In recent years, polymer surfaces have become increasingly popular for biomolecule attachment because of their relatively low cost and desirable bulk physicochemical characteristics. However, the ...chemical inertness of some polymer surfaces poses an obstacle to more expansive implementation of polymer materials in bioanalytical applications. We describe use of argon plasma to generate reactive hydroxyl moieties at the surface of polystyrene microtiter plates. The plates are then selectively functionalized with silanes and cross-linkers suitable for the covalent immobilization of biomolecules. This plasma-based method for microtiter plate functionalization was evaluated after each step by X-ray photoelectron spectroscopy, water contact angle analysis, atomic force microscopy, and bioimmobilization efficacy. We further demonstrate that the plasma treatment followed by silane derivatization supports direct, covalent immobilization of biomolecules on microtiter plates and thus overcomes challenging issues typically associated with simple physisorption. Importantly, biomolecules covalently immobilized onto microtiter plates using this plasma-based method retained functionality and demonstrated attachment efficiency comparable to commercial preactivated microtiter plates.
The new LHC experiments at CERN will have very large numbers of channels to operate. In order to be able to configure and monitor such large systems, a high degree of parallelism is necessary. The ...control system is built as a hierarchy of sub-systems distributed over several computers. A toolkit-SMI++, combining two approaches: finite state machines and rule-based programming, allows for the description of the various sub-systems as decentralized deciding entities, reacting in real-time to changes in the system, thus providing for the automation of standard procedures and for the automatic recovery from error conditions in a hierarchical fashion. In this paper we will describe the principles and features of SMI++ as well as its integration with an industrial SCADA tool for use by the LHC experiments and we will try to show that such tools, can provide a very convenient mechanism for the automation of large scale, high complexity, applications.
In the SMI++ framework, the real world is viewed as a collection of objects behaving as finite state machines. These objects can represent real entities, such as hardware devices or software tasks, ...or they can represent abstract subsystems. A special language SML (State Manager Language) is provided for the object description. The SML description is then interpreted by a Logic Engine (coded in C++) to drive the Control System. This allows rule based automation and error recovery. SMI++ objects can run distributed over a variety of platforms, all communication being handled transparently by an underlying communication system – DIM (Distributed Information Management). This framework has been first used by the DELPHI experiment at CERN since 1990 and subsequently by BaBar experiment at SLAC since 1999 for the design and implementation of their experiment control. SMI++ has been adopted at CERN by all LHC experiments in their detector control systems as recommended by the Joint Controls Project. Since then it has undergone many upgrades to provide for varying needs. The main features of the framework and in particular of SML language as well as recent and near future upgrades will be discussed. SMI++ has, so far, been used only by large particle physics experiments. It is, however, equally suitable for any other control applications.
In the SMI++ framework, the real world is viewed as a collection of objects behaving as finite-state machines. These objects can represent real entities, such as hardware devices or software tasks, ...or they can represent abstract subsystems. A special language (SML) is provided for the object description. The SML description is then interpreted by a logic engine (coded in C++) to drive the control system. This allows rule-based automation and error recovery. SMI++ objects can run distributed over a variety of platforms, all communication being handled transparently by an underlying communication system, DIM. This framework was first used by the DELPHI experiment at CERN for the experiment control. The BaBar experiment at SLAC has adopted this framework for the design and implementation of their Run Control system. For this purpose, the framework was significantly upgraded. The BaBar Run Control and the underlying SMI++ framework has been in production since the beginning of 1999. SMI++ has recently been adopted at CERN by all LHC experiments for their detector control systems, as recommended by the Joint Controls Project. The main features of the framework and, in particular, of the SML language, as well as recent and near future upgrades, will be discussed. SMI++ has, so far, been used only by large particle physics experiments. It is, however, equally suitable for any other control applications.
LHCb's Experiment Control System will handle the configuration, monitoring, and operation of all experimental equipment involved in the various activities of the experiment. A control framework ...(based on an industrial SCADA system) allowing the integration of the various devices into a coherent hierarchical system is being developed in common for the four Large Hadron Collider (LHC) experiments. The aim of this paper is to demonstrate that the same architecture and tools can be used to control and monitor all the different types of devices, from front-end electronics boards to temperature sensors to algorithms in an event filter farm, thus providing LHCb with a homogeneous control system and a coherent interface to all parts of the experiment.
Systemic lupus erythematosus (SLE) is a highly heterogeneous disorder, characterized by differences in autoantibody profile, serum cytokines, and clinical manifestations. SLE-associated ...autoantibodies and high serum interferon alpha (IFN-α) are important heritable phenotypes in SLE which are correlated with each other, and play a role in disease pathogenesis. These two heritable risk factors are shared between ancestral backgrounds. The aim of the study was to detect genetic factors associated with autoantibody profiles and serum IFN-α in SLE.
We undertook a case-case genome-wide association study of SLE patients stratified by ancestry and extremes of phenotype in serology and serum IFN-α. Single nucleotide polymorphisms (SNPs) in seven loci were selected for follow-up in a large independent cohort of 538 SLE patients and 522 controls using a multi-step screening approach based on novel metrics and expert database review. The seven loci were: leucine-rich repeat containing 20 (LRRC20); protein phosphatase 1 H (PPM1H); lysophosphatidic acid receptor 1 (LPAR1); ankyrin repeat and sterile alpha motif domain 1A (ANKS1A); protein tyrosine phosphatase, receptor type M (PTPRM); ephrin A5 (EFNA5); and V-set and immunoglobulin domain containing 2 (VSIG2).
SNPs in the LRRC20, PPM1H, LPAR1, ANKS1A, and VSIG2 loci each demonstrated strong association with a particular serologic profile (all odds ratios > 2.2 and P < 3.5 × 10-4). Each of these serologic profiles was associated with increased serum IFN-α. SNPs in both PTPRM and LRRC20 were associated with increased serum IFN-α independent of serologic profile (P = 2.2 × 10-6 and P = 2.6 × 10-3 respectively). None of the SNPs were strongly associated with SLE in case-control analysis, suggesting that the major impact of these variants will be upon subphenotypes in SLE.
This study demonstrates the power of using serologic and cytokine subphenotypes to elucidate genetic factors involved in complex autoimmune disease. The distinct associations observed emphasize the heterogeneity of molecular pathogenesis in SLE, and the need for stratification by subphenotypes in genetic studies. We hypothesize that these genetic variants play a role in disease manifestations and severity in SLE.
Glass microscope slides are considered by many as the substrate of choice for microarray manufacturing due to their amenability to various surface chemistry modifications. The use of silanes to ...attach various functional groups onto glass slides has provided a versatile tool for the covalent immobilization of many diverse biomolecules of interest. We recently noted a dramatic reduction in biomolecule immobilization efficiency on standard microscope slides prepared using a well-characterized silanization method. A survey of commercial soda-lime slides yielded the surprising result that slides purchased prior to 2008 had superior immobilization efficiencies when compared to those purchased after 2008. Characterization of the slides by X-ray photoelectron spectroscopy (XPS), contact angle measurements, and atomic force microscopy (AFM), revealed a significant correlation (R > 0.9) between magnesium content, surface roughness, and bioimmobilization efficiency. High performance slides had higher magnesium content and higher root-mean-square (rms) roughness (P < 0.005) than slides with lower bioimmobilization efficiencies. Although the exact mechanism of how magnesium content and surface roughness affect silane deposition has not yet been defined, we show that recent changes in the chemical and physical properties of commercial soda-lime slides affect the ability of these slides to be covalently modified.
In the SMI++ framework, the real world is viewed as a collection of objects behaving as finite state machines. These objects can represent real entities, such as hardware devices or software tasks, ...or they can represent abstract subsystems. A special language (SML) is provided for the object description, The SML description is then interpreted by a Logic Engine (coded in C++) to drive the Control System SMI++ objects can run in a variety of platforms all communication being handled transparently by an underlying communication system-DIM. This framework has been used by the DELPHI experiment at CERN for the experiment control. A significantly upgraded version is now being used by BaBar experiment at SLAC.
The LHCb Run Control Alessio, F; Barandela, M C; Callot, O ...
Journal of physics. Conference series,
01/2010, Letnik:
219, Številka:
2
Journal Article
Recenzirano
Odprti dostop
LHCb has designed and implemented an integrated Experiment Control System. The Control System uses the same concepts and the same tools to control and monitor all parts of the experiment: the Data ...Acquisition System, the Timing and the Trigger Systems, the High Level Trigger Farm, the Detector Control System, the Experiment's Infrastructure and the interaction with the CERN Technical Services and the Accelerator. LHCb's Run Control, the main interface used by the experiment's operator, provides access in a hierarchical, coherent and homogeneous manner to all areas of the experiment and to all its sub-detectors. It allows for automated (or manual) configuration and control, including error recovery, of the full experiment in its different running modes. Different instances of the same Run Control interface are used by the various sub-detectors for their stand-alone activities: test runs, calibration runs, etc. The architecture and the tools used to build the control system, the guidelines and components provided to the developers, as well as the first experience with the usage of the Run Control will be presented
LHCb Online event processing and filtering Alessio, F; Barandela, C; Brarda, L ...
Journal of physics. Conference series,
07/2008, Letnik:
119, Številka:
2
Journal Article
Recenzirano
Odprti dostop
The first level trigger of LHCb accepts one million events per second. After preprocessing in custom FPGA-based boards these events are distributed to a large farm of PC-servers using a high-speed ...Gigabit Ethernet network. Synchronisation and event management is achieved by the Timing and Trigger system of LHCb. Due to the complex nature of the selection of B-events, which are the main interest of LHCb, a full event-readout is required. Event processing on the servers is parallelised on an event basis. The reduction factor is typically 1/500. The remaining events are forwarded to a formatting layer, where the raw data files are formed and temporarily stored. A small part of the events is also forwarded to a dedicated farm for calibration and monitoring. The files are subsequently shipped to the CERN Tier0 facility for permanent storage and from there to the various Tier1 sites for reconstruction. In parallel files are used by various monitoring and calibration processes running within the LHCb Online system. The entire data-flow is controlled and configured by means of a SCADA system and several databases. After an overview of the LHCb data acquisition and its design principles this paper will emphasize the LHCb event filter system, which is now implemented using the final hardware and will be ready for data-taking for the LHC startup. Control, configuration and security aspects will also be discussed.
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