The toll-like receptor 4 (TLR4) plays a key role in the activation of innate immune response participating in the recognition of lipopolysaccharides. Changes in the innate immune response are ...involved in the pathogenesis of some metabolic disorders such as metabolic syndrome and type 2 diabetes mellitus (Met-S and T2DM). It has been recently shown the role of gut microbiota in the perpetuation of both insulin resistance and low-grade chronic inflammation. Some studies have reported that TLR4 D299G polymorphism is associated with metabolic disorders, however results have been inconsistent. Two recent meta-analyses showed that D299G is associated with inflammatory bowel disease and gastrointestinal cancers risk, two pathological states in which the luminal microbial flora-host cells interaction may be implicated. We conducted a systemic review of the published data considering all eligible published studies (six studies with 1696 cases and 3388 controls for D299G) and a meta-analysis was performed to evaluate the association between TLR4 D299G polymorphism and the risk for metabolic disorders. Five studies were identified for T2DM: three corresponding to Caucasian populations and two to mixed populations. The remaining study analyzed Met-S in a Caucasian population. We observed a significant association between D299G polymorphism and metabolic disorders (T2DM and Met-S) risk (OR = 0.566, 95 % CI: 0.347–0.925,
p
= 0.023) particularly in Caucasians. No association was found in mixed population subgroup. Our meta-analysis identified that the AG/GG genotypes of D299G are associated with decreased metabolic disorders risk.
Inflammatory bowel disease (IBD) is the most common form of intestinal inflammation associated with a dysregulated immune system response to the commensal microbiota in a genetically susceptible ...host. IBD includes ulcerative colitis (UC) and Crohn’s disease (CD), both of which are remarkably heterogeneous in their clinical presentation and response to treatment. This translates into a notable diagnostic challenge, especially in underdeveloped countries where IBD is on the rise and access to diagnosis or treatment is not always accessible for chronic diseases. The present work characterized, for the first time in our region, epigenetic biomarkers and gut microbial profiles associated with UC and CD patients in the Buenos Aires Metropolitan area and revealed differences between non-IBD controls and IBD patients. General metabolic functions associated with the gut microbiota, as well as core microorganisms within groups, were also analyzed. Additionally, the gut microbiota analysis was integrated with relevant clinical, biochemical and epigenetic markers considered in the follow-up of patients with IBD, with the aim of generating more powerful diagnostic tools to discriminate phenotypes. Overall, our study provides new insights into data analysis algorithms to promote comprehensive phenotyping tools using quantitative and qualitative analysis in a transkingdom interactions network context.
CRAB3 is a workload management tool used by CMS physicists to analyze data acquired by the Compact Muon Solenoid (CMS) detector at the CERN Large Hadron Collider (LHC). Research in high energy ...physics often requires the analysis of large collections of files, referred to as datasets. The task is divided into jobs that are distributed among a large collection of worker nodes throughout the Worldwide LHC Computing Grid (WLCG). Splitting a large analysis task into optimally sized jobs is critical to efficient use of distributed computing resources. Jobs that are too big will have excessive runtimes and will not distribute the work across all of the available nodes. However, splitting the project into a large number of very small jobs is also inefficient, as each job creates additional overhead which increases load on infrastructure resources. Currently this splitting is done manually, using parameters provided by the user. However the resources needed for each job are difficult to predict because of frequent variations in the performance of the user code and the content of the input dataset. As a result, dividing a task into jobs by hand is difficult and often suboptimal. In this work we present a new feature called "automatic splitting" which removes the need for users to manually specify job splitting parameters. We discuss how HTCondor DAGMan can be used to build dynamic Directed Acyclic Graphs (DAGs) to optimize the performance of large CMS analysis jobs on the Grid. We use DAGMan to dynamically generate interconnected DAGs that estimate the processing time the user code will require to analyze each event. This is used to calculate an estimate of the total processing time per job, and a set of analysis jobs are run using this estimate as a specified time limit. Some jobs may not finish within the alloted time; they are terminated at the time limit, and the unfinished data is regrouped into smaller jobs and resubmitted.
AsyncStageOut (ASO) is the component of the CMS distributed data analysis system (CRAB) that manages users transfers in a centrally controlled way using the File Transfer System (FTS3) at CERN. It ...addresses a major weakness of the previous, decentralized model, namely that the transfer of the user's output data to a single remote site was part of the job execution, resulting in inefficient use of job slots and an unacceptable failure rate. Currently ASO manages up to 600k files of various sizes per day from more than 500 users per month, spread over more than 100 sites. ASO uses a NoSQL database (CouchDB) as internal bookkeeping and as way to communicate with other CRAB components. Since ASO/CRAB were put in production in 2014, the number of transfers constantly increased up to a point where the pressure to the central CouchDB instance became critical, creating new challenges for the system scalability, performance, and monitoring. This forced a re-engineering of the ASO application to increase its scalability and lowering its operational effort. In this contribution we present a comparison of the performance of the current NoSQL implementation and a new SQL implementation, and how their different strengths and features influenced the design choices and operational experience. We also discuss other architectural changes introduced in the system to handle the increasing load and latency in delivering output to the user.
Efficient monitoring of CRAB jobs at CMS Silva, J M D; Balcas, J; Belforte, S ...
Journal of physics. Conference series,
10/2017, Letnik:
898, Številka:
9
Journal Article
Recenzirano
Odprti dostop
CRAB is a tool used for distributed analysis of CMS data. Users can submit sets of jobs with similar requirements (tasks) with a single request. CRAB uses a client-server architecture, where a ...lightweight client, a server, and ancillary services work together and are maintained by CMS operators at CERN. As with most complex software, good monitoring tools are crucial for efficient use and longterm maintainability. This work gives an overview of the monitoring tools developed to ensure the CRAB server and infrastructure are functional, help operators debug user problems, and minimize overhead and operating cost. This work also illustrates the design choices and gives a report on our experience with the tools we developed and the external ones we used.
The CDF Silicon Vertex Trigger Ashmanskas, Bill; Barchiesi, A.; Bardi, A. ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
02/2004, Letnik:
518, Številka:
1
Journal Article
Recenzirano
Odprti dostop
The Collider Detector at Fermilab (CDF) experiment's Silicon Vertex Trigger (SVT) is a system of 150 custom 9U VME boards that reconstructs axial tracks in the CDF silicon strip detector in a
15
μs
...pipeline. SVT's
35
μm
impact parameter resolution enables CDF's Level 2 trigger to distinguish primary and secondary particles, and hence to collect large samples of hadronic bottom and charm decays. We review some of SVT's key design features. Speed is achieved with custom VLSI pattern recognition, linearized track fitting, pipelining, and parallel processing. Testing and reliability are aided by built-in logic state analysis and test-data sourcing at each board's input and output, a common interboard data link, and a universal “Merger” board for data fan-in/fan-out. Speed and adaptability are enhanced by use of modern FPGAs.
CMS will require access to more than 125k processor cores for the beginning of Run 2 in 2015 to carry out its ambitious physics program with more and higher complexity events. During Run1 these ...resources were predominantly provided by a mix of grid sites and local batch resources. During the long shut down cloud infrastructures, diverse opportunistic resources and HPC supercomputing centers were made available to CMS, which further complicated the operations of the submission infrastructure. In this presentation we will discuss the CMS effort to adopt and deploy the glideinWMS system as a common resource provisioning layer to grid, cloud, local batch, and opportunistic resources and sites. We will address the challenges associated with integrating the various types of resources, the efficiency gains and simplifications associated with using a common resource provisioning layer, and discuss the solutions found. We will finish with an outlook of future plans for how CMS is moving forward on resource provisioning for more heterogenous architectures and services.
CMS distributed data analysis with CRAB3 Mascheroni, M; Balcas, J; Belforte, S ...
Journal of physics. Conference series,
12/2015, Letnik:
664, Številka:
6
Journal Article
Recenzirano
Odprti dostop
The CMS Remote Analysis Builder (CRAB) is a distributed workflow management tool which facilitates analysis tasks by isolating users from the technical details of the Grid infrastructure. Throughout ...LHC Run 1, CRAB has been successfully employed by an average of 350 distinct users each week executing about 200,000 jobs per day. CRAB has been significantly upgraded in order to face the new challenges posed by LHC Run 2. Components of the new system include 1) a lightweight client, 2) a central primary server which communicates with the clients through a REST interface, 3) secondary servers which manage user analysis tasks and submit jobs to the CMS resource provisioning system, and 4) a central service to asynchronously move user data from temporary storage in the execution site to the desired storage location. The new system improves the robustness, scalability and sustainability of the service. Here we provide an overview of the new system, operation, and user support, report on its current status, and identify lessons learned from the commissioning phase and production roll-out.
CMS production and analysis job submission is based largely on glideinWMS and pilot submissions. The transition from multiple different submission solutions like gLite WMS and HTCondor-based ...implementations was carried out over years and is coming now to a conclusion. The historically explained separate glideinWMS pools for different types of production jobs and analysis jobs are being unified into a single global pool. This enables CMS to benefit from global prioritization and scheduling possibilities. It also presents the sites with only one kind of pilots and eliminates the need of having to make scheduling decisions on the CE level. This paper provides an analysis of the benefits of a unified resource pool, as well as a description of the resulting global policy. It will explain the technical challenges moving forward and present solutions to some of them.
The CMS experiment at the LHC relies on HTCondor and glideinWMS as its primary batch and pilot-based Grid provisioning system. So far we have been running several independent resource pools, but we ...are working on unifying them all to reduce the operational load and more effectively share resources between various activities in CMS. The major challenge of this unification activity is scale. The combined pool size is expected to reach 200K job slots, which is significantly bigger than any other multi-user HTCondor based system currently in production. To get there we have studied scaling limitations in our existing pools, the biggest of which tops out at about 70K slots, providing valuable feedback to the development communities, who have responded by delivering improvements which have helped us reach higher and higher scales with more stability. We have also worked on improving the organization and support model for this critical service during Run 2 of the LHC. This contribution will present the results of the scale testing and experiences from the first months of running the Global Pool.
PDF
