Peakmatch: a simple and robust method for peak list matching

Peak lists are commonly used in NMR as input data for various software tools such as automatic assignment and structure calculation programs. Inconsistencies of chemical shift referencing among different peak lists or between peak and chemical shift lists can cause severe problems during peak assignment. Here we present a simple and robust tool to achieve self-consistency of the chemical shift referencing among a set of peak lists. The Peakmatch algorithm matches a set of peak lists to a specified reference peak list, neither of which have to be assigned. The chemical shift referencing offset between two peak lists is determined by optimizing an assignment-free match score function using either a complete grid search or downhill simplex optimization. It is shown that peak lists from many different types of spectra can be matched reliably as long as they contain at least two corresponding dimensions. Using a simulated peak list, the Peakmatch algorithm can also be used to obtain the optimal agreement between a chemical shift list and experimental peak lists. Combining these features makes Peakmatch a useful tool that can be applied routinely before automatic assignment or structure calculation in order to obtain an optimized input data set.     

MICE: multiple-peak identification, characterization, and estimation

MICE--multiple-peak identification, characterization, and estimation--is a procedure for estimating a lower bound of the number of frequency peaks and for estimating the frequency peak parameters. The leading application is protein structure determination using nuclear magnetic resonance (NMR) experiments. NMR frequency data are multiple-peak data, where each frequency peak corresponds to two connected atoms in the three-dimensional protein structure. We analyze the NMR frequency data through a series of steps: a preliminary step for separating the signal from the background followed by identification of local maxima up to a noise-level-dependent threshold, estimation of the frequency peak parameters using an iterative algorithm, and detection of mixtures of peaks using hypothesis testing.     

The peak oxygen uptake of British children with reference to age, sex and sexual maturity

The purposes of this study were to provide baseline data on the peak oxygen consumption (VO2) of British children, aged 11-16 years and to examine the peak VO2 of children in relation to their pubertal stage of development. The peak VO2 of 226 boys and 194 girls was determined during either treadmill running or cycle ergometry. The sexual maturity of 320 of the children was estimated using Tanner's indices. Peak VO2 increased with chronological age in both sexes and from about the age of 12 years boys exhibited significantly higher (P less than 0.05) values than girls. Boys' peak VO2 in relation to body mass was consistent over the age range studied and was superior (P less than 0.05) to girls' values at all ages. It appears that mass-related peak VO2 is independent of sexual maturity in both sexes. The more mature boys demonstrated a significantly higher (P less than 0.05) peak VO2 (1.min-1) than the less mature boys on both ergometers. The more mature girls demonstrated significantly higher (P less than 0.05) peak VO2 (1.min-1) than the less mature girls only on the cycle ergometer. On both ergometers the differences between the peak VO2 of the girls and boys were more pronounced in the mature children whether expressed in relation to body mass or not. Comparison of the results with earlier data drawn from smaller samples failed to provide evidence to suggest that British children's peak VO2 has declined in recent years. No study with which to compare our maturity peak VO2 data appears to be available.     

A simple exploratory algorithm for the accurate and fast detection of spontaneous synaptic events

We have developed a program for the fast and accurate detection of spontaneous synaptic events. The algorithm identifies each event of which the slope and amplitude which meet criteria. The significant feature of this algorithm is its stepwise and exploratory search for the onset and the peak points. During the first step, the program employing the algorithm makes a rough estimate of the candidate for a synaptic event, and determines a 'temporary' onset data point. The next step is the detection of the true onset data point and 'temporary' peak data point, which probably exist several points after the temporary onset data point. The third step is a backward search to detect the true peak data point. The final step is to check whether the amplitude of the detected event exceeds the threshold. This stepwise and shuttlewise search allows for the accurate detection of the peak points. Using this program, we succeeded in detecting an increased frequency and amplitude of spontaneous excitatory postsynaptic currents in chick cerebral neurons following the application of 12-O-tetradecanoyl-phorbol-13-acetate (TPA). In addition, we demonstrated that the program employing the algorithm was able to be used for the detection of extracellular action potentials.     

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.     

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data

Warp2D is a novel time alignment approach, which uses the overlapping peak volume of the reference and sample peak lists to correct misleading peak shifts. Here, we present an easy-to-use web interface for high-throughput Warp2D batch processing time alignment service using the Dutch Life Science Grid, reducing processing time from days to hours. This service provides the warping function, the sample chromatogram peak list with adjusted retention times and normalized quality scores based on the sum of overlapping peak volume of all peaks. Heat maps before and after time alignment are created from the arithmetic mean of the sum of overlapping peak area rearranged with hierarchical clustering, allowing the quality control of the time alignment procedure. Taverna workflow and command line tool are provided for remote processing of local user data. AVAILABILITY: online data processing service is available at http://www.nbpp.nl/warp2d.html. Taverna workflow is available at myExperiment with title '2D Time Alignment-Webservice and Workflow' at http://www.myexperiment.org/workflows/1283.html. Command line tool is available at http://www.nbpp.nl/Warp2D_commandline.zip. CONTACT: p.l.horvatovich@rug.nl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Predicting time to peak occurrence of insect life-stages usingregression models calibrated from stage-frequency data and ancillary stage-mortality data

1 Integrated Pest Management programmes often require predictions of peak occurrence of particular insect life‐stages to optimize the timing of population monitoring and control operations. 2 Given a known or estimated starting time for a synchronously developing pest population, predictive models estimated from stage‐frequency data alone can only predict the times of peak occurrence assuming a constant mortality rate across stages. 3 Here, continuation ratio regression models of relative stage frequencies estimated from stage‐frequency data are combined with a stage‐specific model of mortality estimated from ancillary mortality data to allow prediction of time of peak occurrence. 4 To calculate time of peak occurrence new mathematical derivations are given for continuation ratio models. 5 The models are used to predict the time of peak occurrence in degree‐day units for each of the first to third larval instars of the Tasmanian Eucalyptus leaf beetle Chrysophtharta bimaculata (Olivier) (Coleoptera: Chrysomelidae), a serious defoliator of Eucalyptus regnans and E. nitens plantations in Tasmania.     

Photoacoustic study of iron-deficiency anaemia

A photoacoustic spectrum of a smear of whole blood clearly shows all of the details of the haem absorption in an optical spectrum and good optical absorption data without a data extraction procedure. There are three peaks; γ (420 nm), β (550 nm), and α (585 nm) in the band 350–700 nm. For iron-deficiency anaemia the peak/peak ratios, ratios of the value of peak γ to that of the peak β and peak α, and the integral/integral ratios, ratios of the value of the integral under the peak γ to that under the peak β, peak α, peak β and peak α are closely related to the variation of haemoglobin concentration. Linear relationships among the ratios and the Hb concentration are found. These ratios could be a good index of haem synthesis disturbance.     

The latitudinal position of peak marine diversity in living and fossil biotas

Aim Peak marine taxonomic diversity has only rarely occurred at or near the equator during the Phanerozoic Eon, in contrast to the present‐day pattern. This fundamental difference is difficult to reconcile because the latitude at which peak diversity occurs for living marine taxa has not yet been explicitly determined at a broad taxonomic and spatial scale. Here, we attempt to determine this value in order to compare the contemporary and fossil patterns directly. Location Our data are global in coverage. Methods We used a literature compilation of 149 present‐day marine latitudinal diversity gradients. We summed the number of marine taxa that exhibited peak diversity within 10° latitudinal bins. In addition, we recorded locality data, general habitat (benthic/pelagic), and the taxonomic level of the study organisms. Results We found that peak diversity for most sampled marine taxa currently occurs between 10° and 20° N, even after correcting for a Northern Hemisphere sampling bias. Moreover, this peak position is a global phenomenon: it is found across habitats and higher taxa, within all sampled ocean basins, and on both sides of the Atlantic and Pacific oceans. Benthic taxa, which dominate our data, exhibit one peak at 10°–20° N, while pelagic taxa exhibit a peak at 10°–20° N and an additional peak at 10°–20° S, producing a distinct trough at the equator. Main conclusions Our data indicate that peak marine diversity for many taxa is currently within 10°–20° N rather than at the equator, and that this is not likely to result from either undersampling at lower latitudes or the pattern being dominated by a particular taxon. Possible explanations may include a coincidence with the intertropical convergence zone, a mid‐domain effect, abundant shallow marine habitat, or high ocean temperatures at latitudes nearest the equator. Regardless of its exact cause, the position of peak diversity should be considered a fundamental feature of the latitudinal diversity gradient that must be accounted for within attempts to explain the latter’s existence.     

Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta

We have developed a novel and robust approach for automatic and unsupervised simultaneous nuclear Overhauser effect (NOE) assignment and structure determination within the CS-Rosetta framework. Starting from unassigned peak lists and chemical shift assignments, autoNOE-Rosetta determines NOE cross-peak assignments and generates structural models. The approach tolerates incomplete and raw NOE peak lists as well as incomplete or partially incorrect chemical shift assignments, and its performance has been tested on 50 protein targets ranging from 50 to 200 residues in size. We find a significantly improved performance compared to established programs, particularly for larger proteins and for NOE data obtained on perdeuterated protein samples. X-ray crystallographic structures allowed comparison of Rosetta and conventional, PDB-deposited, NMR models in 20 of 50 test cases. The unsupervised autoNOE-Rosetta models were often of significantly higher accuracy than the corresponding expert-supervised NMR models deposited in the PDB. We also tested the method with unrefined peak lists and found that performance was nearly as good as for refined peak lists. Finally, demonstrating our method’s remarkable robustness against problematic input data, we provided correct models for an incorrect PDB-deposited NMR solution structure.     

Estimation of 24-Hour Intraocular Pressure Peak Timing and Variation Using a Contact Lens Sensor

Purpose

To compare estimates of 24-hour intraocular pressure (IOP) peak timing and variation obtained using a contact lens sensor (CLS) and using a pneumatonometer.

Methods

Laboratory data collected from 30 healthy volunteers (ages, 20-66 years) in a randomized, controlled clinical trial were analyzed. Participants were housed for 24 hours in a sleep laboratory. One randomly selected right or left eye was fitted with a CLS that monitored circumferential curvature in the corneoscleral region related to the change of IOP. Electronic output signals of 30 seconds were averaged and recorded every 5 minutes. In the contralateral eye, habitual IOP measurements were taken using a pneumatonometer once every two hours. Simulated 24-hour rhythms in both eyes were determined by cosinor fitting. Simulated peak timings (acrophases) and simulated data variations (amplitudes) were compared between the paired eyes.

Results

Bilateral change patterns of average 24-hour data for the group were in parallel. The simulated peak timing in the CLS fitted eye occurred at 4:44 AM ± 210 min (mean ± SD) and the IOP peak timing in the contralateral eye at 4:11 AM ± 120 min (P=0.256, Wilcoxon signed-rank test). There was no significant correlation between the simulated data variations in the paired eyes (P=0.820, linear regression).

Conclusions

The 24-hour CLS data showed a simulated peak timing close to the 24-hour IOP peak timing obtained using the pneumatonometer. However, the simulated variations of 24-hour data in the paired eyes were not correlated. Estimated 24-hour IOP rhythms using the two devices should not be considered interchangeable.     

MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data

SUMMARY: New additional methods are presented for processing and visualizing mass spectrometry based molecular profile data, implemented as part of the recently introduced MZmine software. They include new features and extensions such as support for mzXML data format, capability to perform batch processing for large number of files, support for parallel processing, new methods for calculating peak areas using post-alignment peak picking algorithm and implementation of Sammon's mapping and curvilinear distance analysis for data visualization and exploratory analysis. AVAILABILITY: MZmine is available under GNU Public license from http://mzmine.sourceforge.net/.     

Side peak suppression in responses of an across-frequency integration model to stimuli of varying bandwidth as demonstrated analytically and by implementation

Multiplication-like sound localization models are subjected to phase ambiguities for high-frequency tonal stimuli as multiplication creates several equivalent response peaks in tuning curves. By increasing the bandwidth of the stimulus, phase ambiguities can be reduced, which is often referred to as side peak suppression. In this study we present a Jeffress-based sound localization model, and determine side peak suppression analytically. The results were verified with an implementation of the same model, and compared to physiological data of barn owls. Three types of stimuli were analyzed: pure-tone stimuli, two-tone complexes with varying frequency distances, and noise signals with variable bandwidths. As an additional parameter we also determined the half-width of the main response peak to examine the scaling of tuning curves in azimuth. Results showed that side peak suppression did not only depend on bandwidth, but also on the center frequency and the distance of the side peak to the main response peak. In particular, the analytical model predicted that side peak suppression is a function of relative bandwidth, whereas half-width is inversely proportional to center frequency, with a proportionality factor depending on relative bandwidth. The analytical approach and the implementation yielded equivalent tuning curves (deviation < 1 %). Moreover, the electrophysiological data recorded in barn owls closely matched the predicted tuning curves.     

Peak tree: a new tool for multiscale hierarchical representation and peak detection of mass spectrometry data

Peak detection is one of the most important steps in mass spectrometry (MS) analysis. However, the detection result is greatly affected by severe spectrum variations. Unfortunately, most current peak detection methods are neither flexible enough to revise false detection results nor robust enough to resist spectrum variations. To improve flexibility, we introduce peak tree to represent the peak information in MS spectra. Each tree node is a peak judgment on a range of scales, and each tree decomposition, as a set of nodes, is a candidate peak detection result. To improve robustness, we combine peak detection and common peak alignment into a closed-loop framework, which finds the optimal decomposition via both peak intensity and common peak information. The common peak information is derived and loopily refined from the density clustering of the latest peak detection result. Finally, we present an improved ant colony optimization biomarker selection method to build a whole MS analysis system. Experiment shows that our peak detection method can better resist spectrum variations and provide higher sensitivity and lower false detection rates than conventional methods. The benefits from our peak-tree-based system for MS disease analysis are also proved on real SELDI data.     

Validation of plantar pressure simulations using finite and discrete element modelling in healthy and diabetic subjects

Plantar pressure simulation driven by integrated 3D motion capture data, using both a finite element and a discrete element model, is compared for ten healthy and ten diabetic neuropathic subjects. The simulated peak pressure deviated on average between 16.7 and 34.2% from the measured peak pressure. The error in the position of the peak pressure was on average smaller than 4.2 cm. No method was more accurate than the other although statistical differences were found between them. Both techniques are thus complementary and useful tools to better understand the alteration of diabetic foot biomechanics during gait.     

Differences in the Head Movement During Baseball Batting between Skilled Players and Novices

ABSTRACT: Nakata, H, Miura, A, Yoshie, M, and Kudo, K. Differences in the head movement during baseball batting between skilled players and novices. J Strength Cond Res 26(10): 2632-2640, 2012-We investigated the pattern of head movement during baseball batting in 8 skilled players and 9 unskilled novices, using a high-speed video camera. The 2 directions of head movement were analyzed as an X-axis (from the home plate to the pitcher's plate) and Z-axis (vertical downward). On the X-axis, peak latency, peak value, the distance from the peak to the value at bat-ball impact, and data variability were compared between the 2 groups. On the Z-axis, peak latency, downward distance, and data variability were analyzed. Peak latency on the X-axis occurred significantly earlier in baseball players than in novices (p < 0.001), and the difference between the minimum peak and impact was significantly larger in the players (p < 0.05). The variability in peak latency on the X-axis was significantly larger in the novices (p < 0.05). The variability in peak value on the Z-axis was also significantly larger in the novices (p < 0.05). Our findings showed that the significant differences in head movement between the 2 groups should help baseball players, beginners, coaches, and strength and conditioning professionals to improve performance, be effectively applied to actual practice, and enhance coaching for batting.     

Accurate peak list extraction from proteomic mass spectra for identification and profiling studies

Background  

Mass spectrometry is an essential technique in proteomics both to identify the proteins of a biological sample and to compare proteomic profiles of different samples. In both cases, the main phase of the data analysis is the procedure to extract the significant features from a mass spectrum. Its final output is the so-called peak list which contains the mass, the charge and the intensity of every detected biomolecule. The main steps of the peak list extraction procedure are usually preprocessing, peak detection, peak selection, charge determination and monoisotoping operation.     

Sexual behavior and reproduction ofCercocebus albigena johnstonii in Kibale forest,Western Uganda

Gray-cheeked mangabeys live in multimale social groups. Two groups of these monkeys were studied extensively over a period of 22 months, and a further eight groups were observed opportunistically. Data on the occurrence of sexual swelling infernales were collected and the different phases of swelling and deflation are described in detail together with data on their duration. The data were found to agree broadly with those presented by other workers on captive animals. Pre and postpartum swellings are described. The majority of copulations was observed to occur at peak swelling and a specific gesture, the head flag, was noted as a solicitation. The data on initiation of copulations show that the males initiated more copulations than the females. However, female-initiated copulations ended in ejaculation more often than male-initiated copulations. The behaviors of the mangabeys during precopulation and copulation were found to be broadly similar to those of the macaque. Copulations were observed most often on the day of peak swelling;however, adult males were the only animals to copulate prior to peak swelling. Subadult male copulations were most often after peak swelling. Masturbation was observed to ejaculation on two occasions. The data show gestation periods of between 184 and 189 days. A mean interbirth interval was calculated to be 33.33 ± 15.87 months.     

A generalized linear model for peak calling in ChIP-Seq data

Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) has become a routine for detecting genome-wide protein-DNA interaction. The success of ChIP-Seq data analysis highly depends on the quality of peak calling (i.e., to detect peaks of tag counts at a genomic location and evaluate if the peak corresponds to a real protein-DNA interaction event). The challenges in peak calling include (1) how to combine the forward and the reverse strand tag data to improve the power of peak calling and (2) how to account for the variation of tag data observed across different genomic locations. We introduce a new peak calling method based on the generalized linear model (GLMNB) that utilizes negative binomial distribution to model the tag count data and account for the variation of background tags that may randomly bind to the DNA sequence at varying levels due to local genomic structures and sequence contents. We allow local shifting of peaks observed on the forward and the reverse stands, such that at each potential binding site, a binding profile representing the pattern of a real peak signal is fitted to best explain the observed tag data with maximum likelihood. Our method can also detect multiple peaks within a local region if there are multiple binding sites in the region.