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PubMed2006

Integration of two-dimensional LC-MS with multivariate statistics for comparative analysis of proteomic samples.

LC-MS-based proteomics requires methods with high peak capacity and a high degree of automation, integrated with data-handling tools able to cope with the massive data produced and able to quantitatively compare them. This paper describes an off-line two-dimensional (2D) LC-MS method and its integration with software tools for data preprocessing and multivariate statistical analysis. The 2D LC-MS method was optimized in order to minimize peptide loss prior to sample injection and during the collection step after the first LC dimension, thus minimizing errors from off-column sample handling. The second dimension was run in fully automated mode, injecting onto a nanoscale LC-MS system a series of more than 100 samples, representing fractions collected in the first dimension (8 fractions/sample). As a model study, the method was applied to finding biomarkers for the antiinflammatory properties of zilpaterol, which are coupled to the beta2-adrenergic receptor. Secreted proteomes from U937 macrophages exposed to lipopolysaccharide in the presence or absence of propanolol or zilpaterol were analysed. Multivariate statistical analysis of 2D LC-MS data, based on principal component analysis, and subsequent targeted LC-MS/MS identification of peptides of interest demonstrated the applicability of the approach.

Adrenergic beta-Antagonists↗

PubMed1990

Estimation of microscopic redox potentials of a tetraheme protein, cytochrome c3 of Desulfovibrio vulgaris, Miyazaki F, and partial assignments of heme groups.

The microscopic formal redox potentials of a tetraheme protein, cytochrome c3 from Desulfovibrio vulgaris, Miyazaki F, were estimated from the chemical shifts of the heme methyl signals in its 1H NMR spectrum. All chemical shifts in the five macroscopic oxidation states were determined for eight of the heme methyl protons by the saturation-transfer method. The electron-distribution probability at each heme in each oxidation state was estimated directly from the chemical shifts. To minimize errors due to interheme pseudocontact contributions, the average electron-distribution probability was used for calculation of the microscopic formal redox potentials. By introducing interacting potentials, 32 parameters were reduced to 10. The 10 parameters were determined analytically from the 9 independent electron-distribution probabilities and 2 macroscopic formal redox potentials. The results showed the presence of a strong positive interaction between a pair of particular hemes. The microscopic formal redox potential changes dramatically with the extent of reduction because of the intramolecular interheme interactions. NMR signals of two hemes were assigned to particular hemes in the crystal structures by nuclear Overhauser effect experiments. The results showed that the hemes with the highest and lowest redox potentials in the one-electron reduction process correspond to hemes I and IV in the crystal structure.

Cytochrome c Group↗

PubMedDate not supplied

Transport and kinetic processes underlying biomolecular interactions in the BIACORE optical biosensor.

The transport and kinetic processes describing biomolecular interactions in the BIACORE optical biosensor have been studied with the help of a mathematical model. In comparison to previous models, the model presented here couples, for the first time, transport phenomena in the flow channel with hindered diffusive transport and reactions inside the hydrogel. Simulated experiments based on this model, and two simpler models extant in the literature, are used to identify cases under which the detailed model is essential for accurate prediction of kinetic parameters. It is shown that this model can substantially improve the accuracy of kinetic parameter estimation when transport limitations in the flow channel and/or the hydrogel significantly influence the observed instrument response curves. The model can extend the range of the instrument's applicability to higher concentrations of immobilized species within the hydrogel. It can also be used for accurate design of experiments with the purpose of minimizing errors in the estimation of the kinetic parameters.

Antibodies↗

PubMed1991

One-dimensional and two-dimensional 1H- and 13C-nuclear magnetic resonance (NMR) analysis of vitamin E raw materials or analytical reference standards.

Two-dimensional spectral analysis (COSY, HETCOR) was utilized to make the complete 13C- and 1H-NMR assignments for alpha-, beta-, gamma-, and delta-tocopherol as well as for the acetate and succinate esters of alpha-tocopherol. 13C-NMR was found to be especially useful in distinguishing between the various tocopherols and distinguishing between the d-isomer and the d,l-racemic mixture. HETCOR spectra were also found to be useful for the qualitative identification of mixtures of the tocopherols and sesame oil. Using a procedure designed to minimize errors arising from spin relaxation and nuclear Overhauser effects, 13C-NMR peak integrals were used to quantitate alpha-tocopherol and delta-tocopherol in the presence of sesame oil using benzoic acid as the standard for calibration of the quantitation. The NMR results were compared to a capillary column gas chromatographic analysis of the individual alpha-tocopherol and delta-tocopherol reference materials.

Carbon Isotopes↗

PubMed2005

Finding useful questions: on Bayesian diagnosticity, probability, impact, and information gain.

Several norms for how people should assess a question's usefulness have been proposed, notably Bayesian diagnosticity, information gain (mutual information), Kullback-Liebler distance, probability gain (error minimization), and impact (absolute change). Several probabilistic models of previous experiments on categorization, covariation assessment, medical diagnosis, and the selection task are shown to not discriminate among these norms as descriptive models of human intuitions and behavior. Computational optimization found situations in which information gain, probability gain, and impact strongly contradict Bayesian diagnosticity. In these situations, diagnosticity's claims are normatively inferior. Results of a new experiment strongly contradict the predictions of Bayesian diagnosticity. Normative theoretical concerns also argue against use of diagnosticity. It is concluded that Bayesian diagnosticity is normatively flawed and empirically unjustified.

Bayes Theorem↗

PubMed1978

Manufacture and utilization of antimony pH electrodes.

A new technique for manufacturing single-barreled and double-barreled antimony pH microelectrodes is described. The results of investigations into the accuracy of antimony as a pH sensor disclosed that the pH-voltage response is: 1) within the physiologic range, principally the result of the hydrogen ion activity of the solution in which the voltage is being developed, 2) in part, qualitatively anion-dependent, 3) modified by the presence of significant amounts of at least carbon dioxide, oxygen, and nitrogen gases, and 4) markedly offset by fluctuations in temperature. Our results further indicate that the accuracy of antimony as a pH sensor is determined by the quality of the calibration procedure. We conclude that if the antimony electrode is to accurately determine the pH of a biological fluid, the pH calibration solutions must closely resemble the unknown biological fluid with respect to temperature, PO2, PN2, and types of buffering anions. A calibration procedure is described which can minimize errors with antimony pH estimations when measuring the pH of proximal tubular fluid of the mammalian kidney.

Animals↗

PubMed1985

Autoradiographic studies of solute transport across the toad bladder.

The autoradiography of diffusible, hydrophilic solutes presents special problems in localization of the labeled solute under study. We present studies of the movement of 14C-labeled urea, and 14C- and 3H-labeled sucrose across the isolated urinary bladder of the toad, a vasopressin-sensitive epithelium, using a technique that avoids exposure to water throughout all processing steps and minimizes error caused by isotope scatter. We have shown a significant increase in 14C urea entry into epithelial cells following vasopressin, and a significant decrease following phloretin, an agent that selectively blocks vasopressin-stimulated urea transport. The autoradiographic technique confirms the luminal site of action of phloretin. Studies of 14C and 3H sucrose labeling show that this molecule is virtually excluded from the cell. The current method of grain counting is capable of yielding reliable information in studies of epithelial transport.

Animals↗

PubMed2005

Flexible strategies for sensory integration during motor planning.

When planning target-directed reaching movements, human subjects combine visual and proprioceptive feedback to form two estimates of the arm's position: one to plan the reach direction, and another to convert that direction into a motor command. These position estimates are based on the same sensory signals but rely on different combinations of visual and proprioceptive input, suggesting that the brain weights sensory inputs differently depending on the computation being performed. Here we show that the relative weighting of vision and proprioception depends both on the sensory modality of the target and on the information content of the visual feedback, and that these factors affect the two stages of planning independently. The observed diversity of weightings demonstrates the flexibility of sensory integration and suggests a unifying principle by which the brain chooses sensory inputs so as to minimize errors arising from the transformation of sensory signals between coordinate frames.

Adolescent↗

PubMed2001

Continuous and stopped flow injection for catalytic determination of total iodine in urine.

This paper describes the use of flow injection (FI) techniques for the determination of iodine in urine, based on the catalytic effect of iodide in the redox reaction between Ce(IV) and As(III). The proposed procedures minimize errors in the conventional batch method arising from the reading of absorbance at a fixed time after addition of Ce(IV) reagent. Two FI systems, for the continuous and stopped modes of operation were assembled. In the continuous-FI system, a thermostated bath was used to increase the sensitivity. However this is not necessary for the stopped-FI system. The two systems are comparable in terms of sensitivity, sample throughput and detection limit. The continuous-FI and the stopped-FI exhibited detection limits (3 sigma) of 2.3 and 3 micrograms I l-1 respectively. Both systems have equal sample throughputs of 35 samples h-1. Calibration plots for both techniques are linear. The FI procedures provide very short analysis times compared to the batch procedure. Using the linear regression test, there is no significant difference between the results from the four methods, i.e., continuous-FI, stopped-FI, conventional method and ICP-MS. The proposed methods are readily applicable for automation and can be an alternative to the conventional procedure for the survey of the iodine deficiency disorder. A condition for sample digestion is also proposed to reduce the amount of chloric acid required for complete digestion. Kinetic information of the reaction can also be obtained from the stopped flow mode.

Flow Injection Analysis↗

PubMed1971

Dielectric dispersion in aqueous solutions of oxyhaemoglobin and carboxyhaemoglobin.

The relative permittivity and conductivity of aqueous solutions of oxyhaemoglobin and carboxyhaemoglobin were measured over the frequency range 150kHz-100MHz. To minimize errors of measurement the investigations were carried out with three different samples of each type of haemoglobin, independent apparatus being used in two different laboratories. The dielectric increment and relaxation time were calculated at each of several temperatures from the results. These lead to a dipole moment of 400 Debyes and an activation enthalpy of 17.6+/-1.4kJ.mol(-1), both of which were found to be independent of temperature to within experimental error over the range 3-35 degrees C. The value of the dipole moment shows that the distribution of charge throughout the haemoglobin molecule is nearly symmetrical with respect to the centre of charge. The magnitude of the activation enthalpy is similar to that of the viscosity of water, in accord with the common observation that dielectric relaxation and viscosity are related phenomena. No significant differences are found between the dielectric parameters of oxyhaemoglobin and carboxyhaemoglobin. Combining the results with those obtained from X-ray diffraction of the solid a hydration value of 0.45g of water/g of protein is suggested, subject to the limitations of the model used. Finally, the results indicate the presence of a subsidiary dispersion, which could be attributed to the above quantity of bound water having a static permittivity of about 100 and a relaxation frequency in the region 100-200MHz.

Carbon Monoxide↗

PubMed1999

Obturation of root canals with different sealers using non-instrumentation technology.

AIM: To evaluate and compare the sealing quality of hand- or vacuum-obturated root canals after hand preparation or hydrodynamic cleansing of root canals, respectively. METHODOLOGY: After assessing root curvature, 96 single-rooted deep-frozen teeth were divided into eight comparable groups. The root canals of four groups were instrumented with the balanced force technique. The remaining uninstrumented teeth were connected to a reduced-pressure device (NIT) and the root-canal system perfused with 2.5% NaOCl under alternating pressure fields. This dissolved the pulpal tissues and removed debris from the root-canal system. The canals of the hand-instrumented groups were obturated using the cold lateral condensation method with guttapercha and one of four different sealers (AH26, AH Plus, Apexit and Pulp Canal Sealer EWT). The teeth treated with the alternating pressure device (NIT) were obturated by a vacuum obturation method (NIT) with the same four sealers. The quality of the coronal seal was assessed using a dye penetration method. In order to minimize errors the roots were perfused with water before exposure to the dye, under vacuum. The teeth were then rendered transparent and the depth of penetration of the dye between the wall of the canal and the obturating material was measured with a stereomicroscope. RESULTS: The canals cleaned and filled by NIT showed statistically significantly less dye penetration than those obturated by lateral condensation (P < 0.05). Within the NIT group, Pulp Canal Sealer EWT exhibited significantly more dye penetration than Apexit. Amongst the control lateral condensation groups no significant differences were found between the various sealers. CONCLUSIONS: The present investigation demonstrated the validity of the NIT obturation method in combination with commonly used root-canal sealers.

Bismuth↗

PubMed2001

Transesophageal echocardiographic evaluation of native aortic valve area: utility of the double-envelope technique.

OBJECTIVE: To assess the accuracy of aortic valve area (AVA) calculations using the continuity equation with data obtained from the double envelope (DE) (simultaneously obtained left ventricular outflow tract [V1]) and aortic valve [V2] velocities) during intraoperative transesophageal echocardiography (TEE). DESIGN: Prospective study; measurements were performed on-line. SETTING: University hospital. PARTICIPANTS: Cardiac and noncardiac surgical patients (n = 75) with recent aortic valve assessment (<3 months) undergoing general anesthesia or endotracheal intubation. INTERVENTIONS: Intraoperative AVA was measured by the continuity equation using the DE technique (DE/TEE) and by planimetry (PL/TEE). Left ventricular outflow tract diameter was obtained from midesophageal views, whereas subvalvular (V1) and valvular (V2) velocities were obtained simultaneously using continuous-wave Doppler from transgastric views. V1 was also obtained using pulsed-wave Doppler. Measurements were compared with AVA obtained preoperatively by the Gorlin equation during cardiac catheterization (G/CATH) or by transthoracic echocardiography using the traditional continuity equation (C/TTE) (nonsimultaneously obtained V1 and V2). MEASUREMENTS AND MAIN RESULTS: A DE was obtained in 73 of 75 patients (97%). Four patients had atrial fibrillation at the time of the examination, whereas the rest were in sinus rhythm. PL/TEE was performed in 54 of 71 patients with sinus rhythm (76%). Agreement was good between DE/TEE and G/CATH (mean bias, 0.02 cm(2) [SD, 0.24 cm(2)]), and C/TTE (mean bias, -0.05 cm(2) [SD, 0.16 cm(2)]). Agreement was not as good between PL/TEE and G/CATH (mean bias, -0.07 cm(2) [SD, 0.28 cm(2)]) and C/TTE (mean bias, -0.13 cm(2) [SD, 0.30 cm(2)]). V1 obtained by pulsed-wave Doppler and with DE closely agreed (mean bias, 0.01 m/sec [SD, 0.05 m/sec]). CONCLUSION: TEE evaluation of native AVA using the DE technique is feasible and in good agreement with that obtained by C/TTE and G/CATH. Compared with DE/TEE, PL/TEE did not agree as well. Use of DE/TEE should simplify the continuity equation and may minimize errors resulting from beat-to-beat variability in stroke volume.

Aged↗

PubMed2006

A random-sampling high dimensional model representation neural network for building potential energy surfaces.

We combine the high dimensional model representation (HDMR) idea of Rabitz and co-workers [J. Phys. Chem. 110, 2474 (2006)] with neural network (NN) fits to obtain an effective means of building multidimensional potentials. We verify that it is possible to determine an accurate many-dimensional potential by doing low dimensional fits. The final potential is a sum of terms each of which depends on a subset of the coordinates. This form facilitates quantum dynamics calculations. We use NNs to represent HDMR component functions that minimize error mode term by mode term. This NN procedure makes it possible to construct high-order component functions which in turn enable us to determine a good potential. It is shown that the number of available potential points determines the order of the HDMR which should be used.

Journal Article↗

PubMed2003

Pressure-flow loops and instantaneous input impedance in the thoracic aorta: another way to assess the effect of aortic bypass graft implantation on myocardial, brain, and subdiaphragmatic perfusion.

BACKGROUND: The serious disturbances in ventriculoarterial coupling after thoracic aorta bypass grafting are addressed through aortic entry impedance in the frequency domain from flow-pressure waves. We designed a method for synthesizing pressure and flow waves to evaluate opposal to aortic flow along the cardiac cycle, addressing myocardial, brain, and visceral tissue perfusions from pressure-flow hysteresis loops and forward-backward aortic entry impedance in the ascending aorta, transverse aortic arch, and distal descending aorta, respectively, before and after extra-anatomic grafting of the descending aorta in the swine. METHODS: Twelve pigs underwent extra-anatomic grafting (woven double-velour prosthesis, 18-mm diameter), bypassing the descending aorta. Periarterial flow and endovascular pressure signals were mathematically synthesized (error minimization) to yield continuous functions of flow, pressure along the cardiac cycle before treatment for mean hemodynamics, pressure-flow hysteresis loops, and aortic entry impedance. RESULTS: Grafting of the descending aorta overshadowed pressure-flow hysteresis loops in the ascending aorta by shortening maximum pressure delay on maximum flow and diastolic flow reversal. Clamping of the descending aorta substantially restored hemodynamics in the ascending aorta, although the diastolic flow decrease was accelerated. Identical processes developed in the transverse aorta. Subdiaphragmatic descending aortic flow was flattened after grafting and restored, although thickened, after clamping of the descending aorta. Flow wave peak was framed by a diastolic aortic entry impedance peak, which was damped along the transverse aortic arch (aortic entry impedance peak in the ascending aorta, 1700 +/- 102 kN x s x m(-5); aortic entry impedance peak in the descending aorta, 292 +/- 45 kN x s x m(-5); P <.05). After grafting, the aortic entry impedance peak was transferred to early systole (aortic entry impedance peak in the transverse aortic arch, 2104 +/- 94 kN x s x m(-5); aortic entry impedance peak in the descending aorta, 450 +/- 75 kN x s x m(-5); P <.05). Clamping of the descending aorta attenuated the early systolic aortic entry impedance peak (aortic entry impedance peak in the transverse aortic arch, 1269 +/- 104 kN x s x m(-5); aortic entry impedance peak in the descending aorta, 491 +/- 75 kN x s x m(-5); P <.05), although aortic entry impedance in the descending aorta remained higher than before grafting (P <.05). Specifically, the backward flow ascending aorta to coronary trunks generated a backward aortic entry impedance peak (2234 +/- 350 kN x s x m(-5)) superimposed onto the forward aortic entry impedance peak with asymptotic boundaries that diminished after grafting and further enlarged after clamping of the descending aorta. CONCLUSIONS: Hemodynamic opposition of grafting of the descending aorta are specific to the aortic site and cardiac cycle and are dependent on clamping of the descending aorta. Our approach to thoracic aorta hemodynamics could enable optimization of bypass grafting.

Analysis of Variance↗

PubMed2000

Coordination of grip configurations as a function of force output.

In this investigation, the authors examined the coordination and control of force production by the digits of the hand as a function of criterion force level and grip configuration. Each adult participant (N = 6: 3 men and 3 women) was required to place the thumb and a finger (or fingers) upon load cells that were fixed to a grasping apparatus that was clamped to a table. In the task, participants had to match a criterion continuous constant total force level displayed on a computer screen. There were 10 trials at each grip configuration and criterion force level combination on each of 3 consecutive days. The results showed that (a) different grip configurations minimized error at each force level; (b) there was a specific digit pairing within a given grip configuration that produced the highest correlation of force output; (c) the correlation between the force output of digits generally increased at higher force levels; (d) error was reduced at each force level and grip configuration over the practice period; and (e) the organization of the force output of each digit varied as a function of digit, force level, grip configuration, and practice. The findings are consistent with the hypothesis that coordination of the digits in prehension is reflective of an adaptive, task-specific solution that is modified with practice.

Adult↗

PubMed1989

Effect of immersion on lung capacities and volumes: implications for the densitometric estimation of relative body fat.

Immersion of 18 male subjects in water caused a 20.4% (787 ml) increase (P less than 0.05) in the mean inspiratory capacity (IC) whereas there were no changes (P greater than 0.05) in tidal volume (VT) and the frequency of respiration. All the means for the other pulmonary variables decreased (P less than 0.05) by varying amounts: total lung capacity (TLC) = 8.4% (599 ml), vital capacity (VC) = 5.5% (308 ml), functional residual capacity (FRC) = 42.6% (1386 ml), expiratory reserve volume (ERV) = 61.9% (1095 ml) and residual volume (RV) = 19.7% (292 ml). Variation of only the RV in the body density (BD) formula from which the percentage body fat (%BF) is estimated resulted in a significantly (P less than 0.05) lower mean of 15.2% BF for the RV in air (means = 1482 ml) compared with that of 17.1% BF for the RV in water (means = 1190 ml). All but one of the subjects exhibited a smaller RV in water than in air; the six largest differences were equivalent to 2.4-5.1% BF. These results indicate that the net effect of the hydrostatic pressure (decreases RV), pulmonary vascular engorgement (decreases RV) and diminished compliance (increases RV) is to reduce the ventilated RV. It is therefore advisable to measure the RV when the subject is immersed in order to minimize error in the determination of BD and hence the estimation of % BF.

Adipose Tissue↗

PubMed1997

Image analysis of comet assay measurements.

In the last decade the 'comet assay' or 'single cell gel electrophoresis assay' has been established as a sensitive method for the detection of DNA damage and the measurement of its recovery. The results published in the literature have often been obtained with different methods for comet structure measurement. In most cases these data are not comparable with each other. Even when using similar systems for the analysis, it is difficult to obtain matching data. This presentation will describe some technical aspects of our measurement equipment and evaluation software. It focuses on necessary experimental conditions to minimize errors in obtaining such data. The software developed here allows the rapid analysis of the microscopic samples (< 2 s per image). The image analysis was designed with respect to the morphological shapes of comet cells, which were investigated with a confocal laser microscope. The system is built with standard components which are commercially available. As a measure of the amount of DNA damage the ratio of fluorescence intensity was used inside the comet tail and the fluorescence intensity of the comet head. Other parameters such as DNA content, comet area, head radius, tail length and tail moment are also determined. The reproducibility of the system has been evaluated in several experiments over a period of 5 years.

Ataxia Telangiectasia↗

PubMed2006

Inferring causality assessments from predictive responses: cue interaction without cue competition.

The authors criticize the use of participants' predictive responses during a learning phase as a measure of causal assessments. Simulations demonstrate that a general aim to minimize error as required in the prediction task will produce results in accordance with those observed, in particular apparent cue interaction effects. It is argued that measures estimated from prediction responses do not reflect causal ratings, but are side-effects of learning explained by adaptation in strategy to changes in presented cell frequencies. The results are reinterpreted to be in line with a causal model view, not requiring dual processes or cue competition of lower level associative processes.

Association Learning↗