Calculated Cross-correlation Coefficients Research Articles

Similarities between maternal and fetal RR interval tachograms and their association with fetal development.

An association between maternal and fetal heart rate (HR) has been reported but, so far, little is known about its physiological implication and importance relative to fetal development. Associations between both HRs were investigated previously by performing beat-by-beat coupling analysis and correlation analysis between average maternal and fetal HRs. However, studies reporting on the presence of similarities between maternal and fetal HRs or RR intervals (RRIs) over the short term (e.g., 5-min) at different gestational ages (GAs) are scarce. Here, we demonstrate the presence of similarities in the variations exhibited by maternal and fetal RRl tachograms (RRITs). To quantify the same similarities, a cross-correlation (CC) analysis between resampled maternal and fetal RRITs was conducted; RRITs were obtained from non-invasive electrocardiogram (ECG). The degree of similarity between maternal and fetal RRITs (bmfRRITs) was quantified by calculating four CC coefficients. CC analysis was performed for a total of 330 segments (two 5-min segments from 158 subjects and one 5-min from 14 subjects). To investigate the association of the similarity bmfRRITs with fetal development, the linear correlation between the calculated CC coefficients and GA was calculated. The results from the latter analysis showed that similarities bmfRRITs are common occurrences, they can be negative or positive, and they increase with GA suggesting the presence of a regulation that is associated with proper fetal development. To get an insight into the physiological mechanisms involved in the similarity bmfRRITs, the association of the same similarity with maternal and fetal HR variability (HRV) was investigated by comparing the means of two groups in which one of them had higher CC values compared to the other. The two groups were created by using the data from the 158 subjects where fetal RRI (fRRI) calculation from two 5-min ECG segments was feasible. The results of the comparison showed that the maternal very low frequency (VLF) HRV parameter is potentially associated with the similarity bmfRRITs implying that maternal hormones could be linked to the regulations involved in the similarity bmfRRITs. Our findings in this study reinforce the role of the maternal intrauterine environment on fetal development.

Theoretical characterisation of strand cross-correlation in ChIP-seq

BackgroundStrand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) because of its peak calling independence, it remains unclear what aspects of quality such strand cross-correlation profiles actually measure.ResultsWe introduced a simple model to simulate the mapped read-density of ChIP-seq and then derived the theoretical maximum and minimum of cross-correlation coefficients between strands. The results suggest that the maximum coefficient of typical ChIP-seq samples is directly proportional to the number of total mapped reads and the square of the ratio of signal reads, and inversely proportional to the number of peaks and the length of read-enriched regions. Simulation analysis supported our results and evaluation using 790 ChIP-seq data obtained from the public database demonstrated high consistency between calculated cross-correlation coefficients and estimated coefficients based on the theoretical relations and peak calling results. In addition, we found that the mappability-bias-correction improved sensitivity, enabling differentiation of maximum coefficients from the noise level. Based on these insights, we proposed virtual S/N (VSN), a novel peak call-free metric for S/N assessment. We also developed PyMaSC, a tool to calculate strand cross-correlation and VSN efficiently. VSN achieved most consistent S/N estimation for various ChIP targets and sequencing read depths. Furthermore, we demonstrated that a combination of VSN and pre-existing peak calling results enable the estimation of the numbers of detectable peaks for posterior experiments and assess peak calling results.ConclusionsWe present the first theoretical insights into the strand cross-correlation, and the results reveal the potential and the limitations of strand cross-correlation analysis. Our quality assessment framework using VSN provides peak call-independent QC and will help in the evaluation of peak call analysis in ChIP-seq experiments.

Synchronization of a Pair of Opposed Facing Oscillators in a Side-by-Side Configuration

This study considers two opposed facing fluidic oscillators in a side-by-side layout. Each fluidic oscillator shares one of its feedback channels with the other oscillator thus this configuration provides a mean for communication between fluidic oscillators. As a result of this communication through the shared feedback channel, the exiting jets of the fluidic oscillator pair are synchronized. The details of this synchronization are revealed by means of hot-wire measurements, flow visualizations and validated numerical simulations. The oscillation frequencies for both jets were the same and varied from 123 Hz to 476 Hz for a flow rate range from 5 SLPM to 25 SLPM per inlet corresponding to Reynolds number range of 2,125 to 10,625. The calculated cross-correlation coefficients were over 0.88 for the considered flow rate range. The flow visualizations exposed that the exiting jet of each fluidic oscillator move away from the shared feedback channel and move toward the shared feedback channel simultaneously indicating motion in the same direction. Numerical results indicated that the shared feedback channel plays a pressure balancing role while allowing inter-oscillator flow through each side of the shared feedback channel thus controlling the flow direction of each exiting jet yielding a synchronized output from the fluidic oscillator nozzles.

S21-1. A new analysis method using surface electromyography to assess finger function in patients with severe stroke

We have conducted our research into kinesthetic illusions induced by visual stimuli (KiNvis), which are sensations of being in motion that result from watching artificial images of the body part moving. Our previous studies revealed characteristic neural networks related to KiNvis; since then, we have initiated clinical studies adapting KiNvis in patients with stroke. In patients with severe stroke, it is often difficult to measure joint angles, because voluntary movement does not occur or simultaneous contraction of the agonist and antagonist muscles prevent controlled voluntary joint exercise. Therefore, we have developed an assessment method for finger function in these patients using surface electromyography (EMG). Our method aimed to assess “reciprocal muscle activity” during repetitive exercise. Hence, we calculated cross correlation coefficients between EMG signals recorded during reciprocal muscle activity and pseudo model signals during ideal reciprocal muscle contraction. During reciprocal muscle activity, the peak value of cross correlation coefficient calculated using this method was higher than at rest or during sustained muscle activity. Accordingly, we consider that even in patients with severe stroke in whom changes in motor function cannot be detected with the variable that analyzes EMG signals quantitatively, it may be possible to assess finger function alterations using the analysis method of the present study.

A curvelet-based method to determine wave directions from nautical X-band radar images

A new method to determine wave directions from nautical X-band images is proposed. The signatures of ocean waves show obvious scale and directional characteristics in nautical X-band radar images. Curvelet transform (CT) possesses very high scale and directional sensitivities. Therefore, it has good capability to analyze ocean wave fields. The radar images are decomposed at different scales, in different directions, and at different positions by CT, and curvelet coefficients are obtained. Given to the scale and directional characteristics of surface waves, the information of ocean waves is centralized in the curvelet coefficients of certain directions and at certain scales. Therefore, the wave orientations can be determined. The 180 ambiguity is removed by calculating crosscorrelation coefficients (CCCs) between continuous collected images. The proposed method is verified by the dataset collected on the Northwest coast of the Zhangzi Island in the Yellow Sea of China from March to April 2009.

A study of the correlation between dengue and weather in Kandy City, Sri Lanka (2003 -2012) and lessons learned.

BackgroundWeather variables affect dengue transmission. This study aimed to identify a dengue weather correlation pattern in Kandy, Sri Lanka, compare the results with results of similar studies, and establish ways for better control and prevention of dengue.MethodWe collected data on reported dengue cases in Kandy and mid-year population data from 2003 to 2012, and calculated weekly incidences. We obtained daily weather data from two weather stations and converted it into weekly data. We studied correlation patterns between dengue incidence and weather variables using the wavelet time series analysis, and then calculated cross-correlation coefficients to find magnitudes of correlations.ResultsWe found a positive correlation between dengue incidence and rainfall in millimeters, the number of rainy and wet days, the minimum temperature, and the night and daytime, as well as average, humidity, mostly with a five- to seven-week lag. Additionally, we found correlations between dengue incidence and maximum and average temperatures, hours of sunshine, and wind, with longer lag periods. Dengue incidences showed a negative correlation with wind run.ConclusionOur results showed that rainfall, temperature, humidity, hours of sunshine, and wind are correlated with local dengue incidence. We have suggested ways to improve dengue management routines and to control it in these times of global warming. We also noticed that the results of dengue weather correlation studies can vary depending on the data analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/s40249-015-0075-8) contains supplementary material, which is available to authorized users.

Objective evaluation of through-focus optical performance of presbyopia-correcting intraocular lenses using an optical bench system

TO evaluate spherical aberration and through-focus optical performances of 5 presbyopia-correcting and 2 monofocal intraocular lenses (IOLs). Flaum Eye Institute, University of Rochester, Rochester, New York, USA. Experimental study. Five presbyopia-correcting IOLs (Restor +4D SN6AD3, Restor +3D SN6AD1, Rezoom NXG1, Tecnis multifocal ZM900, Crystalens HD500) were tested using an optical bench system consisting of a model eye, a high-resolution Hartmann-Shack wavefront sensor, and an image-capturing device. Two monofocal IOLs (Sofport AO LI60AOV, Acrysof SN60AT) were measured for comparison. No accommodation was simulated. The spherical aberration profiles of each IOL were measured using the wavefront sensor. Through-focus performance was evaluated by calculating cross-correlation coefficients and comparing the likenesses of captured images of a resolution target and a perfect reference image. With a 5.0 mm entrance pupil, the SN6AD3, SN6AD1, ZM900, NXG1, and HD500 IOLs had spherical aberration of -0.18 μm, -0.14 μm, -0.15 μm, -0.07 μm, and -0.01 μm, respectively. Distance image quality was poorer with multifocal and accommodating IOLs than with monofocal IOLs. All multifocal IOLs had effective distance and near image quality but had a loss in intermediate image quality. The HD 500 accommodating IOL had decreased distance image quality and slightly increased depth of focus compared with the monofocal IOLs because of the bispheric design. The presbyopia-correcting IOLs had different optical characteristics, including spherical aberration profile and through-focus performance. An accurate understanding of the optical characteristics of individual IOLs is essential to selecting the best presbyopia-correcting IOL and thus improving cataract surgery outcomes. No author has a financial or proprietary interest in any material or method mentioned.

Small calcification depiction in ultrasound B-mode images using decorrelation of echoes caused by forward scattered waves.

The purpose of this study is to propose a novel method to depict small calcifications in ultrasound B-mode images using decorrelation of forward scattered waves with no decrease in the frame rate. Since the waveform of an ultrasound pulse changes when it passes through a calcification location, the echo waveform from regions behind the calcification is quite different from that without a calcification. This indicates that the existence of a calcification is predictable based upon the waveform difference between adjacent scan lines by calculating cross-correlation coefficients. In addition, a high-intensity echo should return from the calcification itself. Therefore, the proposed method depicts the high-intensity echo positions with posterior low correlation coefficient regions. Eleven of 15 wires 0.2-0.4mm in diameter were depicted using this method, yielding a sensitivity of 73.3% and a specificity of 100%, even though they might go undetected under clinical inspection of ultrasound B-mode images. This study suggests that an US device could perform well in terms of calcification detection.

Indicator of Small Calcification Detection in Ultrasonography using Decorrelation of Forward Scattered Waves

For the improvement of the ability in detecting small calcifications using Ultrasonography (US) we propose a novel indicator of calcifications in an ultrasound B-mode image without decrease in frame rate. Since the waveform of an ultrasound pulse changes at a calcification position, the decorrelation of adjacent scan lines occurs behind a calcification. Therefore, we employ the decorrelation of adjacent scan lines as an indicator of a calcification. The proposed indicator depicted wires 0.05 mm in diameter at 2 cm depth with a sensitivity of 86.7% and a specificity of 100%, which were hardly detected in ultrasound B-mode images. This study shows the potential of the proposed indicator to approximate the detectable calcification size using an US device to that of an X-ray imager, implying the possibility that an US device will become a convenient, safe, and principal clinical tool for the screening of breast cancer. Keywords—Ultrasonography, Calcification, Decorrelation, Forward scattered wave we reported that the waveform change of the echo caused by a calcification results in the decorrelation between the echoes received at adjacent scan lines (7), (8). These reports indicate that the existence of a small calcification is predictable from the waveform difference between adjacent scan lines by calculating cross-correlation coefficients. In this paper, we propose a novel indicator of calcifications and evaluate the method experimentally using a commercial US device.

Influenza and its relationship to circulatory disorders

Three sources of data (general practice episode data from the Weekly Returns Service of the Royal College of General Practitioners, national hospital admission data for England and national mortality data by date of death) were examined separately in each winter (1994/1995 to 1999/2000) to investigate the impact of influenza on circulatory disease. Weekly data on incidence (clinical new episodes) hospital emergency admissions and deaths certified to circulatory disorders and to respiratory diseases (chapters VII and VIII of ICD9) during influenza epidemic periods (defined from combined clinical/virological surveillance) were examined in age groups 45-64, 65-74 and > or =75 years. Data collected in the four winters in which there were substantial influenza A epidemics were consolidated for the period 6 weeks before to 6 weeks after each peak of the epidemic, and associations between the variables at different time lags examined by calculating cross-correlation coefficients. We also examined deaths due to ischaemic heart disease (IHD) as a proportion of all circulatory deaths and deaths due to influenza/pneumonia as a proportion of all respiratory deaths. There were no increases of GP episodes nor of emergency admissions for circulatory disorders in any of the three age groups during epidemic periods. Increased circulatory deaths occurred in all age groups and particularly in the oldest group. The large cross-correlation coefficients of deaths (circulatory and respiratory) with GP respiratory episodes at weekly lags of 0, -1 and 1 were evidence that the deaths and episode distributions were contemporaneous. The ratios of excess circulatory deaths relative to excess respiratory deaths during epidemic periods were 0.74 (age 45-64), 0.72 (65-74) and 0.57 (> or =75 years). Increased circulatory deaths contemporary with new incident cases of respiratory episodes but with no concomitant increase in admissions suggests rapid death during the acute phase of illness. Influenza contingency planning needs to take account of these deaths in determining policy for prophylaxis and in providing facilities for cardio-respiratory resuscitation.

Possible involvement of collective domain movement in the catalytic reaction of soluble epoxide hydrolase

AbstractThe hydrolysis of 1S,2S‐trans‐methylstyrene oxide by soluble epoxide hydrolases is studied by a 4‐ns molecular dynamics (MD) simulation. An analysis of the extent of correlated motions in the active site was carried out. Based on the calculated cross correlation coefficients form the covariance matrix, a new correlation parameter, termed the supercorrelation coefficient, is introduced. The supercorrelation coefficient indicates the extent to which two amino acid residues move in a correlated manner with respect to all other residues in the protein. The resulting map of the supercorrelation coefficients was used to identify segments of the protein that may show collective domain movements. Interestingly, an anti‐correlated motion is located across the active site, involving the catalytic triad and the tyrosines. This may suggest that if a link exists between enzyme dynamics and catalysis, it may be through an anti‐correlated collective domain movement that compresses the active site, thus initiating the conversion of E–NAC to E–TS. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

制御震源地震探査データの共通散乱点重合法解析による北部フォッサマグナ地域の散乱体分布

Seismic waves are refracted, reflected, or scattered by heterogeneities in the Earth's crust. Small-scale structures less than wave-lengths are difficult to be observed by conventional refraction and/or reflection methods although scattered wave energy is observed as coda waves. In March 1997, a seismic reflection survey was conducted to reveal the active tectonics in the Japan arc across the Northern Fossa Magna in Japan. The profiling revealed a strongly deformed thick sedimentary layer. At the same time, we carried out a seismic array observation using off-line seismic recorders in the same area to image crustal structure. We used four large vibrators as seismic sources with a spacing of 200m. The array consisted of 39 seismometers distributed two dimensionally with a spacing of 100m. We applied the CSP (common scatterer point) stacking method for all the combination of sources and receivers. We assumed 3-D grid points with a spacing of 100m in a studied area. We calculated a travel time field for the 3-D structure by a finite difference method. To investigate whether a scattered energy was really originated from a particular grid point or not, we calculated cross-correlation coefficients between the CSP stacked waveforms and a source waveform. We interpret that the correlation coefficients represent a distribution of point scatterers. The scatterers are distributed near the Earth's surface and at depths of 800m and 1600m. Compared with the reflection profile, scatterers are distributed in severely deformed strata. Since our method strongly depends on the background velocity structure, it is important to use a realistic background velocity structure to estimate scatterer distributions accurately.

Evaluation of automatically generated substructure identification rules from tandem mass spectra

Substructure identification rules for phenothiazine and barbiturate substructures were generated by using a new version of the Method for Analyzing Patterns in Spectra (MAPS) software. This software uses tandem mass spectra and known substructure content of reference compounds to provide “feature-combination” rules. A feature-combination is a series of tandem mass spectral features which are completely unique to compounds containing a specified substructure. The current reference databases contain over 11,000 daughter spectra of 100 compounds acquired at two different collision gas pressures (i.e., single- and multiple-collision conditions). The results of rule evaluation procedures are presented and include a comparison of the spectral features developed in rule generation to those identified in documented fragmentation pahtways of the indicated substructure. Two potential sources of error due to spectral feature and substructure “cross-correlation” were identified. If errors occur, they can be detected by calculating cross-correlation coefficients and edited from the rules. A beneficial cross-correlation involving feature-combinations was also discovered. The rules obtained by using single- and multiple-collision data were further evaluated by applying them to tandem mass spectra of 20 test compounds (compounds not in the reference database). The results of these evaluations give a good indication of the utility rules for use in an automated structure elucidation system for tandem mass spectrometry data.

Independent effects of low frequency magnitude and phase distortion on the recorded electrocardiogram

Electrocardiographic signals must go through electronic amplification and filtering to increase amplitude and to diminish noise before they are recorded. However, amplification and filtering may introduce unwanted magnitude and phase distortion in the recorded signal. The relative importance of inadequate magnitude versus inadequate phase responses of electrocardiographic recording systems has been a subject of debate. Although electrocardiographic signal distortion due to inadequate magnitude response has been identified, 1 there is evidence 2,3 that phase distortion has a greater effect on clinical interpretation of the recorded electrocardiogram. This study was designed to quantify the independent effects of low-frequency magnitude and phase distortion on electrocardiographic signals. Electrocardiographic signals from Holter recordings in 10 patients were digitized and processed by magnitude-modifying and phase-modifying filters. The independent effects of magnitude and phase distortion were evaluated by calculating cross-correlation coefficients between filtered and unfiltered waveforms in each patient.