Chromatographic alignment of LC-MS and LC-MS/MS datasets by genetic algorithm feature extraction

Liquid chromatography-mass spectrometry (LC-MS) datasets can be compared or combined following chromatographic alignment. Here we describe a simple solution to the specific problem of aligning one LC-MS dataset and one LC-MS/MS dataset, acquired on separate instruments from an enzymatic digest of a protein mixture, using feature extraction and a genetic algorithm. First, the LC-MS dataset is searched within a few ppm of the calculated theoretical masses of peptides confidently identified by LC-MS/MS. A piecewise linear function is then fitted to these matched peptides using a genetic algorithm with a fitness function that is insensitive to incorrect matches but sufficiently flexible to adapt to the discrete shifts common when comparing LC datasets. We demonstrate the utility of this method by aligning ion trap LC-MS/MS data with accurate LC-MS data from an FTICR mass spectrometer and show how hybrid datasets can improve peptide and protein identification by combining the speed of the ion trap with the mass accuracy of the FTICR, similar to using a hybrid ion trap-FTICR instrument. We also show that the high resolving power of FTICR can improve precision and linear dynamic range in quantitative proteomics. The alignment software, msalign, is freely available as open source.

The integration of figurative language and static depictions: an eye movement study of fictive motion

Do we view the world differently if it is described to us in figurative rather than literal terms? An answer to this question would reveal something about both the conceptual representation of figurative language and the scope of top-down influences oil scene perception. Previous work has shown that participants will look longer at a path region of a picture when it is described with a type of figurative language called fictive motion (The road goes through the desert) rather than without (The road is in the desert). The current experiment provided evidence that such fictive motion descriptions affect eye movements by evoking mental representations of motion. If participants heard contextual information that would hinder actual motion, it influenced how they viewed a picture when it was described with fictive motion. Inspection times and eye movements scanning along the path increased during fictive motion descriptions when the terrain was first described as difficult (The desert is hilly) as compared to easy (The desert is flat); there were no such effects for descriptions without fictive motion. It is argued that fictive motion evokes a mental simulation of motion that is immediately integrated with visual processing, and hence figurative language can have a distinct effect on perception. (c) 2005 Elsevier B.V. All rights reserved.

Spatial offset of test field elements from surround elements affects the strength of motion aftereffects

Static movement aftereffects (MAEs) were measured after adaptation to vertical square-wave luminance gratings drifting horizontally within a central window in a surrounding stationary vertical grating. The relationship between the stationary test grating and the surround was manipulated by varying the alignment of the stationary stripes in the window and those in the surround, and the type of outline separating the window and the surround [no outline, black outline (invisible on black stripes), and red outline (visible throughout its length)]. Offsetting the stripes in the window significantly increased both the duration and ratings of the strength of MAEs. Manipulating the outline had no significant effect on either measure of MAE strength. In a second experiment, in which the stationary test fields alone were presented, participants judged how segregated the test field appeared from its surround. In contrast to the MAE measures, outline as well as offset contributed to judged segregation. In a third experiment, in which test-stripe offset wits systematically manipulated, segregation ratings rose with offset. However, MAE strength was greater at medium than at either small or large (180 degrees phase shift) offsets. The effects of these manipulations on the MAE are interpreted in terms of a spatial mechanism which integrates motion signals along collinear contours of the test field and surround, and so causes a reduction of motion contrast at the edges of the test field.

Humans ignore motion and stereo cues in favor of a fictional stable world

As we move through the world, our eyes acquire a sequence of images. The information from this sequence is sufficient to determine the structure of a three-dimensional scene, up to a scale factor determined by the distance that the eyes have moved [1, 2]. Previous evidence shows that the human visual system accounts for the distance the observer has walked [3,4] and the separation of the eyes [5-8] when judging the scale, shape, and distance of objects. However, in an immersive virtual-reality environment, observers failed to notice when a scene expanded or contracted, despite having consistent information about scale from both distance walked and binocular vision. This failure led to large errors in judging the size of objects. The pattern of errors cannot be explained by assuming a visual reconstruction of the scene with an incorrect estimate of interocular separation or distance walked. Instead, it is consistent with a Bayesian model of cue integration in which the efficacy of motion and disparity cues is greater at near viewing distances. Our results imply that observers are more willing to adjust their estimate of interocular separation or distance walked than to accept that the scene has changed in size.

Quantitative analysis of accuracy of an inertial/acoustic 6DOF tracking system in motion

An increasing number of neuroscience experiments are using virtual reality to provide a more immersive and less artificial experimental environment. This is particularly useful to navigation and three-dimensional scene perception experiments. Such experiments require accurate real-time tracking of the observer's head in order to render the virtual scene. Here, we present data on the accuracy of a commonly used six degrees of freedom tracker (Intersense IS900) when it is moved in ways typical of virtual reality applications. We compared the reported location of the tracker with its location computed by an optical tracking method. When the tracker was stationary, the root mean square error in spatial accuracy was 0.64 mm. However, we found that errors increased over ten-fold (up to 17 mm) when the tracker moved at speeds common in virtual reality applications. We demonstrate that the errors we report here are predominantly due to inaccuracies of the IS900 system rather than the optical tracking against which it was compared. (c) 2006 Elsevier B.V. All rights reserved.

Perceived spatial displacement of motion-defined contours in peripheral vision

The perceived displacement of motion-defined contours in peripheral vision was examined in four experiments. In Experiment 1, in line with Ramachandran and Anstis' finding [Ramachandran, V. S., & Anstis, S. M. (1990). Illusory displacement of equiluminous kinetic edges. Perception, 19, 611-616], the border between a field of drifting dots and a static dot pattern was apparently displaced in the same direction as the movement of the dots. When a uniform dark area was substituted for the static dots, a similar displacement was found, but this was smaller and statistically insignificant. In Experiment 2, the border between two fields of dots moving in opposite directions was displaced in the direction of motion of the dots in the more eccentric field, so that the location of a boundary defined by a diverging pattern is perceived as more eccentric, and that defined by a converging as less eccentric. Two explanations for this effect (that the displacement reflects a greater weight given to the more eccentric motion, or that the region containing stronger centripetal motion components expands perceptually into that containing centrifugal motion) were tested in Experiment 3, by varying the velocity of the more eccentric region. The results favoured the explanation based on the expansion of an area in centripetal motion. Experiment 4 showed that the difference in perceived location was unlikely to be due to differences in the discriminability of contours in diverging and converging pattems, and confirmed that this effect is due to a difference between centripetal and centrifugal motion rather than motion components in other directions. Our result provides new evidence for a bias towards centripetal motion in human vision, and suggests that the direction of motion-induced displacement of edges is not always in the direction of an adjacent moving pattern. (C) 2008 Elsevier Ltd. All rights reserved.

Variable step LMS algorithm using the accumulated instantaneous error concept

The convergence speed of the standard Least Mean Square adaptive array may be degraded in mobile communication environments. Different conventional variable step size LMS algorithms were proposed to enhance the convergence speed while maintaining low steady state error. In this paper, a new variable step LMS algorithm, using the accumulated instantaneous error concept is proposed. In the proposed algorithm, the accumulated instantaneous error is used to update the step size parameter of standard LMS is varied. Simulation results show that the proposed algorithm is simpler and yields better performance than conventional variable step LMS.

Unsupervised genetic algorithm deployed for intrusion detection

This paper represents the first step in an on-going work for designing an unsupervised method based on genetic algorithm for intrusion detection. Its main role in a broader system is to notify of an unusual traffic and in that way provide the possibility of detecting unknown attacks. Most of the machine-learning techniques deployed for intrusion detection are supervised as these techniques are generally more accurate, but this implies the need of labeling the data for training and testing which is time-consuming and error-prone. Hence, our goal is to devise an anomaly detector which would be unsupervised, but at the same time robust and accurate. Genetic algorithms are robust and able to avoid getting stuck in local optima, unlike the rest of clustering techniques. The model is verified on KDD99 benchmark dataset, generating a solution competitive with the solutions of the state-of-the-art which demonstrates high possibilities of the proposed method.

A new algorithm for OFDM joint data detection and phase noise cancellation

This paper proposes a new iterative algorithm for OFDM joint data detection and phase noise (PHN) cancellation based on minimum mean square prediction error. We particularly highlight the problem of "overfitting" such that the iterative approach may converge to a trivial solution. Although it is essential for this joint approach, the overfitting problem was relatively less studied in existing algorithms. In this paper, specifically, we apply a hard decision procedure at every iterative step to overcome the overfitting. Moreover, compared with existing algorithms, a more accurate Pade approximation is used to represent the phase noise, and finally a more robust and compact fast process based on Givens rotation is proposed to reduce the complexity to a practical level. Numerical simulations are also given to verify the proposed algorithm.

A sparse kernel density estimation algorithm using forward constrained regression

Using the classical Parzen window (PW) estimate as the target function, the sparse kernel density estimator is constructed in a forward constrained regression manner. The leave-one-out (LOO) test score is used for kernel selection. The jackknife parameter estimator subject to positivity constraint check is used for the parameter estimation of a single parameter at each forward step. As such the proposed approach is simple to implement and the associated computational cost is very low. An illustrative example is employed to demonstrate that the proposed approach is effective in constructing sparse kernel density estimators with comparable accuracy to that of the classical Parzen window estimate.

An on-line algorithm of uncertain time delay estimation in a continuous system

In this paper, we present an on-line estimation algorithm for an uncertain time delay in a continuous system based on the observational input-output data, subject to observational noise. The first order Pade approximation is used to approximate the time delay. At each time step, the algorithm combines the well known Kalman filter algorithm and the recursive instrumental variable least squares (RIVLS) algorithm in cascade form. The instrumental variable least squares algorithm is used in order to achieve the consistency of the delay parameter estimate, since an error-in-the-variable model is involved. An illustrative example is utilized to demonstrate the efficacy of the proposed approach.

A relative path attenuation approximation algorithm for DVB-T systems

In the United Kingdom and in fact throughout Europe, the chosen standard for digital terrestrial television is the European Telecommunications Standards Institute (ETSI) ETN 300 744 also known as Digital Video Broadcasting - Terrestrial (DVB-T). The modulation method under this standard was chosen to be Orthogonal Frequency Division Multiplex (0FD4 because of the apparent inherent capability for withstanding the effects of multipath. Within the DVB-T standard, the addition of pilot tones was included that can be used for many applications such as channel impulse response estimation or local oscillator phase and frequency offset estimation. This paper demonstrates a technique for an estimation of the relative path attenuation of a single multipath signal that can be used as a simple firmware update for a commercial set-top box. This technique can be used to help eliminate the effects of multipath(1).

Investigation into the performance of an algorithm for deriving concise descriptions of optic flow fields for real-time control

This paper describes a region-based algorithm for deriving a concise description of a first order optical flow field. The algorithm described achieves performance improvements over existing algorithms without compromising the accuracy of the flow field values calculated. These improvements are brought about by not computing the entire flow field between two consecutive images, but by considering only the flow vectors of a selected subset of the images. The algorithm is presented in the context of a project to balance a bipedal robot using visual information.

Extending the friction cone algorithm for arbitrary polygon based haptic objects

Most haptic environments are based on single point interactions whereas in practice, object manipulation requires multiple contact points between the object, fingers, thumb and palm. The Friction Cone Algorithm was developed specifically to work well in a multi-finger haptic environment where object manipulation would occur. However, the Friction Cone Algorithm has two shortcomings when applied to polygon meshes: there is no means of transitioning polygon boundaries or feeling non-convex edges. In order to overcome these deficiencies, Face Directed Connection Graphs have been developed as well as a robust method for applying friction to non-convex edges. Both these extensions are described herein, as well as the implementation issues associated with them.

Force shading and bump mapping using the friction cone algorithm

Previous work has presented the friction cone algorithm, a generalised method to resolve forces on a simulated haptic object when two or more fingers are in contact. Two extensions to the friction cone algorithm are presented: force shading and bump mapping. Force shading removes the discontinuities that are present when transitioning from one face to the next, whilst bump mapping provides a mechanism for rendering haptic textures on polygonal surfaces. Both these extensions can be combined whilst still maintaining the friction cone algorithm's intrinsic ability to simulate arbitrarily complex friction models.