Long time behaviour of diffusing particles in constrained geometries; application to chromatin motion

Inspired by experiments that use single-particle tracking to measure the regions of confinement of selected chromosomal regions within cell nuclei, we have developed an analytical approach that takes into account various possible positions and shapes of the confinement regions. We show, in particular, that confinement of a particle into a subregion that is entirely enclosed within a spherical volume can lead to a higher limit of the mean radial square displacement value than the one associated with a particle that can explore the entire spherical volume. Finally, we apply the theory to analyse the motion of extrachromosomal chromatin rings within nuclei of living yeast.

Learning Robot Motions from Visual Sensing

Learning from demonstration becomes increasingly popular as an efficient way of robot programming. Not only a scientific interest acts as an inspiration in this case but also the possibility of producing the machines that would find application in different areas of life: robots helping with daily routine at home, high performance automata in industries or friendly toys for children. One way to teach a robot to fulfill complex tasks is to start with simple training exercises, combining them to form more difficult behavior. The objective of the Master’s thesis work was to study robot programming with visual input. Dynamic movement primitives (DMPs) were chosen as a tool for motion learning and generation. Assuming a movement to be a spring system influenced by an external force, making this system move, DMPs represent the motion as a set of non-linear differential equations. During the experiments the properties of DMP, such as temporal and spacial invariance, were examined. The effect of the DMP parameters, including spring coefficient, damping factor, temporal scaling, on the trajectory generated were studied.

Reading Development During Elementary School Years. Evidence from Eye Movements

The present dissertation examined reading development during elementary school years by means of eye movement tracking. Three different but related issues in this field were assessed. First of all, the development of parafoveal processing skills in reading was investigated. Second, it was assessed whether and to what extent sublexical units such as syllables and morphemes are used in processing Finnish words and whether the use of these sublexical units changes as a function of reading proficiency. Finally, the developmental trend in the speed of visual information extraction during reading was examined. With regard to parafoveal processing skills, it was shown that 2nd graders extract letter identity information approx. 5 characters to the right of fixation, 4th graders approx. 7 characters to the right of fixation, and 6th graders and adults approx. 9 characters to the right of fixation. Furthermore, it was shown that all age groups extract more parafoveal information within compound words than across adjectivenoun pairs of similar length. In compounds, parafoveal word information can be extracted in parallel with foveal word information, if the compound in question is of high frequency. With regard to the use of sublexical units in Finnish word processing, it was shown that less proficient 2nd graders use both syllables and morphemes in the course of lexical access. More proficient 2nd graders as well as older readers seem to process words more holistically. Finally, it was shown that 60 ms is enough for 4th graders and adults to extract visual information from both 4-letter and 8-letter words, whereas 2nd graders clearly needed more than 60 ms to extract all information from 8- letter words for processing to proceed smoothly. The present dissertation demonstrates that Finnish 2nd graders develop their reading skills rapidly and are already at an adult level in some aspects of reading. This is not to say that there are no differences between less proficient (e.g., 2nd graders) and more proficient readers (e.g., adults) but in some respects it seems that the visual system used in extracting information from the text is matured by the 2nd grade. Furthermore, the present dissertation demonstrates that the allocation of attention in reading depends much on textual properties such as word frequency and whether words are spatially unified (as in compounds) or not. This flexibility of the attentional system naturally needs to be captured in word processing models. Finally, individual differences within age groups are quite substantial but it seems that by the end of the 2nd grade practically all Finnish children have reached a reasonable level of reading proficiency.

Tracking larval insect movement within soil using high resolution X-ray microtomography

1. In contrast to above-ground insects, comparatively little is known about the behaviour of subterranean insects, due largely to the difficulty of studying them in situ. 2. The movement of newly hatched (neonate) clover root weevil (Sitona lepidus L. Coleoptera: Curculinidae) larvae was studied non-invasively using recently developed high resolution X-ray microtomography. 3. The movement and final position of S. lepidus larvae in the soil was reliably established using X-ray microtomography, when compared with larval positions that were determined by destructively sectioning the soil column. 4. Newly hatched S. lepidus larvae were seen to attack the root rhizobial nodules of their host plant, white clover (Trifolium repens L.). Sitona lepidus larvae travelled between 9 and 27 mm in 9 h at a mean speed of 1.8 mm h(-1). 5. Sitona lepidus larvae did not move through the soil in a linear manner, but changed trajectory in both the lateral and vertical planes.

Short-term movement and retreat sites of Leptodactylus labyrinthicus (Anura : Leptodactylidae) during the breeding season: A spool-and-line tracking study

Capture/recapture studies significantly increase our knowledge of the natural history of anuran amphibians. Many different methods have been employed in these studies, but a number of new techniques still require experimental validation. During two reproductive seasons in a Cerrado remnant in southeastern Brazil, we investigated the movement patterns and habitat use of the pepper frog, Leptodactylus labyrinthicus, using a spool-and-line device. This low-cost device did not appear to interfere with the activities of the frogs and allowed for constant monitoring, showing precise routes of movement and great predictability of relocations. Both sexes were active at night. During the day, males and females made use of retreat sites under vegetation or in burrows constructed by small- and medium-sized mammals. Males and females did not use standardized routes; there were no significant differences between their movements, and movements were not correlated with body size or environmental conditions. Individuals are able to move further than 100 m per day, a characteristic that may enable this species to colonize or recolonize open areas.

An evaluation of home range models for marine fish tracking and fine scale habitat use and movement patterns of age 1 Greenland cod (Gadus macrocephalus ogac)

My thesis examines fine-scale habitat use and movement patterns of age 1 Greenland cod (Gadus macrocephalus ogac) tracked using acoustic telemetry. Recent advances in tracking technologies such as GPS and acoustic telemetry have led to increasingly large and detailed datasets that present new opportunities for researchers to address fine-scale ecological questions regarding animal movement and spatial distribution. There is a growing demand for home range models that will not only work with massive quantities of autocorrelated data, but that can also exploit the added detail inherent in these high-resolution datasets. Most published home range studies use radio-telemetry or satellite data from terrestrial mammals or avian species, and most studies that evaluate the relative performance of home range models use simulated data. In Chapter 2, I used actual field-collected data from age-1 Greenland cod tracked with acoustic telemetry to evaluate the accuracy and precision of six home range models: minimum convex polygons, kernel densities with plug-in bandwidth selection and the reference bandwidth, adaptive local convex hulls, Brownian bridges, and dynamic Brownian bridges. I then applied the most appropriate model to two years (2010-2012) of tracking data collected from 82 tagged Greenland cod tracked in Newman Sound, Newfoundland, Canada, to determine diel and seasonal differences in habitat use and movement patterns (Chapter 3). Little is known of juvenile cod ecology, so resolving these relationships will provide valuable insight into activity patterns, habitat use, and predator-prey dynamics, while filling a knowledge gap regarding the use of space by age 1 Greenland cod in a coastal nursery habitat. By doing so, my thesis demonstrates an appropriate technique for modelling the spatial use of fish from acoustic telemetry data that can be applied to high-resolution, high-frequency tracking datasets collected from mobile organisms in any environment.

Real-time hand tracking for rehabilitation and character animation

Hand and finger tracking has a major importance in healthcare, for rehabilitation of hand function required due to a neurological disorder, and in virtual environment applications, like characters animation for on-line games or movies. Current solutions consist mostly of motion tracking gloves with embedded resistive bend sensors that most often suffer from signal drift, sensor saturation, sensor displacement and complex calibration procedures. More advanced solutions provide better tracking stability, but at the expense of a higher cost. The proposed solution aims to provide the required precision, stability and feasibility through the combination of eleven inertial measurements units (IMUs). Each unit captures the spatial orientation of the attached body. To fully capture the hand movement, each finger encompasses two units (at the proximal and distal phalanges), plus one unit at the back of the hand. The proposed glove was validated in two distinct steps: a) evaluation of the sensors’ accuracy and stability over time; b) evaluation of the bending trajectories during usual finger flexion tasks based on the intra-class correlation coefficient (ICC). Results revealed that the glove was sensitive mainly to magnetic field distortions and sensors tuning. The inclusion of a hard and soft iron correction algorithm and accelerometer and gyro drift and temperature compensation methods provided increased stability and precision. Finger trajectories evaluation yielded high ICC values with an overall reliability within application’s satisfying limits. The developed low cost system provides a straightforward calibration and usability, qualifying the device for hand and finger tracking in healthcare and animation industries.

Colonic movements in healthy subjects as monitored by a Magnet Tracking System.

The Magnet Tracking System (MTS) is a minimally-invasive technique of continuous evaluation of gastrointestinal motility. In this study, MTS was used to analyse colonic propulsive dynamics and compare the transit of a magnetic pill with that of standard radio-opaque markers. MTS monitors the progress in real time of a magnetic pill through the gut. Ten men and 10 women with regular daily bowel movements swallowed this pill and 10 radio-opaque markers at 8 pm. Five hours of recordings were conducted during 2 following mornings. Origin, direction, amplitude and velocity of movements were analysed relative to space-time plots of the pill trajectory. Abdominal radiographs were taken to compare the progress of both pill and markers. The magnetic pill lay idle for 90% of its sojourn in the colon; its total retrograde displacement accounted for only 20% of its overall movement. Analysis of these movements showed a bimodal distribution of velocities: around 1.5 and 50 cm min(-1), the latter being responsible for 2/3 of distance traversed. There were more movements overall and more mass movements in males. Net hourly forward progress was greater in the left than right colon, and greater in males. The position of the magnetic pill correlated well with the advancement of markers. MTS showed patterns and propulsion dynamics of colonic segments with as yet unmet precision. Detailed analysis of slow and fast patterns of colonic progress makes it possible to specify the motility of colonic segments, and any variability in gender. Such analysis opens up promising avenues in studies of motility disorders.

ZHARP: three-dimensional motion tracking from a single image plane.

Three-dimensional imaging and quantification of myocardial function are essential steps in the evaluation of cardiac disease. We propose a tagged magnetic resonance imaging methodology called zHARP that encodes and automatically tracks myocardial displacement in three dimensions. Unlike other motion encoding techniques, zHARP encodes both in-plane and through-plane motion in a single image plane without affecting the acquisition speed. Postprocessing unravels this encoding in order to directly track the 3-D displacement of every point within the image plane throughout an entire image sequence. Experimental results include a phantom validation experiment, which compares zHARP to phase contrast imaging, and an in vivo study of a normal human volunteer. Results demonstrate that the simultaneous extraction of in-plane and through-plane displacements from tagged images is feasible.

Real-time MR imaging of myocardial regional function using strain-encoding (SENC) with tissue through-plane motion tracking.

PURPOSE: To implement real-time myocardial strain-encoding (SENC) imaging in combination with tracking the tissue displacement in the through-plane direction. MATERIALS AND METHODS: SENC imaging was combined with the slice-following technique by implementing three-dimensional (3D) selective excitation. Certain adjustments were implemented to reduce scan time to one heartbeat. A total of 10 volunteers and five pigs were scanned on a 3T MRI scanner. Spatial modulation of magnetization (SPAMM)-tagged images were acquired on planes orthogonal to the SENC planes for comparison. Myocardial infarction (MI) was induced in two pigs and the resulting SENC images were compared to standard delayed-enhancement (DE) images. RESULTS: The strain values computed from SENC imaging with slice-following showed significant difference from those acquired without slice-following, especially during systole (P < 0.01). The strain curves computed from the SENC images with and without slice-following were similar to those computed from the orthogonal SPAMM images, with and without, respectively, tracking the tag line displacement in the strain direction. The resulting SENC images showed good agreement with the DE images in identifying MI in infarcted pigs. CONCLUSION: Correction of through-plane motion in real-time cardiac functional imaging is feasible using slice-following. The strain measurements are more accurate than conventional SENC measurements in humans and animals, as validated with conventional MRI tagging.

Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking.

We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2×2×3 factorial design with the following factors: PMC on or off; 3.0mm or 1.5mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p<0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies.

Skill Development in Music Reading. The Eye-Movement Approach

This dissertation examined skill development in music reading by focusing on the visual processing of music notation in different music-reading tasks. Each of the three experiments of this dissertation addressed one of the three types of music reading: (i) sight-reading, i.e. reading and performing completely unknown music, (ii) rehearsed reading, during which the performer is already familiar with the music being played, and (iii) silent reading with no performance requirements. The use of the eye-tracking methodology allowed the recording of the readers’ eye movements from the time of music reading with extreme precision. Due to the lack of coherence in the smallish amount of prior studies on eye movements in music reading, the dissertation also had a heavy methodological emphasis. The present dissertation thus aimed to promote two major issues: (1) it investigated the eye-movement indicators of skill and skill development in sight-reading, rehearsed reading and silent reading, and (2) developed and tested suitable methods that can be used by future studies on the topic. Experiment I focused on the eye-movement behaviour of adults during their first steps of learning to read music notation. The longitudinal experiment spanned a nine-month long music-training period, during which 49 participants (university students taking part in a compulsory music course) sight-read and performed a series of simple melodies in three measurement sessions. Participants with no musical background were entitled as “novices”, whereas “amateurs” had had musical training prior to the experiment. The main issue of interest was the changes in the novices’ eye movements and performances across the measurements while the amateurs offered a point of reference for the assessment of the novices’ development. The experiment showed that the novices tended to sight-read in a more stepwise fashion than the amateurs, the latter group manifesting more back-and-forth eye movements. The novices’ skill development was reflected by the faster identification of note symbols involved in larger melodic intervals. Across the measurements, the novices also began to show sensitivity to the melodies’ metrical structure, which the amateurs demonstrated from the very beginning. The stimulus melodies consisted of quarter notes, making the effects of meter and larger melodic intervals distinguishable from effects caused by, say, different rhythmic patterns. Experiment II explored the eye movements of 40 experienced musicians (music education students and music performance students) during temporally controlled rehearsed reading. This cross-sectional experiment focused on the eye-movement effects of one-bar-long melodic alterations placed within a familiar melody. The synchronizing of the performance and eye-movement recordings enabled the investigation of the eye-hand span, i.e., the temporal gap between a performed note and the point of gaze. The eye-hand span was typically found to remain around one second. Music performance students demonstrated increased professing efficiency by their shorter average fixation durations as well as in the two examined eye-hand span measures: these participants used larger eye-hand spans more frequently and inspected more of the musical score during the performance of one metrical beat than students of music education. Although all participants produced performances almost indistinguishable in terms of their auditory characteristics, the altered bars indeed affected the reading of the score: the general effects of expertise in terms of the two eye- hand span measures, demonstrated by the music performance students, disappeared in the face of the melodic alterations. Experiment III was a longitudinal experiment designed to examine the differences between adult novice and amateur musicians’ silent reading of music notation, as well as the changes the 49 participants manifested during a nine-month long music course. From a methodological perspective, an opening to research on eye movements in music reading was the inclusion of a verbal protocol in the research design: after viewing the musical image, the readers were asked to describe what they had seen. A two-way categorization for verbal descriptions was developed in order to assess the quality of extracted musical information. More extensive musical background was related to shorter average fixation duration, more linear scanning of the musical image, and more sophisticated verbal descriptions of the music in question. No apparent effects of skill development were observed for the novice music readers alone, but all participants improved their verbal descriptions towards the last measurement. Apart from the background-related differences between groups of participants, combining verbal and eye-movement data in a cluster analysis identified three styles of silent reading. The finding demonstrated individual differences in how the freely defined silent-reading task was approached. This dissertation is among the first presentations of a series of experiments systematically addressing the visual processing of music notation in various types of music-reading tasks and focusing especially on the eye-movement indicators of developing music-reading skill. Overall, the experiments demonstrate that the music-reading processes are affected not only by “top-down” factors, such as musical background, but also by the “bottom-up” effects of specific features of music notation, such as pitch heights, metrical division, rhythmic patterns and unexpected melodic events. From a methodological perspective, the experiments emphasize the importance of systematic stimulus design, temporal control during performance tasks, and the development of complementary methods, for easing the interpretation of the eye-movement data. To conclude, this dissertation suggests that advances in comprehending the cognitive aspects of music reading, the nature of expertise in this musical task, and the development of educational tools can be attained through the systematic application of the eye-tracking methodology also in this specific domain.

The influence of drug-induced dyskinesias on manual tracking in Parkinson's disease

The influence of peak-dose drug-induced dyskinesia (DID) on manual tracking (MT) was examined in 10 dyskinetic patients (OPO), and compared to 10 age/gendermatched non-dyskinetic patients (NDPD) and 10 healthy controls. Whole body movement (WBM) and MT were recorded with a 6-degrees of freedom magnetic motion tracker and forearm rotation sensors, respectively. Subjects were asked to match the length of a computer-generated line with a line controlled via wrist rotation. Results show that OPO patients had greater WBM displacement and velocity than other groups. All groups displayed increased WBM from rest to MT, but only DPD and NDPO patients demonstrated a significant increase in WBM displacement and velocity. In addition, OPO patients exhibited excessive increase in WBM suggesting overflow DID. When two distinct target pace segments were examined (FAST/SLOW), all groups had slight increases in WBM displacement and velocity from SLOW to FAST, but only OPO patients showed significantly increased WBM displacement and velocity from SLOW to FAST. Therefore, it can be suggested that overflow DID was further increased with increased task speed. OPO patients also showed significantly greater ERROR matching target velocity, but no significant difference in ERROR in displacement, indicating that significantly greater WBM displacement in the OPO group did not have a direct influence on tracking performance. Individual target and performance traces demonstrated this relatively good tracking performance with the exception of distinct deviations from the target trace that occurred suddenly, followed by quick returns to the target coherent in time with increased performance velocity. In addition, performance hand velocity was not correlated with WBM velocity in DPO patients, suggesting that increased ERROR in velocity was not a direct result of WBM velocity. In conclusion, we propose that over-excitation of motor cortical areas, reported to be present in DPO patients, resulted in overflow DID during voluntary movement. Furthermore, we propose that the increased ERROR in velocity was the result of hypermetric voluntary movements also originating from the over-excitation of motor cortical areas.