Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS)

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.

A network forensics tool for precise data packet capture and replay in cyber-physical systems

Network data packet capture and replay capabilities are basic requirements for forensic analysis of faults and security-related anomalies, as well as for testing and development. Cyber-physical networks, in which data packets are used to monitor and control physical devices, must operate within strict timing constraints, in order to match the hardware devices' characteristics. Standard network monitoring tools are unsuitable for such systems because they cannot guarantee to capture all data packets, may introduce their own traffic into the network, and cannot reliably reproduce the original timing of data packets. Here we present a high-speed network forensics tool specifically designed for capturing and replaying data traffic in Supervisory Control and Data Acquisition systems. Unlike general-purpose "packet capture" tools it does not affect the observed network's data traffic and guarantees that the original packet ordering is preserved. Most importantly, it allows replay of network traffic precisely matching its original timing. The tool was implemented by developing novel user interface and back-end software for a special-purpose network interface card. Experimental results show a clear improvement in data capture and replay capabilities over standard network monitoring methods and general-purpose forensics solutions.

Design and fabrication of an automated temperature programmed reaction system to evaluate 3-way catalysts Ce1-x-y(La/Y)(x)PtyO2-delta

A completely automated temperature-programmed reaction (TPR) system for carrying out gas-solid catalytic reactions under atmospheric flow conditions is fabricated to study CO and hydrocarbon oxidation, and NO reduction. The system consists of an all-stainless steel UHV system, quadrupole mass spectrometer SX200 (VG Scientific), a tubular furnace and micro-reactor, a temperature controller, a versatile gas handling system, and a data acquisition and analysis system. The performance of the system has been tested under standard experimental conditions for CO oxidation over well-characterized Ce1-x-y(La/Y)(y)O2-delta catalysts. Testing of 3-way catalysis with CO, NO and C2H2 to convert to CO2, N-2 and H2O is done with this catalyst which shows complete removal of pollutants below 325 degrees C. Fixed oxide-ion defects in Pt substituted Ce1-y(La/Y)(y)O2-y/2 show higher catalytic activity than Pt ion-substituted CeO2

Design and fabrication of an automated temperature programmed reaction system to evaluate 3-way catalysts Ce1-x-y(La/Y)(x)PtyO2-delta

A completely automated temperature-programmed reaction (TPR) system for carrying out gas-solid catalytic reactions under atmospheric flow conditions is fabricated to study CO and hydrocarbon oxidation, and NO reduction. The system consists of an all-stainless steel UHV system, quadrupole mass spectrometer SX200 (VG Scientific), a tubular furnace and micro-reactor, a temperature controller, a versatile gas handling system, and a data acquisition and analysis system. The performance of the system has been tested under standard experimental conditions for CO oxidation over well-characterized Ce1-x-y(La/Y)(y)O2-delta catalysts. Testing of 3-way catalysis with CO, NO and C2H2 to convert to CO2, N-2 and H2O is done with this catalyst which shows complete removal of pollutants below 325 degrees C. Fixed oxide-ion defects in Pt substituted Ce1-y(La/Y)(y)O2-y/2 show higher catalytic activity than Pt ion-substituted CeO2.

Requirements for information management system in agricultural contracting

Menneinä vuosikymmeninä maatalouden työt ovat ensin koneellistuneet voimakkaasti ja sittemmin mukaan on tullut automaatio. Nykyään koneiden kokoa suurentamalla ei enää saada tuottavuutta nostettua merkittävästi, vaan työn tehostaminen täytyy tehdä olemassa olevien resurssien käyttöä tehostamalla. Tässä työssä tarkastelun kohteena on ajosilppuriketju nurmisäilörehun korjuussa. Säilörehun korjuun intensiivisyys ja koneyksiköiden runsas määrä ovat työnjohdon kannalta vaativa yhdistelmä. Työn tavoitteena oli selvittää vaatimuksia maatalouden urakoinnin tueksi kehitettävälle tiedonhallintajärjestelmälle. Tutkimusta varten haastateltiin yhteensä 12 urakoitsijaa tai yhteistyötä tekevää viljelijää. Tutkimuksen perusteella urakoitsijoilla on tarvetta tietojärjestelmille.Luonnollisesti urakoinnin laajuus ja järjestelyt vaikuttavat asiaan. Tutkimuksen perusteella keskeisimpiä vaatimuksia tiedonhallinnalle ovat: • mahdollisimman laaja, yksityiskohtainen ja automaattinen tiedon keruu tehtävästä työstä • karttapohjaisuus, kuljettajien opastus kohteisiin • asiakasrekisteri, työn tilaus sähköisesti • tarjouspyyntöpohjat, hintalaskurit • luotettavuus, tiedon säilyvyys • sovellettavuus monenlaisiin töihin • yhteensopivuus muiden järjestelmien kanssa Kehitettävän järjestelmän tulisi siis tutkimuksen perusteella sisältää seuraavia osia: helppokäyttöinen suunnittelu/asiakasrekisterityökalu, toimintoja koneiden seurantaan, opastukseen ja johtamiseen, työnaikainen tiedonkeruu sekä kerätyn tiedon käsittelytoimintoja. Kaikki käyttäjät eivät kuitenkaan tarvitse kaikkia toimintoja, joten urakoitsijan on voitava valita tarvitsemansa osat ja mahdollisesti lisätä toimintoja myöhemmin. Tiukoissa taloudellisissa ja ajallisissa raameissa toimivat urakoitsijat ovat vaativia asiakkaita, joiden käyttämän tekniikan tulee olla toimivaa ja luotettavaa. Toisaalta inhimillisiä virheitä sattuu kokeneillekin, joten hyvällä tietojärjestelmällä työstä tulee helpompaa ja tehokkaampaa.

A Low-Cost System for Measurement and Spectral Analysis of Motor Acoustic Noise

Workplace noise has become one of the major issues in industry not only because of workers’ health but also due to safety. Electric motors, particularly, inverter fed induction motors emit objectionably high levels of noise. This has led to the emergence of a research area, concerned with measurement and mitigation of the acoustic noise. This paper presents a lowcost option for measurement and spectral analysis of acoustic noise emitted by electric motors. The system consists of an electret microphone, amplifier and filter. It makes use of the windows sound card and associated software for data acquisition and analysis. The measurement system is calibrated using a professional sound level meter. Acoustic noise measurements are made on an induction motor drive using the proposed system as per relevant international standards. These measurements are seen to match closely with those of a professional meter.

Instrumentation and control of a two-stage 4-bed silica gel plus water adsorption cooling cum desalination system

This paper presents the instrumentation and control architecture for a laboratory based two-stage 4-bed silica gel + water adsorption system. The system consists of primarily two fluids: refrigerant (water vapour) and heat transfer fluid (water) flowing through various components. Heat input to the system is simulated using multiple heaters and ambient air is used as the heat sink. The laboratory setup incorporates a real time National Instruments (NI) controller to control several digital and analog valves, heaters, pumps and fans along with simultaneous data acquisition from various flow, pressure and temperature sensors. The paper also presents in detail the various automated and manual tasks required for successful operation of the system. Finally the system pressure and temperature dynamics are reported and its performance evaluated for various cycle times. (C) 2015 Elsevier Ltd. All rights reserved.

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and substrate maps from James Island to Ozette Lake, Washington Outer Coast

Without knowledge of basic seafloor characteristics, the ability to address any number of critical marine and/or coastal management issues is diminished. For example, management and conservation of essential fish habitat (EFH), a requirement mandated by federally guided fishery management plans (FMPs), requires among other things a description of habitats for federally managed species. Although the list of attributes important to habitat are numerous, the ability to efficiently and effectively describe many, and especially at the scales required, does not exist with the tools currently available. However, several characteristics of seafloor morphology are readily obtainable at multiple scales and can serve as useful descriptors of habitat. Recent advancements in acoustic technology, such as multibeam echosounding (MBES), can provide remote indication of surficial sediment properties such as texture, hardness, or roughness, and further permit highly detailed renderings of seafloor morphology. With acoustic-based surveys providing a relatively efficient method for data acquisition, there exists a need for efficient and reproducible automated segmentation routines to process the data. Using MBES data collected by the Olympic Coast National Marine Sanctuary (OCNMS), and through a contracted seafloor survey, we expanded on the techniques of Cutter et al. (2003) to describe an objective repeatable process that uses parameterized local Fourier histogram (LFH) texture features to automate segmentation of surficial sediments from acoustic imagery using a maximum likelihood decision rule. Sonar signatures and classification performance were evaluated using video imagery obtained from a towed camera sled. Segmented raster images were converted to polygon features and attributed using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999) for use in a geographical information system (GIS). (PDF contains 41 pages.)

Olympic Coast National Marine Sanctuary Habitat Mapping: Survey report and classification of side scan sonar data from surveys HMPR-114-2004-02 and HMPR-116-2005-01.

The Olympic Coast National Marine Sanctuary (OCNMS) continues to invest significant resources into seafloor mapping activities along Washington’s outer coast (Intelmann and Cochrane 2006; Intelmann et al. 2006; Intelmann 2006). Results from these annual mapping efforts offer a snapshot of current ground conditions, help to guide research and management activities, and provide a baseline for assessing the impacts of various threats to important habitat. During the months of August 2004 and May and July 2005, we used side scan sonar to image several regions of the sea floor in the northern OCNMS, and the data were mosaicked at 1-meter pixel resolution. Video from a towed camera sled, bathymetry data, sedimentary samples and side scan sonar mapping were integrated to describe geological and biological aspects of habitat. Polygon features were created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). For three small areas that were mapped with both side scan sonar and multibeam echosounder, we made a comparison of output from the classified images indicating little difference in results between the two methods. With these considerations, backscatter derived from multibeam bathymetry is currently a costefficient and safe method for seabed imaging in the shallow (<30 meters) rocky waters of OCNMS. The image quality is sufficient for classification purposes, the associated depths provide further descriptive value and risks to gear are minimized. In shallow waters (<30 meters) which do not have a high incidence of dangerous rock pinnacles, a towed multi-beam side scan sonar could provide a better option for obtaining seafloor imagery due to the high rate of acquisition speed and high image quality, however the high probability of losing or damaging such a costly system when deployed as a towed configuration in the extremely rugose nearshore zones within OCNMS is a financially risky proposition. The development of newer technologies such as intereferometric multibeam systems and bathymetric side scan systems could also provide great potential for mapping these nearshore rocky areas as they allow for high speed data acquisition, produce precisely geo-referenced side scan imagery to bathymetry, and do not experience the angular depth dependency associated with multibeam echosounders allowing larger range scales to be used in shallower water. As such, further investigation of these systems is needed to assess their efficiency and utility in these environments compared to traditional side scan sonar and multibeam bathymetry. (PDF contains 43 pages.)

Developing A Microfluidic-Based System To Quantify Cell Capture Efficiency

Micro-fabrication technology has substantial potential for identifying molecular markers expressed on the surfaces of tissue cells and viruses. It has been found in several conceptual prototypes that cells with such markers are able to be captured by their antibodies immobilized on microchannel substrates and unbound cells are flushed out by a driven flow. The feasibility and reliability of such a microfluidic-based assay, however, remains to be further tested. In the current work, we developed a microfluidic-based system consisting of a microfluidic chip, an image grabbing unit, data acquisition and analysis software, as well as a supporting base. Specific binding of CD59-expressed or BSA-coupled human red blood cells (RBCs) to anti-CD59 or anti-BSA antibody-immobilized chip surfaces was quantified by capture efficiency and by the fraction of bound cells. Impacts of respective flow rate, cell concentration, antibody concentration and site density were tested systematically. The measured data indicated that the assay was robust. The robustness was further confirmed by capture efficiencies measured from an independent ELISA-based cell binding assay. These results demonstrated that the system developed provided a new platform to effectively quantify cellular surface markers effectively, which promoted the potential applications in both biological studies and clinical diagnoses.

Computer system support for data analysis

This thesis is an investigation into the nature of data analysis and computer software systems which support this activity.

The first chapter develops the notion of data analysis as an experimental science which has two major components: data-gathering and theory-building. The basic role of language in determining the meaningfulness of theory is stressed, and the informativeness of a language and data base pair is studied. The static and dynamic aspects of data analysis are then considered from this conceptual vantage point. The second chapter surveys the available types of computer systems which may be useful for data analysis. Particular attention is paid to the questions raised in the first chapter about the language restrictions imposed by the computer system and its dynamic properties.

The third chapter discusses the REL data analysis system, which was designed to satisfy the needs of the data analyzer in an operational relational data system. The major limitation on the use of such systems is the amount of access to data stored on a relatively slow secondary memory. This problem of the paging of data is investigated and two classes of data structure representations are found, each of which has desirable paging characteristics for certain types of queries. One representation is used by most of the generalized data base management systems in existence today, but the other is clearly preferred in the data analysis environment, as conceptualized in Chapter I.

This data representation has strong implications for a fundamental process of data analysis -- the quantification of variables. Since quantification is one of the few means of summarizing and abstracting, data analysis systems are under strong pressure to facilitate the process. Two implementations of quantification are studied: one analagous to the form of the lower predicate calculus and another more closely attuned to the data representation. A comparison of these indicates that the use of the "label class" method results in orders of magnitude improvement over the lower predicate calculus technique.

The importance of high frequency data in ecological modelling.

The purpose of this note is to discuss the role of high frequency data in ecological modelling and to identify some of the data requirements for the further development of ecological models for operational oceanography. There is a pressing requirement for the establishment of data acquisition systems for key ecological variables with a high spatial and temporal coverage. Such a system will facilitate the development of operational models. It is envisaged that both in-situ and remotely sensed measurements will need to combined to achieve this aim.

Microcontroller based double beam modulation system for atomic scattering experiments

Double beam modulation is widely used in atomic collision experiments in the case where the noise arising froth each of the beams exceeds the measured signal. A method for minimizing the statistical uncertainty in a measured signal in a given time period is discussed, and a flexible modulation and counting system based on a low cost PIC microcontroller is described. This device is capable of modifying the acquisition parameters in real time during the course of an experimental run. It is shown that typical savings in data acquisition time of approximately 30% can be achieved using this optimized modulation scheme.

A single microphone capillary-based system for measuring the complex input impedance of musical wind instruments

Capillary-based systems for measuring the input impedance of musical wind instruments were first developed in the mid-20th century and remain in widespread use today. In this paper, the basic principles and assumptions underpinning the design of such systems are examined. Inexpensive modifications to a capillary-based impedance measurement set-up made possible due to advances in computing and data acquisition technology are discussed. The modified set-up is able to measure both impedance magnitude and impedance phase even though it only contains one microphone. In addition, a method of calibration is described that results in a significant improvement in accuracy when measuring high impedance objects on the modified capillary-based system. The method involves carrying out calibration measurements on two different objects whose impedances are well-known theoretically. The benefits of performing two calibration measurements (as opposed to the one calibration measurement that has been traditionally used) are demonstrated experimentally through input impedance measurements on two test objects and a Boosey and Hawkes oboe. © S. Hirzel Verlag · EAA.

Rule-Based Intrusion Detection System for SCADA Networks

Increased complexity and interconnectivity of Supervisory Control and Data Acquisition (SCADA) systems in Smart Grids potentially means greater susceptibility to malicious attackers. SCADA systems with legacy communication infrastructure have inherent cyber-security vulnerabilities as these systems were originally designed with little consideration of cyber threats. In order to improve cyber-security of SCADA networks, this paper presents a rule-based Intrusion Detection System (IDS) using a Deep Packet Inspection (DPI) method, which includes signature-based and model-based approaches tailored for SCADA systems. The proposed signature-based rules can accurately detect several known suspicious or malicious attacks. In addition, model-based detection is proposed as a complementary method to detect unknown attacks. Finally, proposed intrusion detection approaches for SCADA networks are implemented and verified using a ruled based method.