Exploring the spatial variation of tides for seafloor mapping data corrections

Senior thesis written for Oceanography 445

Temporal precision of interceptive action: differential effects of target size and speed

The duration of movements made to intercept moving targets decreases and movement speed increases when interception requires greater temporal precision. Changes in target size and target speed can have the same effect on required temporal precision, but the response to these changes differs: changes in target speed elicit larger changes in response speed. A possible explanation is that people attempt to strike the target in a central zone that does not vary much with variation in physical target size: the effective size of the target is relatively constant over changes in physical size. Three experiments are reported that test this idea. Participants performed two tasks: (1) strike a moving target with a bat moved perpendicular to the path of the target; (2) press on a force transducer when the target was in a location where it could be struck by the bat. Target speed was varied and target size held constant in experiment 1. Target speed and size were co-varied in experiment 2, keeping the required temporal precision constant. Target size was varied and target speed held constant in experiment 3 to give the same temporal precision as experiment 1. Duration of hitting movements decreased and maximum movement speed increased with increases in target speed and/or temporal precision requirements in all experiments. The effects were largest in experiment 1 and smallest in experiment 3. Analysis of a measure of effective target size (standard deviation of strike locations on the target) failed to support the hypothesis that performance differences could be explained in terms of effective size rather than actual physical size. In the pressing task, participants produced greater peak forces and shorter force pulses when the temporal precision required was greater, showing that the response to increasing temporal precision generalizes to different responses. It is concluded that target size and target speed have independent effects on performance.

Perceptual speed does not cause intelligence, and intelligence does not cause perceptual speed

There is ongoing debate whether the efficiency of local cognitive processes leads to global cognitive ability or whether global ability feeds the efficiency of basic processes. A prominent example is the well-replicated association between inspection time (IT), a measure of perceptual discrimination speed, and intelligence (IQ), where it is not known whether increased speed is a cause or consequence of high IQ. We investigated the direction of causation between IT and IQ in 2012 genetically related subjects from Australia and The Netherlands. Models in which the reliable variance of each observed variable was specified as a latent trait showed IT correlations of -0.44 and -0.33 with respective Performance and Verbal IQ; heritabilities were 57% (IT), 83% (PIQ) and 77% (VIQ). Directional causation models provided poor fits to the data, with covariation best explained by pleiotropic genes (influencing variation in both IT and IQ). This finding of a common genetic factor provides a better target for identifying genes involved in cognition than genes which are unique to specific traits.

Systematic changes in the duration and precision of interception in response to variation of amplitude and effector size

The results of two experiments are reported that examined how performance in a simple interceptive action (hitting a moving target) was influenced by the speed of the target, the size of the intercepting effector and the distance moved to make the interception. In Experiment 1, target speed and the width of the intercepting manipulandum (bat) were varied. The hypothesis that people make briefer movements, when the temporal accuracy and precision demands of the task are high, predicts that bat width and target speed will divisively interact in their effect on movement time (MT) and that shorter MTs will be associated with a smaller temporal variable error (VE). An alternative hypothesis that people initiate movement when the rate of expansion (ROE) of the target's image reaches a specific, fixed criterion value predicts that bat width will have no effect on MT. The results supported the first hypothesis: a statistically reliable interaction of the predicted form was obtained and the temporal VE was smaller for briefer movements. In Experiment 2, distance to move and target speed were varied. MT increased in direct proportion to distance and there was a divisive interaction between distance and speed; as in Experiment 1, temporal VE was smaller for briefer movements. The pattern of results could not be explained by the strategy of initiating movement at a fixed value of the ROE or at a fixed value of any other perceptual variable potentially available for initiating movement. It is argued that the results support pre-programming of MT with movement initiated when the target's time to arrival at the interception location reaches a criterion value that is matched to the pre-programmed MT. The data supported completely open-loop control when MT was less than between 200 and 240 ms with corrective sub-movements increasingly frequent for movements of longer duration.

Delay of light in an optical bottle resonator with nanoscale radius variation : dispersionless, broadband, and low-loss

It is shown theoretically that an optical bottle resonator with a nanoscale radius variation can perform a multinanosecond long dispersionless delay of light in a nanometer-order bandwidth with minimal losses. Experimentally, a 3 mm long resonator with a 2.8 nm deep semiparabolic radius variation is fabricated from a 19??µm radius silica fiber with a subangstrom precision. In excellent agreement with theory, the resonator exhibits the impedance-matched 2.58 ns (3 bytes) delay of 100 ps pulses with 0.44??dB/ns intrinsic loss. This is a miniature slow light delay line with the record large delay time, record small transmission loss, dispersion, and effective speed of light.

Delay of light in an optical bottle resonator with nanoscale radius variation:dispersionless, broadband, and low-loss

It is shown theoretically that an optical bottle resonator with a nanoscale radius variation can perform a multinanosecond long dispersionless delay of light in a nanometer-order bandwidth with minimal losses. Experimentally, a 3 mm long resonator with a 2.8 nm deep semiparabolic radius variation is fabricated from a 19??µm radius silica fiber with a subangstrom precision. In excellent agreement with theory, the resonator exhibits the impedance-matched 2.58 ns (3 bytes) delay of 100 ps pulses with 0.44??dB/ns intrinsic loss. This is a miniature slow light delay line with the record large delay time, record small transmission loss, dispersion, and effective speed of light.

Interpreting Human Genetic Variation through Genomics and In Vivo Models

Improvements in genomic technology, both in the increased speed and reduced cost of sequencing, have expanded the appreciation of the abundance of human genetic variation. However the sheer amount of variation, as well as the varying type and genomic content of variation, poses a challenge in understanding the clinical consequence of a single mutation. This work uses several methodologies to interpret the observed variation in the human genome, and presents novel strategies for the prediction of allele pathogenicity.

Using the zebrafish model system as an in vivo assay of allele function, we identified a novel driver of Bardet-Biedl Syndrome (BBS) in CEP76. A combination of targeted sequencing of 785 cilia-associated genes in a cohort of BBS patients and subsequent in vivo functional assays recapitulating the human phenotype gave strong evidence for the role of CEP76 mutations in the pathology of an affected family. This portion of the work demonstrated the necessity of functional testing in validating disease-associated mutations, and added to the catalogue of known BBS disease genes.

Further study into the role of copy-number variations (CNVs) in a cohort of BBS patients showed the significant contribution of CNVs to disease pathology. Using high-density array comparative genomic hybridization (aCGH) we were able to identify pathogenic CNVs as small as several hundred bp. Dissection of constituent gene and in vivo experiments investigating epistatic interactions between affected genes allowed for an appreciation of several paradigms by which CNVs can contribute to disease. This study revealed that the contribution of CNVs to disease in BBS patients is much higher than previously expected, and demonstrated the necessity of consideration of CNV contribution in future (and retrospective) investigations of human genetic disease.

Finally, we used a combination of comparative genomics and in vivo complementation assays to identify second-site compensatory modification of pathogenic alleles. These pathogenic alleles, which are found compensated in other species (termed compensated pathogenic deviations [CPDs]), represent a significant fraction (from 3 – 10%) of human disease-associated alleles. In silico pathogenicity prediction algorithms, a valuable method of allele prioritization, often misrepresent these alleles as benign, leading to omission of possibly informative variants in studies of human genetic disease. We created a mathematical model that was able to predict CPDs and putative compensatory sites, and functionally showed in vivo that second-site mutation can mitigate the pathogenicity of disease alleles. Additionally, we made publically available an in silico module for the prediction of CPDs and modifier sites.

These studies have advanced the ability to interpret the pathogenicity of multiple types of human variation, as well as made available tools for others to do so as well.

Seawater carbonate chemistry and sperm swimming speed of the polychaete Galeolaria caespitosa in lab experiment

The rapidity of ocean acidification intensifies selection pressure for resilient phenotypes, particularly during sensitive early life stages. The scope for selection is greater in species with greater within-species variation in responses to changing environments, thus enhancing the potential for adaptation. We investigated among-male variation in sperm swimming responses (percent motility and swimming speeds) of the serpulid polychaete Galeolaria caespitosa to near- (delta pH 0.3) and far-future ocean acidification (delta pH 0.5). Responses of sperm swimming to acidification varied significantly among males and were overall negative. Robust sperm swimming behavior under near-future ocean acidification in some males may ameliorate climate change impacts, if traits associated with robustness are heritable, and thereby enhance the potential for adaptation to far-future conditions. Reduced sperm swimming in the majority of male G. caespitosa may decrease their fertilization success in a high CO2 future ocean. Resultant changes in offspring production could affect recruitment success and population fitness downstream.

Seawater carbonate chemistry and sperm swimming speed, fertilization success of the Australasian sea urchin Heliocidaris erythrogramma in lab experiment

Background: Climate change will lead to intense selection on many organisms, particularly during susceptible early life stages. To date, most studies on the likely biotic effects of climate change have focused on the mean responses of pooled groups of animals. Consequently, the extent to which inter-individual variation mediates different selection responses has not been tested. Investigating this variation is important, since some individuals may be preadapted to future climate scenarios. Methodology/Principal Findings: We examined the effect of CO2-induced pH changes ("ocean acidification") in sperm swimming behaviour on the fertilization success of the Australasian sea urchin Heliocidaris erythrogramma, focusing on the responses of separate individuals and pairs. Acidification significantly decreased the proportion of motile sperm but had no effect on sperm swimming speed. Subsequent fertilization experiments showed strong inter-individual variation in responses to ocean acidification, ranging from a 44% decrease to a 14% increase in fertilization success. This was partly explained by the significant relationship between decreases in percent sperm motility and fertilization success at delta pH = 0.3, but not at delta pH = 0.5. Conclusions and Significance: The effects of ocean acidification on reproductive success varied markedly between individuals. Our results suggest that some individuals will exhibit enhanced fertilization success in acidified oceans, supporting the concept of 'winners' and 'losers' of climate change at an individual level. If these differences are heritable it is likely that ocean acidification will lead to selection against susceptible phenotypes as well as to rapid fixation of alleles that allow reproduction under more acidic conditions. This selection may ameliorate the biotic effects of climate change if taxa have sufficient extant genetic variation upon which selection can act.

Intraspecific individual variation of temperature tolerance associated with oxygen demand in the European sea bass (Dicentrarchus labrax)

The European sea bass (Dicentrarchus labrax) is an economically important fish native to the Mediterranean and Northern Atlantic. Its complex life cycle involves many migrations through temperature gradients that affect the energetic demands of swimming. Previous studies have shown large intraspecific variation in swimming performance and temperature tolerance, which could include deleterious and advantageous traits under the evolutionary pressure of climate change. However, little is known of the underlying determinants of this individual variation. We investigated individual variation in temperature tolerance in 30 sea bass by exposing them to a warm temperature challenge test. The eight most temperature-tolerant and eight most temperature-sensitive fish were then studied further to determine maximal swimming speed (U-CAT), aerobic scope and post-exercise oxygen consumption. Finally, ventricular contractility in each group was determined using isometric muscle preparations. The temperature-tolerant fish showed lower resting oxygen consumption rates, possessed larger hearts and initially recovered from exhaustive exercise faster than the temperature-sensitive fish. Thus, whole-animal temperature tolerance was associated with important performance traits. However, the temperature-tolerant fish also demonstrated poorer maximal swimming capacity (i.e. lower UCAT) than their temperature-sensitive counterparts, which may indicate a trade-off between temperature tolerance and swimming performance. Interestingly, the larger relative ventricular mass of the temperature-tolerant fish did not equate to greater ventricular contractility, suggesting that larger stroke volumes, rather than greater contractile strength, may be associated with thermal tolerance in this species.

Effects of Drive Speed Modulation on Dynamics of Slender Rotating Structures

Slender rotating structures are used in many mechanical systems. These structures can suffer from undesired vibrations that can affect the components and safety of a system. Furthermore, since some these structures can operate in a harsh environment, installation and operation of sensors that are needed for closed-loop and collocated control schemes may not be feasible. Hence, the need for an open-loop non-collocated scheme for control of the dynamics of these structures. In this work, the effects of drive speed modulation on the dynamics of slender rotating structures are studied. Slender rotating structures are a type of mechanical rotating structures, whose length to diameter ratio is large. For these structures, the torsion mode natural frequencies can be low. In particular, for isotropic structures, the first few torsion mode frequencies can be of the same order as the first few bending mode frequencies. These situations can be conducive for energy transfer amongst bending and torsion modes. Scenarios with torsional vibrations experienced by rotating structures with continuous rotor-stator contact occur in many rotating mechanical systems. Drill strings used in the oil and gas industry are an example of rotating structures whose torsional vibrations can be deleterious to the components of the drilling system. As a novel approach to mitigate undesired vibrations, the effects of adding a sinusoidal excitation to the rotation speed of a drill string are studied. A portion of the drill string located within a borewell is considered and this rotating structure has been modeled as an extended Jeffcott rotor and a sinusoidal excitation has been added to the drive speed of the rotor. After constructing a three-degree-of-freedom model to capture lateral and torsional motions, the equations of motions are reduced to a single differential equation governing torsional vibrations during continuous stator contact. An approximate solution has been obtained by making use of the Method of Direct Partition of Motions with the governing torsional equation of motion. The results showed that for a rotor undergoing forward or backward whirling, the addition of sinusoidal excitation to the drive speed can cause an increase in the equivalent torsional stiffness, smooth the discontinuous friction force at contact, and reduce the regions of negative slope in the friction coefficient variation with respect to speed. Experiments with a scaled drill string apparatus have also been conducted and the experimental results show good agreement with the numerical results obtained from the developed models. These findings suggest that the extended Jeffcott rotordynamics model can be useful for studies of rotor dynamics in situations with continuous rotor-stator contact. Furthermore, the results obtained suggest that the drive speed modulation scheme can have value for attenuating drill-string vibrations.

Geographic Variation of Notified Ross River Virus Infections in Queensland, Australia, 1985-1996

The spatial and temporal variations of Ross River virus infections reported in Queensland, Australia, between 1985 and 1996 were studied by using the Geographic Information System. The notified cases of Ross River virus infection came from 489 localities between 1985 and 1988, 805 between 1989 and 1992, and 1,157 between 1993 and 1996 (chi2(df = 2) = 680.9; P < 0.001). There was a marked increase in the number of localities where the cases were reported by 65 percent for the period of 1989-1992 and 137 percent for 1993-1996, compared with that for 1985-1988. The geographic distribution of the notified Ross River virus cases has expanded in Queensland over recent years. As Ross River virus disease has impacted considerably on tourism and industry, as well as on residents of affected areas, more research is required to explore the causes of the geographic expansion of the notified Ross River virus infections.