Using XDAQ in Application Scenarios of the CMS Experiment

XDAQ is a generic data acquisition software environment that emerged from a rich set of of use-cases encountered in the CMS experiment. They cover not the deployment for multiple sub-detectors and the operation of different processing and networking equipment as well as a distributed collaboration of users with different needs. The use of the software in various application scenarios demonstrated the viability of the approach. We discuss two applications, the tracker local DAQ system for front-end commissioning and the muon chamber validation system. The description is completed by a brief overview of XDAQ.Comment: Conference CHEP 2003 (Computing in High Energy and Nuclear Physics, La Jolla, CA

The CMS Event Builder

The data acquisition system of the CMS experiment at the Large Hadron Collider will employ an event builder which will combine data from about 500 data sources into full events at an aggregate throughput of 100 GByte/s. Several architectures and switch technologies have been evaluated for the DAQ Technical Design Report by measurements with test benches and by simulation. This paper describes studies of an EVB test-bench based on 64 PCs acting as data sources and data consumers and employing both Gigabit Ethernet and Myrinet technologies as the interconnect. In the case of Ethernet, protocols based on Layer-2 frames and on TCP/IP are evaluated. Results from ongoing studies, including measurements on throughput and scaling are presented. The architecture of the baseline CMS event builder will be outlined. The event builder is organised into two stages with intelligent buffers in between. The first stage contains 64 switches performing a first level of data concentration by building super-fragments from fragments of 8 data sources. The second stage combines the 64 super-fragments into full events. This architecture allows installation of the second stage of the event builder in steps, with the overall throughput scaling linearly with the number of switches in the second stage. Possible implementations of the components of the event builder are discussed and the expected performance of the full event builder is outlined.Comment: Conference CHEP0

Metabolic regulation of regulatory T cell development and function

It is now well established that the effector T cell (Teff) response is regulated by a series of metabolic switches. Quiescent T cells predominantly require ATP-generating processes, whereas proliferating Teff require high metabolic flux through growth-promoting pathways, such as glycolysis. Pathways that control metabolism and immune cell function are intimately linked, and changes in cell metabolism at both the cell and system levels have been shown to enhance or suppress specific T cell effector functions. Furthermore, functionally distinct T cell subsets have been shown to require distinct energetic and biosynthetic pathways to support their specific functional needs. In particular, naturally occurring regulatory T cells (Treg) are characterized by a unique metabolic signature distinct to that of conventional Teff cells. We here briefly review the signaling pathways that control Treg metabolism and how this metabolic phenotype integrates their differentiation and function. Ultimately, these metabolic features may provide new opportunities for the therapeutic modulation of unwanted immune responses

Evaluation of Four Commercial IgG- and IgM-specific Enzyme Immunoassays for Detecting Mycoplasma pneumoniae Antibody: Comparison with Particle Agglutination Assay

Diagnosis of Mycoplasma pneumoniae infection is important due to its variable clinical manifestations and absence of response to beta-lactams. Introduction of enzyme immunoassays (EIAs) for serologic diagnosis of M. pneumoniae has made it possible to separate the analyses of specific IgG and IgM antibodies. We compared four different commercial EIAs, ImmunoWELL IgG, IgM (GenBio), Medac IgG, IgA, IgM (Medac), Platelia IgG, IgM (Sanofi Pasteur), and Ridascreen IgG, IgA, IgM (r-Biopharm) with indirect particle agglutination assay (PA), Serodia-MycoII (Fujirebio). We tested 91 specimens from 73 pediatric patients (2-17 yr) hospitalized at a tertiary-care hospital between December 2005 and January 2006. The measurements of IgM EIAs were correlated with PA titers (Spearman's correlation coefficient, from 0.89 to 0.92) with high concordance rates, ranging from 82.4% to 92.3%. However, some negative IgM-EIA results in PA-positive specimens indicated that serial samplings with convalescent sera would be necessary to confirm M. pneumoniae infection

Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

<p>Abstract</p> <p>Background</p> <p>Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two domains that are separated by a conserved hinge. The hinge allows the protein to cycle between open (apo) and closed (ligated) conformations. Conformational changes within the proteins depend on a complex interplay of mechanical and thermodynamic response, which is manifested as an increase in thermal stability and decrease of flexibility upon ligand binding.</p> <p>Results</p> <p>We use a distance constraint model (DCM) to quantify the give and take between thermodynamic stability and mechanical flexibility across the bPBP family. Quantitative stability/flexibility relationships (QSFR) are readily evaluated because the DCM links mechanical and thermodynamic properties. We have previously demonstrated that QSFR is moderately conserved across a mesophilic/thermophilic RNase H pair, whereas the observed variance indicated that different enthalpy-entropy mechanisms allow similar mechanical response at their respective melting temperatures. Our predictions of heat capacity and free energy show marked diversity across the bPBP family. While backbone flexibility metrics are mostly conserved, cooperativity correlation (long-range couplings) also demonstrate considerable amount of variation. Upon ligand removal, heat capacity, melting point, and mechanical rigidity are, as expected, lowered. Nevertheless, significant differences are found in molecular cooperativity correlations that can be explained by the detailed nature of the hydrogen bond network.</p> <p>Conclusion</p> <p>Non-trivial mechanical and thermodynamic variation across the family is explained by differences within the underlying H-bond networks. The mechanism is simple; variation within the H-bond networks result in altered mechanical linkage properties that directly affect intrinsic flexibility. Moreover, varying numbers of H-bonds and their strengths control the likelihood for energetic fluctuations as H-bonds break and reform, thus directly affecting thermodynamic properties. Consequently, these results demonstrate how unexpected large differences, especially within cooperativity correlation, emerge from subtle differences within the underlying H-bond network. This inference is consistent with well-known results that show allosteric response within a family generally varies significantly. Identifying the hydrogen bond network as a critical determining factor for these large variances may lead to new methods that can predict such effects.</p

Secondary education reform in Lesotho and Zimbabwe and the needs of rural girls: Pronouncements, policy and practice

Analysis of the educational needs of rural girls in Lesotho and Zimbabwe suggests a number of shortcomings in the current form of secondary education, and ways in which it might be modified so as to serve this sizeable group of students better. Several of the shortcomings, notably in relation to curricular irrelevance and excessive focus on examinations, have long been recognised, including by politicians. Yet political pronouncements are seldom translated into policy, and even where policy is formulated, reforms are seldom implemented in schools. This paper makes use of interviews with educational decision-makers in the two southern African countries and a range of documentary sources to explore why, despite the considerable differences between the two contexts, much needed educational reforms have been implemented in neither

CMS DAQ Event Builder Based on Gigabit Ethernet

The CMS Data Acquisition system is designed to build and filter events originating from approximately 500 data sources from the detector at a maximum Level 1 trigger rate of 100 kHz and with an aggregate throughput of 100 GByte/s. For this purpose different architectures and switch technologies have been evaluated. Events will be built in two stages: the first stage, the FED Builder, will be based on Myrinet technology and will pre-assemble groups of about 8 data sources. The next stage, the Readout Builder, will perform the building of full events. The requirement of one Readout Builder is to build events at 12.5 kHz with average size of 16 kBytes from 64 sources. In this paper we present the prospects of a Readout Builder based on TCP/IP over Gigabit Ethernet. Various Readout Builder architectures that we are considering are discussed. The results of throughput measurements and scaling performance are outlined as well as the preliminary estimates of the final performance. All these studies have been carried out at our test-bed farms that are made up of a total of 130 dual Xeon PCs interconnected with Myrinet and Gigabit Ethernet networking and switching technologies