The ATLAS experiment at the LHC collects billions of events each data-taking year, and processes them to make them available for physics analysis in several different formats. An even larger amount ...of events is in addition simulated according to physics and detector models and then reconstructed and analysed to be compared to real events. The EventIndex is a catalogue of all events in each production stage; it includes for each event a few identification parameters, some basic non-mutable information coming from the online system, and the references to the files that contain the event in each format (plus the internal pointers to the event within each file for quick retrieval). Each EventIndex record is logically simple but the system has to hold many tens of billions of records, all equally important. The Hadoop technology was selected at the start of the EventIndex project development in 2012 and proved to be robust and flexible to accommodate this kind of information; both the insertion and query response times are acceptable for the continuous and automatic operation that started in Spring 2015. This paper describes the EventIndex data input and organisation in Hadoop and explains the operational challenges that were overcome in order to achieve the expected performance.
Abstract Chlorothalonil and thiophanate-methyl are fungicides widely used in agriculture. The aim of this study was to assess maternal toxicity and embryotoxic potential of exposure to chlorothalonil ...and thiophanate-methyl during organogenesis period in rats. Pregnant rats were divided into four groups: control and exposed to 400 (CT400), 800 (CT800) and 1200 mg-1kg bw-1 day (CT1200) of commercial formulation constituted of 200 g of thiophanate-methyl kg−1 and 500 g of chlorothalonil kg−1 by gavage, from 6th to 15th gestational day. Maternal toxicity, liver, kidney and placenta histology, reproductive performance, and external, skeletal and visceral malformations of fetuses were evaluated. Maternal liver weight was decreased in CT1200 group and focal necrosis and microvesicular steatosis, inflammatory infiltrate and hepatocytes with pyknotic nucleus were observed in CT800 and CT1200 groups. Reproductive performance was similar among groups. The percentage of fetuses small for pregnancy age was increase in CT400 and CT800 groups. Moreover, incidence of skeletal anomalies was increased in the three groups exposed to fungicides. Chlorothalonil and thiophanate-methyl exposure showed affect the prenatal development and induce maternal toxicity.
The EventIndex is the complete catalogue of all ATLAS events, keeping the references to all files that contain a given event in any processing stage. It replaces the TAG database, which had been in ...use during LHC Run 1. For each event it contains its identifiers, the trigger pattern and the GUIDs of the files containing it. Major use cases are event picking, feeding the Event Service used on some production sites, and technical checks of the completion and consistency of processing campaigns. The system design is highly modular so that its components (data collection system, storage system based on Hadoop, query web service and interfaces to other ATLAS systems) could be developed separately and in parallel during LSI. The EventIndex is in operation for the start of LHC Run 2. This paper describes the high-level system architecture, the technical design choices and the deployment process and issues. The performance of the data collection and storage systems, as well as the query services, are also reported.
In this study we investigated the effects of subacute exposure to methylmercury (MeHg) on male reproductive functions in rats by means of determination of alterations in structural and functional ...parameters. Adult male Wistar rats received 0, 0.5, 1.0 or 3.0
mg/kg/body weight/day orally, daily MeHg for 14 days. Sperm motility, the relative sperm count and transit time in the caput/corpus epididymis, were all reduced at all doses. The lowest dose increased the number of sperm head abnormalities; daily sperm production was elevated at the intermediate dose; while at the highest dose there was a decrease in serum testosterone levels and a rise in mercury (Hg) content in reproductive organs, liver and kidneys. In conclusion, MeHg exposure produced damages on male reproductive functions which may be attributed, at least in part, to the reduction in serum testosterone levels. These consequences could potentially result in infertility in rats.
The ATLAS EventIndex has been running in production since mid-2015, reliably collecting information worldwide about all produced events and storing them in a central Hadoop infrastructure at CERN. A ...subset of this information is copied to an Oracle relational database for fast dataset discovery, event-picking, crosschecks with other ATLAS systems and checks for event duplication. The system design and its optimization is serving event picking from requests of a few events up to scales of tens of thousand of events, and in addition, data consistency checks are performed for large production campaigns. Detecting duplicate events with a scope of physics collections has recently arisen as an important use case. This paper describes the general architecture of the project and the data flow and operation issues, which are addressed by recent developments to improve the throughput of the overall system. In this direction, the data collection system is reducing the usage of the messaging infrastructure to overcome the performance shortcomings detected during production peaks; an object storage approach is instead used to convey the event index information, and messages to signal their location and status. Recent changes in the Producer/Consumer architecture are also presented in detail, as well as the monitoring infrastructure.
Obesity is rapidly becoming a worldwide epidemic that affects children and adults. Some studies have shown a relationship between obesity and infertility, but until now it remains controversial. ...Thus, the aim of the present study was to investigate the effect of high-fat diet-induced obesity on male reproductive parameters.
In a first experiment, male Wistar rats were fed a high-fat diet (HFD) or standard chow (SD) for 15, 30 or 45 weeks, after which they were evaluated by adiposity index, serum leptin levels, reproductive organ weights and sperm counts. In a second experiment, rats received HFD or SD only for 15 weeks, long enough to cause obesity. Sexual hormones and sexual behavior were evaluated in these animals, as well as fertility after natural mating. Another group of rats was submitted to motility analysis and fertility evaluation after in utero insemination.
After 15, 30 or 45 weeks, HFD-fed animals presented significant increases in obesity index and serum leptin levels. Reproductive organ weights and sperm counts in the testis and epididymis were similar between the two groups at all timepoints studied. Sexual behavior was not altered by the diet regimen, and HFD fertility after natural mating was also similar to SD-fed animals. Intergroup testosterone levels were also comparable, but estradiol levels were increased in HFD rats. Furthermore, sperm quality was reduced in HFD animals as evidenced by their decreased percentage of sperm with progressive movement. This altered motility parameter was followed by a trend toward reduction in fertility potential after artificial in utero insemination.
The results reported herein showed that obesity can affect sperm quality, by reducing sperm motility, without affecting other sperm parameters. The low sperm quality caused a slight reduction in fertility potential, showing that obesity may lead to impairment in male fertility.
The ATLAS Pixel Detector is the innermost detector of the ATLAS experiment at the Large Hadron Collider at CERN, providing high-resolution measurements of charged particle tracks in the high ...radiation environment close to the collision region. This capability is very important for the identification and measurement of proper decay times of long-lived particles such as b-hadrons, and thus vital for the ATLAS physics program. The detector provides hermetic coverage with three cylindrical layers of pixel detectors and three layers end-caps on each side. It consists of approximately 80×106 pixels that are individually read out via chips bump-bonded to 1744 n-in-n silicon substrates. The detector performance is excellent: ∼96% of the pixels are operational, noise occupancy and hit efficiency exceed the design specification, and a good alignment allows high quality track resolution.
The ATLAS EventIndex is a data catalogue system that stores event-related metadata for all (real and simulated) ATLAS events, on all processing stages. As it consists of different components that ...depend on other applications (such as distributed storage, and different sources of information) we need to monitor the conditions of many heterogeneous subsystems, to make sure everything is working correctly. This paper describes how we gather information about the EventIndex components and related subsystems: the Producer-Consumer architecture for data collection, health parameters from the servers that run EventIndex components, EventIndex web interface status, and the Hadoop infrastructure that stores EventIndex data. This information is collected, processed, and then displayed using CERN service monitoring software based on the Kibana analytic and visualization package, provided by CERN IT Department. EventIndex monitoring is used both by the EventIndex team and ATLAS Distributed Computing shifts crew.
The Event Index project consists in the development and deployment of a complete catalogue of events for experiments with large amounts of data, such as the ATLAS experiment at the LHC accelerator at ...CERN. Data to be stored in the EventIndex are produced by all production jobs that run at CERN or the GRID; for every permanent output file, a snippet of information, containing the file unique identifier and the relevant attributes for each event, is sent to the central catalogue. The estimated insertion rate during the LHC Run 2 is about 80 Hz of file records containing ∼15 kHz of event records. This contribution describes the system design, the initial performance tests of the full data collection and cataloguing chain, and the project evolution towards the full deployment and operation by the end of 2014.
The ATLAS EventIndex is the catalogue of the event-related metadata for the information collected from the ATLAS detector. The basic unit of this information is the event record, containing the event ...identification parameters, pointers to the files containing this event as well as trigger decision information. The main use case for the EventIndex is event picking, as well as data consistency checks for large production campaigns. The EventIndex employs the Hadoop platform for data storage and handling, as well as a messaging system for the collection of information. The information for the EventIndex is collected both at Tier-0, when the data are first produced, and from the Grid, when various types of derived data are produced. The EventIndex uses various types of auxiliary information from other ATLAS sources for data collection and processing: trigger tables from the condition metadata database (COMA), dataset information from the data catalogue AMI and the Rucio data management system and information on production jobs from the ATLAS production system. The ATLAS production system is also used for the collection of event information from the Grid jobs. EventIndex developments started in 2012 and in the middle of 2015 the system was commissioned and started collecting event metadata, as a part of ATLAS Distributed Computing operations.
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