Evaluation of reference-based two-color methods for measurement of gene expression ratios using spotted cDNA microarrays

Abstract Background Spotted cDNA microarrays generally employ co-hybridization of fluorescently-labeled RNA targets to produce gene expression ratios for subsequent analysis. Direct comparison of two RNA samples in the same microarray provides the highest level of accuracy; however, due to the number of combinatorial pair-wise comparisons, the direct method is impractical for studies including large number of individual samples (e.g., tumor classification studies). For such studies, indirect comparisons using a common reference standard have been the preferred method. Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard. Results We performed hybridizations using a fixed amount of Cy3-labeled reference oligonucleotide (RefOligo) against distinct Cy5-labeled targets from prostate, breast and kidney tumor samples. Reconstructed ratios between all tissue pairs were derived from ratios between each tissue sample and RefOligo. Reconstructed ratios were compared to (i) ratios obtained in parallel from direct pair-wise hybridizations of tissue samples, and to (ii) reconstructed ratios derived from hybridization of each tissue against a reference RNA pool (RefPool). To evaluate the effect of the external references, reconstructed ratios were also calculated directly from intensity values of single-channel (One-Color) measurements derived from tissue sample data collected in the RefOligo experiments. We show that the average coefficient of variation of ratios between intra- and inter-slide replicates derived from RefOligo, RefPool and One-Color were similar and 2 to 4-fold higher than ratios obtained in direct hybridizations. Correlation coefficients calculated for all three tissue comparisons were also similar. In addition, the performance of all indirect methods in terms of their robustness to identify genes deemed as differentially expressed based on direct hybridizations, as well as false-positive and false-negative rates, were found to be comparable. Conclusion RefOligo produces ratios as precise and accurate as ratios reconstructed from a RNA pool, thus representing a reliable alternative in reference-based hybridization experiments. In addition, One-Color measurements alone can reconstruct expression ratios without loss in precision or accuracy. We conclude that both methods are adequate options in large-scale projects where the amount of a common reference RNA pool is usually restrictive.

Measurement of K(892)*0 resonance production in Pb-Pb collisions with the ALICE experiment at the LHC

The analysis of the K(892)*0 resonance production in Pb–Pb collisions at √sNN = 2.76 TeV with the ALICE detector at the LHC is presented. The analysis is motivated by the interest in the measurement of short-lived resonances production that can provide insights on the properties of the medium produced in heavy-ion collisions both during its partonic (Quark-Gluon Plasma) and hadronic phase. This particular analysis exploits particle identification of the ALICE Time-Of-Flight detector. The ALICE experiment is presented, with focus on the performance of the Time-Of-Flight system. The aspects of calibration and data quality controls are discussed in detail, while illustrating the excellent and very stable performance of the system in different collision environments at the LHC. A full analysis of the K*0 resonance production is presented: from the resonance reconstruction to the determination of the efficiency and the systematic uncertainty. The results show that the analysis strategy discussed is a valid tool to measure the K∗0 up to intermediate momenta. Preliminary results on K*0 resonance production at the LHC are presented and confirmed to be a powerful tool to study the physics of ultra-relativistic heavy-ion collisions.

Tracking, b-tagging and measurement of the b-jet production cross section with the ATLAS detector

The Standard Model of elementary particle physics was developed to describe the fundamental particles which constitute matter and the interactions between them. The Large Hadron Collider (LHC) at CERN in Geneva was built to solve some of the remaining open questions in the Standard Model and to explore physics beyond it, by colliding two proton beams at world-record centre-of-mass energies. The ATLAS experiment is designed to reconstruct particles and their decay products originating from these collisions. The precise reconstruction of particle trajectories plays an important role in the identification of particle jets which originate from bottom quarks (b-tagging). This thesis describes the step-wise commissioning of the ATLAS track reconstruction and b-tagging software and one of the first measurements of the b-jet production cross section in pp collisions at sqrt(s)=7 TeV with the ATLAS detector. The performance of the track reconstruction software was studied in great detail, first using data from cosmic ray showers and then collisions at sqrt(s)=900 GeV and 7 TeV. The good understanding of the track reconstruction software allowed a very early deployment of the b-tagging algorithms. First studies of these algorithms and the measurement of the b-tagging efficiency in the data are presented. They agree well with predictions from Monte Carlo simulations. The b-jet production cross section was measured with the 2010 dataset recorded by the ATLAS detector, employing muons in jets to estimate the fraction of b-jets. The measurement is in good agreement with the Standard Model predictions.

DensiProbe Spine: a novel instrument for intraoperative measurement of bone density in transpedicular screw fixation

STUDY DESIGN.: Cadaver study. OBJECTIVE.: To determine bone strength in vertebrae by measuring peak breakaway torque or indentation force using custom-made pedicle probes. SUMMARY OF BACKGROUND DATA.: Screw performance in dorsal spinal instrumentation is dependent on bone quality of the vertebral body. To date no intraoperative measuring device to validate bone strength is available. Destructive testing may predict bone strength in transpedicular instrumentations in osteoporotic vertebrae. Insertional torque measurements showed varying results. METHODS.: Ten human cadaveric vertebrae were evaluated for bone mineral density (BMD) measurements by quantitative computed tomography. Peak torque and indentation force of custom-made probes as a measure for mechanical bone strength were assessed via a transpedicular approach. The results were correlated to regional BMD and to biomechanical load testing after pedicle screw implementation. RESULTS.: Both methods generated a positive correlation to failure load of the respective vertebrae. The correlation of peak breakaway torque to failure load was r = 0.959 (P = 0.003), therewith distinctly higher than the correlation of indentation force to failure load, which was r = 0.690 (P = 0.040). In predicting regional BMD, measurement of peak torque also performed better than that of indentation force (r = 0.897 [P = 0.002] vs. r = 0.777 [P = 0.017]). CONCLUSION.: Transpedicular measurement of peak breakaway torque is technically feasible and predicts reliable local bone strength and implant failure for dorsal spinal instrumentations in this experimental setting.

Effective compression ratio-A new measurement of the quality of thorax compression during CPR

PURPOSE: Computer-based feedback systems for assessing the quality of cardiopulmonary resuscitation (CPR) are widely used these days. Recordings usually involve compression and ventilation dependent variables. Thorax compression depth, sufficient decompression and correct hand position are displayed but interpreted independently of one another. We aimed to generate a parameter, which represents all the combined relevant parameters of compression to provide a rapid assessment of the quality of chest compression-the effective compression ratio (ECR). METHODS: The following parameters were used to determine the ECR: compression depth, correct hand position, correct decompression and the proportion of time used for chest compressions compared to the total time spent on CPR. Based on the ERC guidelines, we calculated that guideline compliant CPR (30:2) has a minimum ECR of 0.79. To calculate the ECR, we expanded the previously described software solution. In order to demonstrate the usefulness of the new ECR-parameter, we first performed a PubMed search for studies that included correct compression and no-flow time, after which we calculated the new parameter, the ECR. RESULTS: The PubMed search revealed 9 trials. Calculated ECR values ranged between 0.03 (for basic life support [BLS] study, two helpers, no feedback) and 0.67 (BLS with feedback from the 6th minute). CONCLUSION: ECR enables rapid, meaningful assessment of CPR and simplifies the comparability of studies as well as the individual performance of trainees. The structure of the software solution allows it to be easily adapted to any manikin, CPR feedback devices and different resuscitation guidelines (e.g. ILCOR, ERC).

Thickness measurement of dynamic thin liquid films generated by plug-annular flow in non-wetting microchannels

Surface tension forces are significant at millimeter length-scales, causing profoundly different flow morphologies in microchannels than in macroscale flows. The existence and morphology of thin liquid films is particularly relevant for predicting performance and operational stability of devices containing microscale two phase flows. Analytical, computational, and experimental methods previously employed in the study of thin liquid films are discussed. Thicknesses before and after a novel film morphology, referred to as a `shock,' are measured with a novel film thickness measurement technique that uses confocal microscopy. Film thicknesses predicted by previous work are compared to experimental results. Methods for increasing the accuracy of the confocal film thickness measurement technique are discussed.

A Physiological Controller for Turbodynamic Ventricular Assist Devices Based on a Measurement of the Left Ventricular Volume

The current article presents a novel physiological control algorithm for ventricular assist devices (VADs), which is inspired by the preload recruitable stroke work. This controller adapts the hydraulic power output of the VAD to the end-diastolic volume of the left ventricle. We tested this controller on a hybrid mock circulation where the left ventricular volume (LVV) is known, i.e., the problem of measuring the LVV is not addressed in the current article. Experiments were conducted to compare the response of the controller with the physiological and with the pathological circulation, with and without VAD support. A sensitivity analysis was performed to analyze the influence of the controller parameters and the influence of the quality of the LVV signal on the performance of the control algorithm. The results show that the controller induces a response similar to the physiological circulation and effectively prevents over- and underpumping, i.e., ventricular suction and backflow from the aorta to the left ventricle, respectively. The same results are obtained in the case of a disturbed LVV signal. The results presented in the current article motivate the development of a robust, long-term stable sensor to measure the LVV.

DensiProbe Spine: an intraoperative measurement of bone quality in spinal instrumentation. A clinical feasibility study

BACKGROUND CONTEXT A new device, DensiProbe, has been developed to provide surgeons with intraoperative information about bone strength by measuring the peak breakaway torque. In cases of low bone quality, the treatment can be adapted to the patient's condition, for example, by improving screw-anchorage with augmentation techniques. PURPOSE The objective of this study was to investigate the feasibility of DensiProbe Spine in patients undergoing transpedicular fixation. STUDY DESIGN Prospective feasibility study on consecutive patients. PATIENT SAMPLE Fourteen women and 16 men were included in this study. OUTCOME MEASURES Local and general bone quality. METHODS These consecutive patients scheduled for transpedicular fixation were evaluated for bone mineral density (BMD), which was measured globally by dual-energy X-ray absorptiometry and locally via biopsies using quantitative microcomputed tomography. The breakaway torque force within the vertebral body was assessed intraoperatively via the transpedicular approach with the DensiProbe Spine. The results were correlated with the areal BMD at the lumbar spine and the local volumetric BMD (vBMD) and a subjective impression of bone strength. The feasibility of the method was evaluated, and the clinical and radiological performance was evaluated over a 1-year follow-up. This study was funded by an AO Spine research grant; DensiProbe was developed at the AO Research Institute Davos, Switzerland; the AO Foundation is owner of the intellectual property rights. RESULTS In 30 patients, 69 vertebral levels were examined. The breakaway torque consistently correlated with an experienced surgeon's quantified impression of resistance as well as with vBMD of the same vertebra. Beyond a marginal prolongation of surgery time, no adverse events related to the usage of the device were observed. CONCLUSIONS The intraoperative transpedicular measurement of the peak breakaway torque was technically feasible, safe, and reliably predictive of local vBMD during dorsal spinal instrumentations in a clinical setting. Larger studies are needed to define specific thresholds that indicate a need for the augmentation or instrumentation of additional levels.

Noise Figure Measurement of Differential Amplifiers Using non-Ideal Baluns

This paper analyzes the noise and gain measurement of microwave differential amplifiers using two passive baluns. A general model of the baluns is considered, including potential losses and phase/amplitude unbalances. This analysis allows de-embedding the actual gain and noise performance of the isolated amplifier by using single-ended measurements of the cascaded system and baluns. Finally, measured results from two amplifier prototypes are used to validate the theoretical principles.

On the design and measurement of a novel non-orthogonal multi-beam network for triangular arrays of three radiating elements

An innovative dissipative multi-beam network for triangular arrays of three radiating elements is proposed. This novel network provides three orthogonal beams in θ0 elevation angle and a fourth one in the broadside steering direction. The network is composed of 90º hybrid couplers and fixed phase shifters. In this paper, a relation between network components, radiating element distance and beam steering directions will be shown. Application of the proposed dissipative network to the triangular cells of three radiating elements that integrate the intelligent antenna GEODA will be exhibited. This system works at 1.7 GHz, it has a 60º single radiating element beamwidth and a distance between array elements of 0.57 λ. Both beam patterns, theoretical and simulated, obtained with the network will be depicted. Moreover, the whole system, dissipative network built with GEODA cell array, has been measured in the anechoic chamber of the Radiation Group of Technical University of Madrid, demonstrating expected performance.

The impacts of market orientation and corporate social responsibility on firm performance:evidence from China

Purpose – The purpose of this paper is to investigate the joint effects of market orientation (MO) and corporate social responsibility (CSR) on firm performance. Design/methodology/approach – Data were collected via a questionnaire survey of star-rated hotels in China and a total of 143 valid responses were received. The hypotheses were tested by employing structural equation modelling with a maximum likelihood estimation option. Findings – It was found that although both MO and CSR could enhance performance, once the effects of CSR are accounted for, the direct effects of MO on performance diminish considerably to almost non-existent. Although this result may be due to the fact that the research is conducted in China, a country where CSR might be crucially important to performance given the country's socialist legacy, it nonetheless provides strong evidence that MO's impact on organizational performance is mediated by CSR. Research limitations/implications – The main limitations include the use of cross-sectional data, the subjective measurement of performance and the uniqueness of the research setting (China). The findings provide an additional important insight into the processes by which a market oriented culture is transformed into superior organizational performance. Originality/value – This paper is one of the first to examine the joint effects of MO and CSR on business performance. The empirical evidence from China adds to the existing literature on the respective importance of MO and CSR.

Evaluation and measurement of multiprocessor systems with shared memory

This study is concerned with several proposals concerning multiprocessor systems and with the various possible methods of evaluating such proposals. After a discussion of the advantages and disadvantages of several performance evaluation tools, the author decides that simulation is the only tool powerful enough to develop a model which would be of practical use, in the design, comparison and extension of systems. The main aims of the simulation package developed as part of this study are cost effectiveness, ease of use and generality. The methodology on which the simulation package is based is described in detail. The fundamental principles are that model design should reflect actual systems design, that measuring procedures should be carried out alongside design that models should be well documented and easily adaptable and that models should be dynamic. The simulation package itself is modular, and in this way reflects current design trends. This approach also aids documentation and ensures that the model is easily adaptable. It contains a skeleton structure and a library of segments which can be added to or directly swapped with segments of the skeleton structure, to form a model which fits a user's requirements. The study also contains the results of some experimental work carried out using the model, the first part of which tests• the model's capabilities by simulating a large operating system, the ICL George 3 system; the second part deals with general questions and some of the many proposals concerning multiprocessor systems.

Measurement of implicit leadership theories and their effect on leadership processes and outcomes

The leadership categorisation theory suggests that followers rely on a hierarchical cognitive structure in perceiving leaders and the leadership process, which consists of three levels; superordinate, basic and subordinate. The predominant view is that followers rely on Implicit Leadership Theories (ILTs) at the basic level in making judgments about managers. The thesis examines whether this presumption is true by proposing and testing two competing conceptualisations; namely the congruence between the basic level ILTs (general leader) and actual manager perceptions, and subordinate level ILTs (job-specific leader) and actual manager. The conceptualisation at the job-specific level builds on context-related assertions of the ILT explanatory models: leadership categorisation, information processing and connectionist network theories. Further, the thesis addresses the effects of ILT congruence at the group level. The hypothesised model suggests that Leader-Member Exchange (LMX) will act as a mediator between ILT congruence and outcomes. Three studies examined the proposed model. The first was cross-sectional with 175 students reporting on work experience during a 1-year industrial placement. The second was longitudinal and had a sample of 343 students engaging in a business simulation in groups with formal leadership. The final study was a cross-sectional survey in several organisations with a sample of 178. A novel approach was taken to congruence analysis; the hypothesised models were tested using Latent Congruence Modelling (LCM), which accounts for measurement error and overcomes the majority of limitations of traditional approaches. The first two studies confirm the traditional theorised view that employees rely on basic-level ILTs in making judgments about their managers with important implications, and show that LMX mediates the relationship between ILT congruence and work-related outcomes (performance, job satisfaction, well-being, task satisfaction, intragroup conflict, group satisfaction, team realness, team-member exchange, group performance). The third study confirms this with conflict, well-being, self-rated performance and commitment as outcomes.

Direct measurement of coherency limits for strain relaxation in heteroepitaxial core/shell nanowires

The growth of heteroepitaxially strained semiconductors at the nanoscale enables tailoring of material properties for enhanced device performance. For core/shell nanowires (NWs), theoretical predictions of the coherency limits and the implications they carry remain uncertain without proper identification of the mechanisms by which strains relax. We present here for the Ge/Si core/shell NW system the first experimental measurement of critical shell thickness for strain relaxation in a semiconductor NW heterostructure and the identification of the relaxation mechanisms. Axial and tangential strain relief is initiated by the formation of periodic a/2 〈110〉 perfect dislocations via nucleation and glide on {111} slip-planes. Glide of dislocation segments is directly confirmed by real-time in situ transmission electron microscope observations and by dislocation dynamics simulations. Further shell growth leads to roughening and grain formation which provides additional strain relief. As a consequence of core/shell strain sharing in NWs, a 16 nm radius Ge NW with a 3 nm Si shell is shown to accommodate 3% coherent strain at equilibrium, a factor of 3 increase over the 1 nm equilibrium critical thickness for planar Si/Ge heteroepitaxial growth. © 2012 American Chemical Society.

Application of calorimetric method for loss measurement of a SynRM drive system

Synchronous reluctance motors (SynRMs) are gaining in popularity in industrial drives due to their permanent magnet-free, competitive performance, and robust features. This paper studies the power losses in a 90-kW converter-fed SynRM drive by a calorimetric method in comparison of the traditional input-output method. After the converter and the motor were measured simultaneously in separate chambers, the converter was installed inside the large-size chamber next to the motor and the total drive system losses were obtained using one chamber. The uncertainty of both measurement methods is analyzed and discussed.