Clustering mass spectrometry data using order statistics

Mass spectrometry data is inherently uncertain. Rather than compare peak heights across samples, a comparison can be made of the relative ordering of the peak height across samples. Order statistics are used to provide a distance metric between each ordered list of peak heights from the samples. A principal component analysis is performed on the set of distance vectors to highlight to important components.     

Considerations that affect optimised simulation in a running jump for height

This study used a computer simulation model to investigate various considerations that affect optimum peak height in a running jump. A planar eight-segment computer simulation model with extensor and flexor torque generators at five joints was formulated and customised to an elite male high jumper. A simulation was matched to a recorded high jumping performance by varying the activation profiles of each of the torque generators giving a simulated peak height of 1.99m compared to the recorded performance of 2.01 m. In order to maximise the peak height reached by the mass centre in the flight phase, the activation profiles were varied, keeping the same initial conditions as in the matching simulation. Optimisations were carried out without any constraints, with constraints on the angular momentum at take-off, with further constraints on joint angles, and with additional requirements of robustness to perturbations of activation timings. A peak height of 2.37 m was achieved in the optimisation without constraints. Introducing the three constraints in turn resulted in peak heights of 2.21, 2.14 and 1.99m. With all three types of constraints included, the peak height was similar to that achieved in the recorded performance. It is concluded that such considerations have a substantial influence on optimum technique and must be included in studies using optimised simulations.     

Image processing and pattern recognition algorithms for evaluation of crossed immunoelectrophoretic patterns (crossed radioimmunoelectrophoresis analysis manager; CREAM)

A computerized method for automatic evaluation and comparison of crossed immunoelectrophoretic and crossed radioimmunoelectrophoretic patterns that requires limited hardware resources has been developed. For the initial reading of the plates an ordinary video camera is used. Feature extractors that allow the computer to recognize a point on the precipitation curve as being a peak point have been developed. After this automatic procedure the program allows for an interactive menu-driven proofreading phase during which it is possible to force the system to take into consideration any number of extra points along the precipitation curve in the curve-fitting process. The system has been tested on crossed immunoelectrophoretic patterns as well as crossed radioimmunoelectrophoretic patterns and it has been shown that the system can recognize the same precipitation curves on different immunoplates and autoradiographs. In addition, the system reports the mean, the variance, and the area of the precipitation curves, thus allowing not only a qualitative comparison of two or more plates but also a quantitation of individual antigens or antibodies.     

THE PROBABILITY OF PEAK SHIFTS IN A FOUNDER POPULATION. II. AN ADDITIVE POLYGENIC TRAIT

Stochastic shifts between two alternative stable equilibria in an additive polygenic system are modelled. The effect of selection on the character is represented by a double-peaked function relating individual fitness to phenotypic value. The mean of a large population will equilibrate near one of the two peaks, although with weak selection there may be a substantial displacement from the closest peak, due to the attraction exerted by the other peak. It is assumed that a small population is founded as a random sample from a large population at equilibrium under selection, and that genetic drift and selection interact to determine the evolution of the mean and variance of the polygenic character during the phase of exponential population growth that follows the foundation of the population. The effects on the frequencies of peak shifts of selectively induced linkage disequilibrium, randomly induced linkage disequilibrium, and random deviations from Hardy-Weinberg equilibrium are investigated by computer simulation. The results are compared with the probabilities of shifts calculated by an approximate analytic method. It is found that the approximations are reasonably accurate when the heights of the peaks in fitness are similar, but the approximations fail when one of the peaks is much higher than the other. The probability of a peak shift is shown to be a decreasing function of the strength of selection on the character. Although substantial changes in phenotypic mean can be induced by a founder event, the probability of a peak shift that induces a significant degree of reproductive isolation is low. The significance of these findings in relation to theories of speciation is discussed.     

Estimation of descriptive parameters of overlapping chromatographic peaks: a simulation study

The characteristics of a non-linear optimization technique for resolution of overlapping chromatographic peaks are examined. A modified Meiron-Marquardt method was used. The estimates of the parameters of overlapping peaks in simulated chromatograms were investigated to indicate the limitations of present mathematical methods and, hopefully, to improve their ultimate utility. Gaussian shapes as well as exponential-Gaussian convolutes were used to simulate the chromatographic peaks. Effects on the overall performance of varying heights, widths, and separation of two peaks were determined. Random additive noise and base line drift were also simulated. For illustrative purposes, the performance of the parameter estimation techniques was expressed in terms of relative errors in estimating the second (or smaller) peak's area, height and location. The results presented indicate the relative importance of noise, skewness, height and width ratios and peak separation on the maximum resolution achievable by numerical methods in an automated chromatographic system.     

Correlation between ground reaction force and tibial acceleration in vertical jumping

Modern electronics allow for the unobtrusive measurement of accelerations outside the laboratory using wireless sensor nodes. The ability to accurately measure joint accelerations under unrestricted conditions, and to correlate them with jump height and landing force, could provide important data to better understand joint mechanics subject to real-life conditions. This study investigates the correlation between peak vertical ground reaction forces, as measured by a force plate, and tibial axial accelerations during free vertical jumping. The jump heights calculated from force-plate data and accelerometer measurements are also compared. For six male subjects participating in this study, the average coefficient of determination between peak ground reaction force and peak tibial axial acceleration is found to be 0.81. The coefficient of determination between jump height calculated using force plate and accelerometer data is 0.88. Data show that the landing forces could be as high as 8 body weights of the jumper. The measured peak tibial accelerations ranged up to 42 g. Jump heights calculated from force plate and accelerometer sensors data differed by less than 2.5 cm. It is found that both impact accelerations and landing forces are only weakly correlated with jump height (the average coefficient of determination is 0.12). This study shows that unobtrusive accelerometers can be used to determine the ground reaction forces experienced in a jump landing. Whereas the device also permitted an accurate determination of jump height, there was no correlation between peak ground reaction force and jump height.     

Effects of various midsole densities of basketball shoes on impact attenuation during landing activities

The purpose of this study was to examine effects of shoe midsole densities and mechanical demands (landing heights) on impact shock attenuation and lower extremity biomechanics during a landing activity. Nine healthy male college athletes performed 5 trials of step-off landing in each of 9 test conditions, i.e., a combination of landings in shoes of 3 midsole densities (soft, normal, hard) from each of 3 landing potential energy (PE) levels (low, median, high). Ground reaction forces (GRF), accelerations (ACC) of the tibia and forehead, and sagittal kinematic data were sampled simultaneously. A 3 x 3 two-way (surface x height) repeated-measures analysis of variance (ANOVA) was performed on selected kinematic, ACC, and GRF variables; a 3 x 3 x 3 three-way (surface x height x joint) ANOVA was performed on variables related to eccentric muscular work. The GRF results showed that the forefoot peak GRF in the normal and hard midsoles was significantly greater than the soft midsole at the low and median PEs. Rearfoot peak GRF was significantly greater for the hard midsole than for the soft and normal midsoles at the median and high PEs, respectively. The peak head and tibia peak ACC were also attenuated in similar fashion. Kinematic variables did not vary significantly across different midsoles, nor did energy absorbed through lower extremity extensors in response to the increased shoe stiffness. Knee joint extensors were shown to be dominant in attenuating the forefoot impact force across the landing heights. The results showed limited evidence of impact-attenuating benefits of the soft midsole in the basketball shoes.     

Line-shape analysis of NMR difference spectra of an anti-spin-label antibody

Specifically deuteriated Fab fragments of the anti-spin-label antibody AN02 were prepared. NMR difference spectra were obtained, in which the spectrum of Fab with some fraction of the binding sites occupied with spin-label hapten was subtracted from the spectrum of Fab with no spin-label. The peak heights were analyzed as a function of the fractional occupation of the binding site, using a computer program that calculates a best fit to the observed spectra. This method treats all of the peaks in the spectra simultaneously. Analyzing all peaks at once allows for the interdependencies in the spectra arising from overlap of positive and negative signals from different peaks. The fitting program calculates line widths for the peaks arising from protons in the binding site region. Almost all of the line widths calculated for the spectrum of the Fab complex with diamagnetic hapten dinitrophenyldiglycine were found to be narrower than the line widths of the corresponding resonances in the spectrum of Fab with an empty binding site. The distances of the binding site region protons from the unpaired electron of the hapten were also obtained from this calculation. Two tyrosine protons were found to be close (less than A) to this electron. These line-width and distance results are discussed with respect to the structure and dynamics of the antibody binding site.     

New dye-labeled terminators for improved DNA sequencing patterns.

We have used two new dye sets for automated dye-labeled terminator DNA sequencing. One set consists of four, 4,7-dichlororhodamine dyes (d-rhodamines). The second set consists of energy-transfer dyes that use the 5-carboxy-d-rhodamine dyes as acceptor dyes and the 5- or 6-carboxy isomers of 4'-aminomethylfluorescein as the donor dye. Both dye sets utilize a new linker between the dye and the nucleotide, and both provide more even peak heights in terminator sequencing than the dye-terminators consisting of unsubstituted rhodamine dyes. The unsubstituted rhodamine terminators produced electropherograms in which weak G peaks are observed after A peaks and occasionally C peaks. The number of weak G peaks has been reduced or eliminated with the new dye terminators. The general improvement in peak evenness improves accuracy for the automated base-calling software. The improved signal-to-noise ratio of the energy-transfer dye-labeled terminators combined with more even peak heights results in successful sequencing of high molecular weight DNA templates such as bacterial artificial chromosome DNA.     

Peak quantification in surface-enhanced laser desorption/ionization by using mixture models

Surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) is a mass spectrometry technology for measuring the composition of a sampled protein mixture. A mass spectrum contains peaks corresponding to proteins in the sample. The peak areas are proportional to the measured concentrations of the corresponding proteins. Quantifying peak areas is difficult for existing methods because peak shapes are not constant across a spectrum and because peaks often overlap. We present a new method for quantifying peak areas. Our method decomposes a spectrum into peaks and a baseline using so-called statistical finite mixture models. We illustrate our method in detail on 8 samples from culture media of adipose tissue and globally on 64 samples from serum to compare our method to the standard Ciphergen method. Both methods give similar estimates for singleton peaks, but not for overlapping peaks. The Ciphergen method overestimates the heights of such peaks while our method still gives appropriate estimates. Peak quantification is an important step in pre-processing SELDI-TOF data and improvements therein will pay off in the later biomarker discovery phase.     

A flexible new computer program for handling DNA sequence data.

A compact new computer program for handling nucleic acid sequence data is presented. It consists of a number of different subsets, which may be used according to a given code system. The program is designed for the determination of restriction enzyme and other recognition sites in correlation with translation patterns, and allows tabulation of codon frequencies and protein molecular weights within specified gene boundaries. The program is especially designed for detection of overlapping genes. The language, is FORTRAN and thus the program may be used on small computers; it may also be used without any prior computer experience. Copies are available on request.     

Robust protein quantitation in chromatographic fractions using MALDI-MS of tryptic peptides

A method is introduced to evaluate protein concentrations using the height sum of all MALDI-MS peaks that unambiguously match theoretic tryptic peptide masses of the protein sought after. The method uses native chromatographic protein fractionation prior to digestion but does not require any depletion, labeling, derivatization, or preparation of a compound similar to the analyte. All peak heights of tryptic peptides are normalized with the peak height of a unique standard peptide added to the MALDI-MS samples. The sum of normalized peak heights, S(n), or the normalized mean peak height, M(n), reflects the concentration of the respective protein. For fractions containing various proteins, S(n) and M(n) can be used to compare concentrations of a protein between different fractions. For fractions with one predominating protein, they can be used to estimate concentration ratios between fractions, or to quantify the fractional protein concentration after calibration with pure protein solutions. Initial native fractionation retains the possibility to apply all conventional analytic procedures. Moreover, it renders the method relatively robust to MS mass accuracy. The method was validated with albumin, transferrin, alpha1-antitrypsin, and immunoglobulin G within highly complex chromatographic fractions of pathological and normal sera, which contained the respective intact native protein in dominating as well as minor concentrations. The correlation found between S(n) and the protein concentration as determined with ELISA showed that the method can be applied to select markers for distinguishing between normal and pathological serum samples.     

Determination of d- and l-aspartate in cell culturing medium,within cells of MPT1 cell line and in rat blood by a column-switching high-performance liquid chromatographic method

HPLC fluorometric methods have been used to analyze trace amounts of d-amino acids in biological samples. In this study, we established an expedient column-switching fluorometric HPLC system that would improve the analysis of d-amino acids, in particular d-aspartate (Asp). Our system consists of the fluorogenic derivatization of amino acids with NBD-F and two chromatographic steps, one that separates individual amino acids in reverse phase mode and another that separates the chiral forms of each amino acid in normal-phase mode. The two separation steps are linked through a trapping column by an automated column-switching system. In addition, sample preparation is simplified and improved, where trichloroacetic acid is used for deproteinization, and borate buffer, pH 9.5 is employed for the fluorescent derivatization. The detection limit for d-Asp in culturing medium is 5 nM. The resulting peak heights correlated well with concentrations that ranged from 12.5 to 250 nM for both d- and l-Asp. The present method was applied to determine d- and l-Asp levels in cell culturing medium, and within cells of MPT1 cell line. The detected cellular levels of d- and l-Asp agree with those detected by our previous method. In addition, this method was used to measure d- and l-Asp levels in rat blood samples, and the results are consistent with the reported values.     

Reaction pathways for Zn(II)-catalyzed carboxylic acid esters hydrolysis

Reaction pathways have been investigated by quantum-mechanical procedures on gas phase models for the hydrolysis of methyl acetate catalyzed by a monohydroxo-Zn(II) complex formed by a phenanthroline-containing polyamine macrocycle. Based on consideration of energy barrier heights, the hydrolysis process is predicted to be bimolecular, consistently with kinetic data obtained for the hydrolysis of p-nitrophenyl acetate promoted by the modelled catalyst. Differences with respect to results of theoretical studies on the more extensively investigated hydrolysis processes catalyzed by the OH⁻ anion are discussed and appear to be mostly due to the presence of the metal centre close to the OH function in the system now investigated. The pervasive presence and path-controlling role of hydrogen bonds are also discussed.     

Effect of landing height on frontal plane kinematics, kinetics and energy dissipation at lower extremity joints

Lack of the necessary magnitude of energy dissipation by lower extremity joint muscles may be implicated in elevated impact stresses present during landing from greater heights. These increased stresses are experienced by supporting tissues like cartilage, ligaments and bones, thus aggravating injury risk. This study sought to investigate frontal plane kinematics, kinetics and energetics of lower extremity joints during landing from different heights. Eighteen male recreational athletes were instructed to perform drop-landing tasks from 0.3- to 0.6-m heights. Force plates and motion-capture system were used to capture ground reaction force and kinematics data, respectively. Joint moment was calculated using inverse dynamics. Joint power was computed as a product of joint moment and angular velocity. Work was defined as joint power integrated over time. Hip and knee joints delivered significantly greater joint power and eccentric work (p<0.05) than the ankle joint at both landing heights. Substantial increase (p<0.05) in eccentric work was noted at the hip joint in response to increasing landing height. Knee and hip joints acted as key contributors to total energy dissipation in the frontal plane with increase in peak ground reaction force (GRF). The hip joint was the top contributor to energy absorption, which indicated a hip-dominant strategy in the frontal plane in response to peak GRF during landing. Future studies should investigate joint motions that can maximize energy dissipation or reduce the need for energy dissipation in the frontal plane at the various joints, and to evaluate their effects on the attenuation of lower extremity injury risk during landing.     

The interaction of mequitazine with phospholipid model membranes

The effect of increasing concentrations of mequitazine, a quinuclidinylmethyl-phenothiazine, on the phase transition temperature (T_c), the broadening of the transition peak, the enthalpy and entropy of transition of dimyristoyl-, dipalmitoyl- and distearoylphosphatidylcholine (DPPC) liposomes was studied. Pest critical micelle concentrations of mequitazine (CMC = 5.23 X 10^?2M), caused broadening of the transition peak and lowering of the T_c of pure liposomes. The ratio of peak heights from the nuclear magnetic resonance (NMR) spectra of egg phosphatidycholine liposomes was used as a criterion for assessing the interaction of the drug with phospholipid membranes. Mequitazine interacts with both the polar head groups and hydrophobic membrane interior.     

Modelling three-dimensional flow over spur-and-groove morphology

Spur-and-groove (SAG) morphology characterizes the fore reef of many coral reefs worldwide. Although the existence and geometrical properties of SAG have been well documented, an understanding of the hydrodynamics over them is limited. Here, the three-dimensional flow patterns over SAG formations, and a sensitivity of those patterns to waves, currents, and SAG geometry were characterized using the physics-based Delft3D-FLOW and SWAN models. Shore-normal shoaling waves over SAG formations were shown to drive two circulation cells: a cell on the lower fore reef with offshore flow over the spurs and onshore flow over the grooves, except near the seabed where velocities were always onshore, and a cell on the upper fore reef with offshore surface velocities and onshore bottom currents, which result in depth-averaged onshore and offshore flow over the spurs and grooves, respectively. The mechanism driving this flow results from the net of the radiation stress gradients and pressure gradient, which is balanced by the Reynolds stress gradients and bottom friction that differ over the spur and over the groove. Waves were the primary driver of variations in modelled flow over SAG, with the flow strength increasing for increasing wave heights and periods. Spur height, SAG wavelength, and the water depth at peak spur height were the dominant influences on the hydrodynamics, with spur heights directly proportional to the strength of SAG circulation cells. SAG formations with shorter SAG wavelengths only presented one circulation cell on the shallower portion of the reef, as opposed to the two circulation cells for longer SAG wavelengths. SAG formations with peak spur heights occurring in shallower water had stronger circulation than those with peak spur heights occurring in deeper water. These hydrodynamic patterns also likely affect coral and reef development through sediment and nutrient fluxes.

     

Quantitative evaluation of sphingomyelin and glucosylceramide using matrix-assisted laser desorption ionization time-of-flight mass spectrometry with sphingosylphosphorylcholine as an internal standard. Practical application to tissues from patients with Niemann-Pick disease types A and C, and Gaucher disease

Niemann-Pick disease types A and C, and Gaucher disease are glycolipid storage disorders characterized by the systemic deposition of glycosphingolipids, i.e., sphingomyelin in Niemann-Pick disease types A and C tissues and glucosylceramide in Gaucher disease ones, respectively. Using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS), we analyzed the sphingolipids in liver and spleen specimens from patients with Niemann-Pick disease types A and C, and Gaucher disease. Crude lipids were extracted from tissue containing 5mg protein with chloroform and methanol. After mild alkaline treatment of the crude lipids, a sphingolipid fraction was prepared and analyzed by MALDI-TOF/MS. The results were as follows: (a) ion peaks with m/z values corresponding to different sphingomyelin and ceramide monohexoside (CMH) species were clearly detected. (b) With sphingosylphosphorylcholine as the internal standard for quantification of sphingomyelin and CMH, the relative peak heights of sphingomyelin and CMH were calculated and plotted versus their contents. The relative peak heights of sphingomyelin and CMH showed linearity between 50 and 1500 ng sphingomyelin content, and between 5 and 150 ng CMH content, respectively. (c) Quantitative analysis revealed the accumulation of sphingomyelin in the liver and spleen specimens from the patients with Niemann-Pick disease types A and C. Striking accumulation of CMH was also detected in the liver and spleen specimens from the patients with Gaucher disease. This investigation indicated that accumulated sphingomyelin and CMH in small amounts of tissues from sphingolipidosis patients can be detected quantatively with the MALDI-TOF/MS method. This method will be useful not only for the diagnosis but also for biochemical pathophysiology evaluation of patients with various sphingolipidosis.     

Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) is a culture-independent method of obtaining a genetic fingerprint of the composition of a microbial community. Comparisons of the utility of different methods of (i) including peaks, (ii) computing the difference (or distance) between profiles, and (iii) performing statistical analysis were made by using replicated profiles of eubacterial communities. These samples included soil collected from three regions of the United States, soil fractions derived from three agronomic field treatments, soil samples taken from within one meter of each other in an alfalfa field, and replicate laboratory bioreactors. Cluster analysis by Ward's method and by the unweighted-pair group method using arithmetic averages (UPGMA) were compared. Ward's method was more effective at differentiating major groups within sets of profiles; UPGMA had a slightly reduced error rate in clustering of replicate profiles and was more sensitive to outliers. Most replicate profiles were clustered together when relative peak height or Hellinger-transformed peak height was used, in contrast to raw peak height. Redundancy analysis was more effective than cluster analysis at detecting differences between similar samples. Redundancy analysis using Hellinger distance was more sensitive than that using Euclidean distance between relative peak height profiles. Analysis of Jaccard distance between profiles, which considers only the presence or absence of a terminal restriction fragment, was the most sensitive in redundancy analysis, and was equally sensitive in cluster analysis, if all profiles had cumulative peak heights greater than 10,000 fluorescence units. It is concluded that T-RFLP is a sensitive method of differentiating between microbial communities when the optimal statistical method is used for the situation at hand. It is recommended that hypothesis testing be performed by redundancy analysis of Hellinger-transformed data and that exploratory data analysis be performed by cluster analysis using Ward's method to find natural groups or by UPGMA to identify potential outliers. Analyses can also be based on Jaccard distance if all profiles have cumulative peak heights greater than 10,000 fluorescence units.