Cross-correlation Profiles Research Articles

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.

Simultaneous electrophysiological and morphological assessment of functional damage to neural networks in vitro after 30\u2013300\u2009g impacts

An enigma of mild traumatic brain injury are observations of substantial behavior and performance deficits in the absence of bleeding or other observable structural damage. Altered behavior and performance reflect changes in action potential (AP) patterns within neuronal networks, which could result from subtle subcellular responses that affect synaptic efficacy and AP production. The aim of this study was to investigate and quantify network activity changes after simulated concussions in vitro and therewith develop a platform for simultaneous and direct observations of morphological and electrophysiological changes in neural networks. We used spontaneously active networks grown on microelectrode arrays (MEAs) to allow long-term multisite monitoring with simultaneous optical observations before and after impacts delivered by a ballistic pendulum (30 to 300 g accelerations). The monitoring of AP waveshape templates for long periods before and after impact provided an internal control for cell death or loss of cell-electrode coupling in the observed set of neurons. Network activity patterns were linked in real-time to high power phase contrast microscopy. There was no overt loss of glial or neuronal adhesion, even at high-g impacts. All recording experiments showed repeatable spike production responses: a loss of activity with recovery to near reference in 1 hr, followed by a slow activity decay to a stable, level plateau approximately 30–40% below reference. The initial recovery occurred in two steps: a rapid return of activity to an average 24% below reference, forming a level plateau lasting from 5 to 20 min, followed by a climb to within 10% of reference where a second plateau was established for 1 to 2 hrs. Cross correlation profiles revealed changes in firing hierarchy as well as in Phase 1 in spontaneous network oscillations that were reduced by as much as 20% 6–8 min post impact with only a partial recovery at 30 min. We also observed that normally stable nuclei developed irregular rotational motion after impact in 27 out of 30 networks. The evolution of network activity deficits and recovery can be linked with microscopically observable changes in the very cells that are generating the activity. The repeatable electrophysiological impact response profiles and oscillation changes can provide a quantitative basis for systematic evaluations of pharmacological intervention strategies. Future expansion to include fluorescent microscopy should allow detailed investigations of damage mechanisms on the subcellular level.

Accuracy improvement in OFDR-based distributed sensing system by image processing

The measurement repeatability and accuracy encounter rapid deterioration when the gauge length drops below several millimeters in optical frequency domain reflectometry (OFDR) based distributed sensing system. To improve the measurement accuracy when the gauge length is short, an approach based on the image processing is presented in this work. We have demonstrated the process of making the original 1D signal derived from the OFDR-based distributed sensing system be a 2D image. The image processing is then applied to denoise the image, which could make use of the 2D information from the measured data. The quality of each 1D cross-correlation profile is enhanced, and therefore the accuracy of the peak detection for the calculation of the spectrum deviation induced by the strain change could be improved. Three image processing methods are introduced, evaluated and compared in a thoughtful way. The strategy of overlapped window is introduced to reduce the deterioration effect on the spatial resolution due to image processing. The distributed strain with a gauge length of 0.4 mm is measured. Five- to tenfold reduction on the measurement standard deviation when the gauge length is less than 3 mm has been achieved. The results are helpful for high spatial resolution sensing applications. Furthermore, the non-local means algorithmic acceleration technique based on the summed square image scheme and fast Fourier Transform is illustrated and used to speed up the non-local means algorithm, making the processing speed over 30 times faster.

V643 Orionis: A detached, evolved, post-mass-exchange eclipsing binary

Context. One of the greatest uncertainties in modelling the mass-exchange phases during the evolution of a binary system is the quantity of mass and angular momentum that has been lost from the system. To constrain this problem, a favourable, evolved, and detached real binary system is valuable as an example of the end result of this process. Aims. We study the 52-day post-mass-exchange eclipsing binary V643 Ori from complete uvby light curves and high-resolution spectra. V643 Ori is double-lined and shows total primary eclipses. The orbit is accurately circular and the rotation of the two stars is synchronised with the orbit, but the photometry from a single year (1993) shows signs of weak spot activity (0.02 mag) around the primary eclipse. Results. We determined accurate masses of 3.3 and 1.9 M⊙ from the spectroscopic orbit and solved the four light curves to determine radii of 16 and 21 R⊙, using the Wilson-Devinney photometric code. The rotational velocities from the cross-correlation profiles agree well with those computed from the known radii and orbital parameters. All observable parameters are thus very precisely determined, but the masses and radii of V643 Ori are incompatible with undisturbed post-main-sequence evolution. Conclusions. We have attempted to simulate the past evolutionary history of V643 Ori under both conservative and non-conservative Case B mass transfer scenarios. In the non-conservative case we varied the amounts of mass and angular momentum loss needed to arrive at the present masses in a circular 52-day orbit, keeping the two stars detached and synchronised as now observed, but without following the evolution of other stellar properties in any detail. Multiple possible solutions were found. Further attempts were made using both the BSE formalism and the binary MESA code in order to track stellar evolution more closely, and make use of the measured radii and temperatures as important additional constraints. Those efforts yielded no satisfactory solutions, possibly due to limitations in handling mass transfer in evolved stars such as these. We remain hopeful that future theoreticians can more fully model the system under realistic conditions.

R Coronae Borealis: radial velocity and other observations, 1950–2007

Radial-velocity observations made on more than a thousand nights are presented for the type star of the R Coronae Borealis (RCB) class. There are four principal sources: the Lick Observatory (1950-1953), the original Cambridge radial-velocity spectrometer (1968-1991), and the Haute-Provence and Cambridge Coravels (1986-1998 and 1997- 2007, respectively). In the case of the last set the size (equivalent width) and width (expressed as if Vsin(i)) of the Coravel cross-correlation ('dip') profiles are also given, and the variation and complexity of those profiles are discussed. Although there is often evidence of cyclical behaviour in radial velocity, no coherent periodicity is found in any of the series. From time to time, and especially over 100 days before the great decline of 2007, the atmosphere was highly disturbed, with evidence of high-velocity components. We suggest that those are associated with large turbulent elements and result in mass ejection to sufficient distances for the formation of soot and other solids and thus the initiation of RCB-type declines. We associate the changes in light and radial velocity near maximum light primarily with the combined effect of such turbulent elements, and not with coherent pulsation. There is some evidence for a variation in the mean radial velocity on a time scale of about ten thousand days.

Spectroscopic monitoring of bright A-F type candidate hybrid stars discovered by the Kepler mission

We report on a study of 250 optical spectra for 50 bright A/F-type candidate hybrid pulsating stars from the Kepler field. Most of the spectra have been collected with the high-resolution spectrograph HERMES attached to the Mercator telescope, La Palma. We determined the radial velocities (RVs), projected rotational velocities, fundamental atmospheric parameters and provide a classification based on the appearance of the cross-correlation profiles and the behaviour of the RVs with time in order to find true hybrid pulsators. Additionally, we also detected new spectroscopic binary and multiple systems in our sample and determined the fraction of spectroscopic systems. In order to be able to extend this investigation to the fainter A-F type candidate hybrid stars, various high-quality spectra collected with 3–4 m sized telescopes suitably equipped with a high-resolution spectrograph and furthermore located in the Northern hemisphere would be ideal. This programme could be done using the new instruments installed at the Devasthal Observatory.

High-cadence spectroscopy of M dwarfs – I. Analysis of systematic effects in HARPS-N line profile measurements on the bright binary GJ 725A+B

Understanding the sources of instrumental systematic noise is a must to improve the design of future spectrographs. In this study, we alternated observations of the well-suited pair of M-stars GJ 725A+B to delve into the sub-night HARPS-N response. Besides the possible presence of a low-mass planet orbiting GJ 725B, our observations reveal changes in the spectral energy distribution (SED) correlated with measurements of the width of the instrumental line profile and, to a lower degree, with the Doppler measurements. To study the origin of these effects, we searched for correlations among several quantities defined and measured on the spectra and on the acquisition images. We find that the changes in apparent SED are very likely related to flux losses at the fibre input. Further tests indicate that such flux losses do not seriously affect the shape of the instrumental point spread function of HARPS-N, but identify an inefficient fitting of the continuum as the most likely source of the systematic variability observed in the FWHM. This index, accounting for the HARPS-N cross-correlation profiles width, is often used to decorrelate Doppler time-series. We show that the Doppler measurement obtained by a parametric least-squares fitting of the spectrum accounting for continuum variability is insensitive to changes in the slope of the SED, suggesting that forward modeling techniques to measure moments of the line profile are the optimal way to achieve higher accuracy. Remaining residual variability at ~1 m/s suggests that for M-stars Doppler surveys the current noise floor still has an instrumental origin.

Inferring synaptic structure in presence of neural interaction time scales.

Biological networks display a variety of activity patterns reflecting a web of interactions that is complex both in space and time. Yet inference methods have mainly focused on reconstructing, from the network’s activity, the spatial structure, by assuming equilibrium conditions or, more recently, a probabilistic dynamics with a single arbitrary time-step. Here we show that, under this latter assumption, the inference procedure fails to reconstruct the synaptic matrix of a network of integrate-and-fire neurons when the chosen time scale of interaction does not closely match the synaptic delay or when no single time scale for the interaction can be identified; such failure, moreover, exposes a distinctive bias of the inference method that can lead to infer as inhibitory the excitatory synapses with interaction time scales longer than the model’s time-step. We therefore introduce a new two-step method, that first infers through cross-correlation profiles the delay-structure of the network and then reconstructs the synaptic matrix, and successfully test it on networks with different topologies and in different activity regimes. Although step one is able to accurately recover the delay-structure of the network, thus getting rid of any a priori guess about the time scales of the interaction, the inference method introduces nonetheless an arbitrary time scale, the time-bin dt used to binarize the spike trains. We therefore analytically and numerically study how the choice of dt affects the inference in our network model, finding that the relationship between the inferred couplings and the real synaptic efficacies, albeit being quadratic in both cases, depends critically on dt for the excitatory synapses only, whilst being basically independent of it for the inhibitory ones.

A novel edge detection for buried target extraction after SVD-2D wavelet processing

Abstract In this letter, a novel approach to analyze the edge and recognize targets of ground-penetrating radar (GPR) images is proposed. The performance of target recognition depends on the accuracy of edge detection. Cross-correlation calculation of the separated background and target signals is introduced to improve the accuracy. A novel edge detection scheme designed based on wavelet modulus maxima is applied on the cross-correlation profiles to reduce the false detection possibility caused by the noise. A novel filtering scheme based on singular value decomposition (SVD)-2D wavelet procedure is proposed to separate the target from background. The procedure can not only enhance the target reflection while suppressing the noise by improving the signal to noise ratio (SNR), but also separate the background and reflection signals. Experimental results including simulation and field application justify the effect of this scheme.

Observation and modelling of main-sequence star chromospheres - XVII. Rotation of dM4 stars★

Using two different spectrographs, High Accuracy Radial velocity Planet Searcher (European Southern Observatory) and SOPHIE (Observatoire de Haute Provence), we have measured v sini for a sample of 23 dM4 stars. These are the first measurements of v sini for most of the stars studied here. We measured v sini to a precision of 0.3 km s −1 and a detection limit of about 0.5–1 km s −1 . All our targets have similar (R − I)C colour. This is an advantage and facilitates the determination of the narrowest cross-correlation profiles for v sini ∼ 0. In our sample, we detected rotation for 21 stars (12 dM4e stars and nine dM4 stars) and we did not detect rotation in a further two stars. This result shows that there are many dM4 fast rotators (of the order of 5 d), and many more than in the case of dM1 stars. We determined radii and effective temperatures for all our target stars. The effective temperatures were derived using the (R − I)C colour and empirical far-red colour–effective temperature correlations. We derived the radii from the standard formulae relating Mbol, bolometric correction (BC) and T eff. We find that the distribution of P/sini (the projected rotation period) is bimodal with a maximum for slow rotators around 14 d and for fast rotators around 6 d, similar to dM1 stars. The rotation period appears to decrease with decreasing radius, both among dM4 and dM4e stars. The same finding was obtained in our previous study of dM1 stars.

Abundances and physical parameters for stars in the open clusters NGC 5822 and IC 4756

Classical chemical analyses may be affected by systematic errors that would cause observed abundance differences between dwarfs and giants. For some elements, however, the abundance difference could be real. We address the issue by observing 2 solar--type dwarfs in NGC 5822 and 3 in IC 4756, and comparing their composition with that of 3 giants in either of the aforementioned clusters. We determine iron abundance and stellar parameters of the dwarf stars, and the abundances of calcium, sodium, nickel, titanium, aluminium, chromium, silicon and oxygen for both the giants and dwarfs. We acquired UVES high-resolution, of high signal--to--noise ratio (S/N) spectra. The width of the cross correlation profiles was used to measure rotation velocities. For abundance determinations, the standard equivalent width analysis was performed differentially with respect to the Sun. For lithium and oxygen, we derived abundances by comparing synthetic spectra with observed line features. We find an iron abundance for dwarf stars equal to solar to within the margins of error for IC 4756, and slightly above for NGC 5822 ([Fe/H]= 0.01 and 0.05 dex respectively). The 3 stars in NG 4756 have lithium abundances between Log N(Li) 2.6 and 2.8 dex, the two stars in NGC 5822 have Log N(Li) ~ 2.8 and 2.5, respectively. For sodium, silicon, and titanium, we show that abundances of giants are significantly higher than those of the dwarfs of the same cluster (about 0.15, 0.15, and 0.35 dex).

Analysis tools for non-radially pulsating objects

At the University of Canterbury we have been developing a set of tools for the analysis of spectra of varying types of non-radially pulsating objects. This set currently includes: calculation of the moments, calculations of the phase across the profile as well as basic binary profile fitting for determination of orbital characteristics and projected rotational velocity (v sin i ) measurement. Recently the ability to calculate cross-correlation profiles using either specified or synthesized line lists has been added, all implemented in MATLAB. A number of observations of γ Doradus candidates is currently being used to test these tools. For information on our observing facilities see Pollard et al. (2007).

Pulsations detected in the line profile variations of red giants

Context.So far, red giant oscillations have been studied from radial velocity and/or light curve variations, which reveal frequencies of the oscillation modes. To characterise radial and non-radial oscillations, line profile variations are a valuable diagnostic. Here we present for the first time a line profile analysis of pulsating red giants, taking into account the small line profile variations and the predicted short damping and re-excitation times. We do so by modelling the time variations in the cross correlation profiles in terms of oscillation theory.

Highly time-resolved correlation measurement between laser and synchrotron radiation pulses without synchronization control

A mode-locked laser has been introduced in combination with synchrotron radiation to establish a versatile technique for highly time-resolved correlation measurements utilizing the short-pulse and high-pulse frequency characteristics of both photon sources. Successive pulse timing delay detected by nonlinear optical mixing between the two sources yields a cross-correlation profile capable of accurate measurement of the picosecond pulse profile of the synchrotron radiation without any synchronization control. Although the experiment was performed in the visible spectral domain, the present technique opens up a methodology for time-resolved spectroscopy in femtosecond and higher-energy domains by introducing a suitable nonlinear process that informs of the pulse coincidence between the two radiation sources.

WZ Cas – variability on multiple time-scales

We present results on our long-term velocity monitoring of the C-rich semi-regular variable WZ Cas with a Coravel instrument. Our findings are compared with light changes of the star. We suggest that the two main periods, 366 and 186 d, are due to radial pulsation. Furthermore, we find an interesting variation of the width and depth of the cross-correlation profile over a time-scale of at least 1000 d. Several possible explanations for this behaviour are discussed by comparison of time-scales and expected variability amplitudes. The influence of movements of large convective cells on the line profiles seems to be the most likely explanation of some of the observed phenomena.

The X-ray variability of the narrow-line type 1 Seyfert galaxy IRAS 13224-3809 from anXMM-Newtonobservation

We report on the XMM‐Newton timing properties of the most X-ray variable, radio-quiet, narrow-line type 1 Seyfert galaxy IRAS 13224‐3809. IRAS 13224‐3809 continues to display the extremely variable behaviour that was previously observed with ROSAT and ASCA ;h owever, no giant, rapid flaring events are observed. We detect variations by a factor as high as ∼8 during the 64-ks observation and the variability is persistent throughout the light curve. Dividing the light curve into 9-min segments, we found almost all of the segments to be variable at >3σ . When the time-averaged cross-correlation function is calculated for the 0.3‐0.8 keV band with the 3‐10 keV band, the cross-correlation profile is skewed, indicating a possible smearing of the signal to longer times (the soft band leading the hard). A correlation between count rate and hardness ratio is detected in four energy bands. In three cases, the correlation is consistent with spectral hardening at lower count rates, which can be explained in terms of a partial-covering model. The other band displays the reverse effect, showing spectral hardening at higher count rates. We can explain this trend as a more variable power-law component compared with the soft component. We also detect a delay between the 0.3‐1.5 keV count rate and the 0.8‐1.5 to 0.3‐0.8 keV hardness ratio, implying flux-induced spectral variability. Such delays and asymmetries in the cross-correlation functions could suggest reprocessing of soft and hard photons. In general, much of the timing behaviour can be attributed to erratic eclipsing behaviour associated with the partial covering phenomenon, in addition to intrinsic variability in the source. The variability behaviour of IRAS 13224‐3809 suggests a complicated combination of effects which we have started to disentangle with this present analysis.

Kinematic analysis of manual tracking in monkeys: characterization of movement intermittencies during a circular tracking task.

Segmentation of the velocity profiles into the submovements has been observed in reaching and tracking limb movements and even in isometric tasks. Submovements have been implicated in both feed-forward and feedback control. In this study, submovements were analyzed during manual tracking in the nonhuman primate with the focus on the amplitude-duration scaling of submovements and the error signals involved in their control. The task consisted of the interception and visually guided pursuit of a target moving in a circle. The submovements were quantified based on their duration and amplitude in the speed profile. Control experiments using passive movements demonstrated that these intermittencies were not instrumentation artifacts. Submovements were prominent in both the interception and tracking phases and their amplitude scaled linearly with duration. The scaling factors increased with tracking speed at the same rate for both interception and pursuit. A cross-correlation analysis between a variety of error signals and the speed profile revealed that direction and speed errors were temporally coupled to the submovements. The cross-correlation profiles suggest that submovements are initiated when speed error reaches a certain limit and when direction error is minimized. The scaling results show that in monkeys submovements characterize both the interception and pursuit portions of the task and that these submovements have similar scaling properties consistent with 1) the concept of stereotypy and 2) adding constant acceleration/force at a specific tracking speed. The correlation results show involvement of speed and direction error signals in controlling the submovements.

Power supply transient signal analysis for defect-oriented test

Transient signal analysis (TSA) is a testing method that is based on the analysis of a set of V/sub DD/ transient waveforms measured simultaneously at each supply port. Defect detection is performed by applying linear regression analysis to the time or frequency domain representations of these signals. Chip-wide process variation effects introduce signal variations that are correlated across the individual power port measurements. In contrast, defects introduce uncorrelated local variations across these measurements that can be detected as anomalies in the cross-correlation profile derived (using regression analysis) from the power port measurements of defect-free chips. This paper focuses on the application of TSA to the detection of delay faults.

Envelope tomography of long-period variable stars

This paper presents statistics of the line-doubling phenomenon in a sample of 81 long-period variable (LPV) stars of various periods, spectral types and brightness ranges. The set of observations consists of 315 high-resolution optical spectra collected with the spectrograph ELODIE at the Haute-Provence Observatory, during 27 observing nights at one-month intervals and spanning two years. When correlated with a mask mimicking a K0III spectrum, 54% of the sample stars clearly showed a double-peaked cross-correlation profile around maximum light, reflecting double absorption lines. Several pieces of evidence are presented that point towards the double absorption lines as being caused by the propagation of a shock wave through the photosphere. The observation of the Balmer lines appearing in emission around maximum light in these stars corroborates the presence of a shock wave. The observed velocity discontinuities, ranging between 10 and 25 km s-1, are not correlated with the brightness ranges. A comparison with the center-of-mass (COM) velocity obtained from submm CO lines originating in the circumstellar envelope reveals that the median velocity between the red and blue peaks is blueshifted with respect to the COM velocity, as expected if the shock moves upwards. The LPVs clearly exhibiting line-doubling around maximum light with the K0III mask appear to be the most compact ones, the stellar radius being estimated from their effective temperatures (via the spectral type) and luminosities (via the period-luminosity relationship). It is not entirely clear whether or not this segregation between compact and extended LPVs is an artefact of the use of the K0III mask. Warmer masks (F0V and G2V) applied to the most extended and coolest LPVs yield asymmetric cross-correlation functions which suggest that line doubling is occurring in those stars as well. Although a firm conclusion on this point is hampered by the large correlation noise present in the CCFs of cool LPVs obtained with warm masks, the occurrence of line doubling in those stars is confirmed by the double CO lines observed around 1.6 μm by Hinkle et al. (1984, ApJS, 56, 1). Moreover, the Hδ line in emission, which is another signature of the presence of shocks, is observed as well in the most extended stars, although with a somewhat narrower profile. This is an indication that the shock is weaker in extended than in compact LPVs, which may also contribute to the difficulty of detecting line doubling in cool, extended LPVs.

Onset of coherent oscillations in turbulent Rayleigh-Bénard convection.

We report temperature cross correlation and velocity profile measurements in the aspect-ratio-one convection cell filled with water. A sharp transition from a random chaotic state to a correlated turbulent state of finite coherence time is found when the Rayleigh number becomes larger than a critical value Ra(c) approximately equal to 5 x 10(7). The experiment reveals a unique mechanism for the onset of coherent oscillations in turbulent Rayleigh-Bénard convection.