all the physical processes involved from the primary ionization up to the signal formation, e.g. the avalanche multiplication and the effect of the diffusion on the electrons. In the case of gas detectors, existing software such as Garfield already perform a very detailed simulation but are CPU time consuming. A description of a reliable but faster simulation is presented here: it uses a parametric description of the variables of interest obtained by suitable preliminary Garfield simulations and tuned to the test beam data. It can reproduce the real values of the charge measured by the strip, needed to reconstruct the position with the Charge Centroid method. In addition, particular attention was put to the simulation of the timing information, which permits to apply also the micro-Time Projection Chamber position reconstruction, for the first time on a triple-GEM. A comparison between simulation and experimental values of some sentinel variables in different conditions of magnetic field, high voltage settings and incident angle will be shown.
Interleukin-8 delays spontaneous and tumor necrosis factor-α-mediated apoptosis of human neutrophils. During inflammation, polymorphonuclear neutrophils (PMN) are exposed to and influenced by various ...cytokines, including the chemoattractant interleukin-8 (IL-8). We tested the hypothesis that IL-8 affects apoptosis in PMN. We investigated which IL-8 receptor (RI or RII) might be involved, as well as the role of Bcl-2. Human PMN were isolated and cultured up to 30 hours. Apoptosis was detected by UV and light microscopy, as well as by DNA-fragmentation assay, and quantitated by flow cytometry. Interleukin-8 significantly delayed spontaneous apoptosis at 10, 20, and 30 hours in a dose-dependent fashion. Polymorphonuclear neutrophil treatment with the highest concentration of IL-8 (100nM) decreased the percentage of apoptotic cells from 2.1 ± 1.5 to 0.8 ± 0.2 after 10 hours, from 31 ± 14 to 8 ± 5 after 20 hours, and from 47 ± 15 to 18 ± 8 after 30 hours of incubation (P < 0.05 for all time points, N = 6). Interleukin-8 also inhibited TNFα-mediated PMN apoptosis. Incubation with 20 ng/ml TNFα resulted in 23 ± 6% apoptotic cells at four hours, whereas pretreatment with IL-8 (50nM) decreased this percentage to 11 ± 3 (N = 5, P < 0.05). We next studied the role of both types of IL-8 receptors, RI and RII, by comparing the effect of IL-8 and the product of growth-related oncogene alpha (Groα) on PMN cultured for 20 hours. Both IL-8 and Groα attenuated apoptosis, although IL-8 was more effective than Groα. Bcl-2 was detected by intracellular fluorescent antibody cell sorter analysis, Western blot, and reverse transcription-polymerase chain reaction (RT-PCR). Neither resting PMN nor IL-8-treated neutrophils expressed BCL-2 protein, which was readily detected in control cells. Furthermore, we could not detect BCL-2 gene expression by RT-PCR. We conclude that IL-8 prolongs the lifespan of human neutrophils in vitro by delaying apoptosis. This effect may be important for a controlled and effective inflammatory response. The delay in apoptosis can be mediated by the IL-8 RII, while RI may provide an added effect. The actions of IL-8 on apoptosis are Bcl-2 independent.
One of the challenges a scientific computing center has to face is to keep delivering well consolidated computational frameworks (i.e. the batch computing farm), while conforming to modern computing ...paradigms. The aim is to ease system administration at all levels (from hardware to applications) and to provide a smooth end-user experience. Within the INDIGO- DataCloud project, we adopt two different approaches to implement a PaaS-level, on-demand Batch Farm Service based on HTCondor and Mesos. In the first approach, described in this paper, the various HTCondor daemons are packaged inside pre-configured Docker images and deployed as Long Running Services through Marathon, profiting from its health checks and failover capabilities. In the second approach, we are going to implement an ad-hoc HTCondor framework for Mesos. Container-to-container communication and isolation have been addressed exploring a solution based on overlay networks (based on the Calico Project). Finally, we have studied the possibility to deploy an HTCondor cluster that spans over different sites, exploiting the Condor Connection Broker component, that allows communication across a private network boundary or firewall as in case of multi-site deployments. In this paper, we are going to describe and motivate our implementation choices and to show the results of the first tests performed.
Urinary tract infections (UTIs) are among the most common bacterial infections and account for a significant part of the workload in clinical microbiology laboratories. Enteric bacteria (in ...particular, Escherichia coli) remain the most frequent cause of UTIs, although the distribution of pathogens that cause UTIs is changing. More important is the increase in resistance to some antimicrobial agents, particularly the resistance to trimethoprim-sulfamethoxazole seen in E. coli. Physicians distinguish UTIs from other diseases that have similar clinical presentations with use of a small number of tests, none of which, if used individually, have adequate sensitivity and specificity. Among the diagnostic tests, urinalysis is useful mainly for excluding bacteriuria. Urine culture may not be necessary as part of the evaluation of outpatients with uncomplicated UTIs, but it is necessary for outpatients who have recurrent UTIs, experience treatment failures, or have complicated UTIs, as well as for inpatients who develop UTIs.
Accounting in a production-level Grid infrastructure is of paramount importance in order to measure the utilization of the available resources. While several CPU accounting systems are deployed ...within the European Grid Infrastructure (EGI), storage accounting systems, stable enough to be adopted in a production environment are not yet available. As a consequence, there is a growing interest in storage accounting and work on this is being carried out in the Open Grid Forum (OGF) where a Usage Record (UR) definition suitable for storage resources has been proposed for standardization. In this paper we present a storage accounting system which is composed of three parts: a sensor layer, a data repository with a transport layer (Distributed Grid Accounting System - DGAS) and a web portal providing graphical and tabular reports (HLRmon). The sensor layer is responsible for the creation of URs according to the schema (described in this paper) that is currently being discussed within OGF. DGAS is one of the CPU accounting systems used within EGI, in particular by the Italian Grid Infrastructure (IGI) and some other National Grid Initiatives (NGIs) and projects. DGAS architecture is evolving in order to collect Usage Records for different types of resources. This improvement allows DGAS to be used as a ‘general’ data repository and transport layer. HLRmon is the web portal acting as an interface to DGAS. It has been improved to retrieve storage accounting data from the DGAS repository and create reports in an easy way. This is very useful not only for the Grid users and administrators but also for the stakeholders.
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