Representational difference analysis:Critical appraisal and method development for the identification of unique DNA sequences from prokaryotes

Representational difference analysis (RDA) has great potential for preferential amplification of unique but uncharacterised DNA sequences present in one source such as a whole genome, but absent from a related genome or other complex population of sequences. While a few examples of its successful exploitation have been published, the method has not been well dissected and robust, detailed published protocols are lacking. Here we examine the method in detail, suggest improvements and provide a protocol that has yielded key unique sequences from a pathogenic bacterial genome. © 2003 Elsevier Science B.V. All rights reserved.

Build-up of auditory stream segregation induced by tone sequences of constant or alternating frequency and the resetting effects of single deviants

Three experiments investigated the dynamics of auditory stream segregation. Experiment 1 used a 2.0-s constant-frequency inducer (10 repetitions of a low-frequency pure tone) to promote segregation in a subsequent, 1.2-s test sequence of alternating low- and high-frequency tones. Replacing the final inducer tone with silence reduced reported test-sequence segregation substantially. This reduction did not occur when either the 4th or 7th inducer was replaced with silence. This suggests that a change at the induction/test-sequence boundary actively resets buildup, rather than less segregation occurring simply because fewer inducer tones were presented. Furthermore, Experiment 2 found that a constant-frequency inducer produced its maximum segregation-promoting effect after only 3 tone cycles - this contrasts with the more gradual build-up typically observed for alternating sequences. Experiment 3 required listeners to judge continuously the grouping of 20-s test sequences. Constant-frequency inducers were considerably more effective at promoting segregation than alternating ones; this difference persisted for ∼10 s. In addition, resetting arising from a single deviant (longer tone) was associated only with constant-frequency inducers. Overall, the results suggest that constant-frequency inducers promote segregation by capturing one subset of test-sequence tones into an on-going, pre-established stream and that a deviant tone may reduce segregation by disrupting this capture. © 2013 Acoustical Society of America.

Analysis of foveation sequences in congenital nystagmus

Congenital nystagmus (CN) is an ocular-motor disorder that appears at birth or during the first few months of life; it is characterised by involuntary, conjugated, bilateral to and fro ocular oscillations. Pathogenesis of congenital nystagmus is still unknown. Eye movement recording allow to extract and analyse nystagmus main features such as shape, amplitude and frequency; depending on the morphology of the oscillations nystagmus can be classified in different categories (pendular, jerk, horizontal unidirectional, bidirectional). In general, CN patient show a considerable decrease of the visual acuity: image fixation on the retina is disturbed by nystagmus continuous oscillations; however, image stabilisation is still achieved during the short foveation periods in which eye velocity slows down while the target image is placed onto the fovea. Visual acuity was found to be mainly dependent on foveation periods duration, but cycle-to-cycle foveation repeatability and reduction of retinal image velocities also contribute in increasing visual acuity. This study concentrate on cycle-to-cycle image position variation onto fovea, trying to characterise the sequences of foveation positions. Eye-movement (infrared oculographic or electro oculographic) recordings, relative to different gaze positions and belonging to more than 30 CN patients, were analysed. Preliminary results suggest that sequences of foveations show a cyclic pattern with a dominant frequency (around 0.3 Hz on average) much lower than that of the nystagmus (about 3.3 Hz on average). Sequences of foveations reveals an horizontal ocular swing of more than 2 degree on average, which can explain the low visual acuity of the CN patient. Current CN therapies, pharmacological treatment or surgery of the ocular muscles, mainly aim to increase the patient's visual acuity. Hence, it is fundamental to have an objective parameter (expected visual acuity) for therapy planning. The information about sequences of foveations can improve estimation of patient visual acuity. © 2008 Springer-Verlag.

Detection of foveation windows and analysis of foveation sequences in congenital nystagmus

Congenital nystagmus (CN) is an ocular-motor disorder characterised by involuntary, conjugated ocular oscillations, that can arise since the first months of life. Pathogenesis of congenital nystagmus is still under investigation. In general, CN patients show a considerable decrease of their visual acuity: image fixation on the retina is disturbed by nystagmus continuous oscillations, mainly horizontal. However, image stabilisation is still achieved during the short periods in which eye velocity slows down while the target image is placed onto the fovea (called foveation intervals). To quantify the extent of nystagmus, eye movement recording are routinely employed, allowing physicians to extract and analyse nystagmus main features such as shape, amplitude and frequency. Using eye movement recording, it is also possible to compute estimated visual acuity predictors: analytical functions which estimates expected visual acuity using signal features such as foveation time and foveation position variability. Use of those functions add information to typical visual acuity measurement (e.g. Landolt C test) and could be a support for therapy planning or monitoring. This study focus on robust detection of CN patients' foveations. Specifically, it proposes a method to recognize the exact signal tracts in which a subject foveates, This paper also analyses foveation sequences. About 50 eyemovement recordings, either infrared-oculographic or electrooculographic, from different CN subjects were acquired. Results suggest that an exponential interpolation for the slow phases of nystagmus could improve foveation time computing and reduce influence of breaking saccades and data noise. Moreover a concise description of foveation sequence variability can be achieved using non-fitting splines. © 2009 Springer Berlin Heidelberg.