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Predators impose a strong selective pressure on the behavioural traits of prey species. Group living, or sociability, allows individuals to reduce their own risk of predation through avoidance, dilution, and confusion effects. Another potentially beneficial mechanism is behavioural lateralisation, or "handedness", the asymmetrical expression of cognitive brain functions through a directional bias in visual or motor tasks. In my thesis, I explore the interaction between behavioural lateralisation, sociability, and predation in both natural and captive populations of Trinidadian guppies (Poecilia reticulata). In Chapter Two, I examine the consistency between current behavioural lateralisation methodologies and assess the assumptions behind these methods, including the number of incorporated turn choices and the impact of random chance. In Chapter Three, I present the use of environmental DNA in assessing natural piscine guppy predator communities at six sites across the Northern Range of Trinidad. Using this measure of predation, I assess its viability in predicting differentiation of adaptive anti-predatory behaviours in natural guppies, including sociability, activity, and both visual and motor lateralisation. In Chapter Four, I assess the visual lateralisation of guppies tested either solitarily or in groups in the presence or absence of a live predator, the blue acara (Andinoacara pulcher). Using a repeated measures design, I investigate the repeatability of guppies' visual lateralisation in terms of personality variation across the investigated contexts. In Chapter Five, I assess the visual lateralisation of natural guppies when viewing a social stimulus and their sociability across a gradient of predation risk using nineteen sites in the Northern Range of Trinidad. Overall, my research demonstrates relatively low levels of lateralisation throughout contexts and populations. However, subtle trends in the lateralisation of eye-use when viewing a predatory or social stimulus appear to exist in relation to predation risk, with an apparent social conformity in lateralisation when assessed in groups.

The nuclear industry requires routine monitoring and the characterisation of environments before they can be decommissioned. Part of the characterisation of potentially contaminated assets is done through analysing swabs that are taken by operators and analysed in laboratories to identify chemical, biological and radiological hazards. The use of human operators in potentially hazardous environments has safety, cost and time implications; and this is accompanied by an understanding that human operators have limited reliability in swabbing scenarios. For these reasons, there is a desire to develop robots that can replace human operators in accessing and characterising radioactive facilities. Swabbing is a sample retrieval process which involves the removal of contamination from a surface using a porous substrate (swab). There is a lack of understanding of the cause of uncertainties in the swabbing process and this hinders the applicability and usefulness of swabbing. This project provides an analysis of swabbing which can inform best practice and aid the development of a new generation of swabbing robots. This thesis makes major contributions to our understanding of swabbing, presenting a systematic evaluation of swabbing inputs, as well as providing the first study which measures human performance in swabbing tasks. In addition to this, a feasibility study which focuses on the use of Chrysoidine G as a chemosensor used for the detection of common radionuclides is presented in this thesis. In addition to the contributions from these experiments, the development of equipment and a number of novel methodologies are detailed. The effect of swabbing force, force application area, contaminant mass and the number of swab passes on the pick-up factor of loose contamination are all studied, with these experiments providing a foundation to better understand the role of different swabbing inputs on the swabbing process. It was found that altering swabbing force did affect swab efficacy, with swabbing force causing a total variation of approximately 16% in mean pick-up factor performance; with a 6% minimum and 22% maximum mean performance. Force application area was found to influence pick-up factor to a greater extent, with an approximate 20% range in mean pick-up factors observed. These results also highlight the importance of leading-edge accumulation, with this mechanism greatly impacting overall swabbing efficacy. Human operators are widely thought to be a large source of swabbing uncertainty, and studies have been undertaken to quantify this uncertainty. It was found that swabbing area recreation had a coefficient of variation (C.O.V.) of approximately 18% and swabbing force recreation was subject to far greater variation with a C.O.V. of 61%. These results provide clear confirmation that human performance in swabbing tasks has a low repeatability, and that human operators do contribute significantly to overall swabbing uncertainty. The repeatability achieved with automated robotic systems in these swabbing tasks is far greater than that achieved by the participants in this study, with these results confirming that robotic platforms could be used to reduce uncertainty in swabbing tasks. Further to increasing sample retrieval capability, the development of in situ sample analysis techniques is a crucial step in removing humans from harm in the characterisation of radioactive facilities. A feasibility study for one such in situ characterisation technique was performed. Chrysoidine G (CG) is seen as a promising candidate for colorimetric detection of the abundant fission products, Sr-90 and Cs-137, which are known to be prevalent across many nuclear sites. This sensor's performance in likely conditions for its use is assessed. Ultimately the response of this sensor was found to be incompatible for use on an in situ characterisation robot. The colorimetric response of CG was found to be greatly affected by pH, necessitating careful pH adjustment before sensing could be performed. This thesis contributes towards efforts in the nuclear industry to improve in situ characterisation capability, through providing a greater understanding of sample retrieval and through advancing our knowledge of chemical sensing techniques. It is thought that through performing more characterisation in environments, the safety, costs and time for decommissioning can be improved. Through analysing the performance of human operators in swabbing tasks, it is clear that humans are likely a large source for error in swabbing, and thus the use of automated systems can improve the accuracy of swabbing. This thesis has demonstrated the key variables which are important in determining swabbing repeatability, and this will assist in the development of new swabbing robots.

Introduction: Myopia is a refractive error associated with an increased risk of sight threatening ocular pathology. Its aetiology is heterogenous in nature, with a combination of genetic and environmental factors, such as less time spent outdoors, intensive education and increased near work (Rudnicka et al., 2016; Xiong, Sankaridurg, et al., 2017), shown to play a role in its development and progression (Morgan and Rose, 2019). Animal studies and some clinical observations suggest that relative peripheral hyperopia also promotes the development and progression of myopia (Nathan, 1985; Smith and Hung, 1998; Mutti et al., 2007; Sankaridurg et al., 2011; Santodomingo-Rubido et al., 2016; Chamberlain et al., 2019; Lam et al., 2019). The Northern Ireland Childhood Errors of Refraction 1.0 (NICER 1.0) Study, an epidemiological study of the prevalence of refractive error in white UK school children (Lisa O'Donoghue et al., 2010), commenced in 2006/2008. Since 2008 electronic devices have dramatically risen in popularity among UK children (Ofcom, 2011, 2020), which some researchers have implicated in the global surge in childhood myopia prevalence (Holden et al., 2016; Lanca and Saw, 2020). Aims: The overall aim of this thesis was to re-evaluate the prevalence of refractive error among white UK school children to determine trends in the prevalence and age of onset of myopia over the last decade. The present work also evaluated the relationship between relative peripheral refraction and changes in central refraction and axial length over one year in children. Methods: The present study employed identical sampling methodology and cycloplegic examination procedures to The NICER 1.0 Study (Lisa O'Donoghue et al., 2010). Comparisons were drawn between contemporary refractive data and data from age- and ethnicity-matched children in 2006/2008. Baseline measures of spherical equivalent refraction (SER) in the central and peripheral horizontal retina and axial length were recorded, and measurements were repeated after 12-months on a sub-group of children. Results and conclusions: This thesis established that the prevalence of childhood myopia has remained relatively unchanged in the UK over the last 12 years. There is no evidence that the age of onset of myopia has decreased in this time. The present work found that a hyperopic relative peripheral refraction in the nasal retina is a statistically significant predictor for accelerated eye growth in teenage myopes. Eye care clinicians should consider myopia control options that reduce relative peripheral hyperopia in cases of established myopes to slow further axial elongation.

Since the adaptation of medical imaging as a standard clinical diagnostic tool, an ever-growing number of images has been taken. Radiomics took the big-data approach to extract quantitative features from medical images invisible to the naked eye to support clinical decision making, known as biomarkers. Over 440 radiomics features are available including size and shape based features, features derived from intensity histogram and texture features that describes the relationship between voxels. To date, there are no widely accepted biomarkers like tumour, nodes and metastases (TNM) staging in oncology due to concerns on the robustness of features. This thesis presents a detailed robustness study of 43 commonly used radiomics mainly 3-dimensional texture features extracted from the CT part of PET/CT images of patients diagnosed with non-small cell lung cancer (NSCLC) in two aspects: repeatability and reproducibility. Repeatability of features were studied using an open source dataset with 31 sets of repeat scans taken 15 minutes apart on quantisation parameters including quantisation method; levels of quantisation and the use of an intensity threshold. Reproducibility of features were studied using a locally acquired dataset of 50 scans on acquisition parameters including scanner model/make and the embedded reconstruction method; variation in tumour delineation and the afore mentioned quantisation parameters. The robust features were validated using the two independent dataset before highly correlated features were identified to reduce type one error caused by over-fitting. The robust texture features were applied to clinical applications from patient stratification to tumour delineation. Features were extremely sensitive to changes in the quantisation parameters. Stability of features were improved by quantising with an intensity threshold and at high levels of quantisation such as 128. The group uniform quantiser (GUQ) produced the most stable results among the four quantisers tested. Using the same quantisation parameters, radiomics features were highly repeatable, 31/43 features had a Spearman's rank correlation (rs) greater than 0.9 across all quantisers. Features were highly reproducible to scanner make/model and variation in tumour delineation under the same quantisation parameters. Features were not reproducible to different quantisation methods, using features quantised with GUQ at 128 intensity levels as a reference, 32 features correlated (rs > 0.8) when quantised using other quantisers with a threshold, 26 features correlated when quantised using other quantisers without a threshold. 7 features correlated with tumour volume (rs > 0.8). All features expect GLSZM GLN and ZSN features were successfully validated. The robust features were able to stratify patients and improve delineation accuracy in clinical applications. Robustness and validation of 43 commonly used radiomics features were investigated from CT scans of patients with NSCLC. Features were extremely sensitive to quantisation parameters. Features were repeatable, reproducible and validated successfully using the same quantisation parameters. Based on the results of this study, it is suggested to quantise using GUQ at 128 intensity levels with a threshold.

Assessment and diagnosis of dry eye disease (DED) is a challenging task. The conventional ways of diagnosing DED are problematic due to their invasiveness, poor test reliability and significant test duration. Previously, ocular surface thermography has been shown to be able to detect early inflammation and dry eye. However, its diagnostic ability and ocular temperature metrics that can best diagnose DED are not clear. The objectives of this thesis were manyfold. First, the prevalence of dry eye in Singapore population was investigated as a helpful basis for the rest of the project. A cross-sectional dry eye survey was carried out using McMonnies dry eye questionnaire. Members of the public were interviewed at 46 (out of 62) selected mass rapid transit stations in Singapore and its vicinity. 1004 questionnaires were collected from participants aged 15 - 83 years and various ethnicity. Prevalence of symptomatic dry eye (SDE) was found to be 12.3% (about 0.5 million Singaporeans). Risk factors associated with SDE were found to be age, gender, ethnicity, hypertension and contact lens wear. Smoking was not associated with SDE.The main part of this thesis sought to evaluate the efficacy of ocular thermography in diagnosing DED. A new infrared detector (NEC Thermo Tracer TH 9260) with relatively high resolution was used. Inter-image, inter-occasion and inter-examiner repeatability was first studied on 21 healthy and 15 DED subjects. Ocular surface marking and ocular surface temperature (OST) acquisition was performed with a novel 'diamond' method using a custom-designed OST analysis V2 software. Ten out of the twelve tested OST indices were shown to be highly repeatable for three studied time points: 0 s, 5 s and 10 s. They were temperatures of the geometric center of the cornea (GCC), mean temperature (MOST) of the region of interest (ROI), maximum (MaxT) and minimum (MinT) temperatures of the ROI, extreme temporal (T1) and nasal conjunctiva (T4), mid temporal (CT) and nasal conjunctiva (CN) and temporal (LT) and nasal limbal (LN). Another 62 DED and 63 age- and sex-matched controls were then recruited and the ten static and dynamic OST indices were evaluated. Static measures were study of absolute OST at t = 0 s, 5 s and 10 s after eye opening. Dynamic measures were study of mean change and net change in OST over 10 s of sustained eye opening. Static measures on eight OST indices (GCC, MOST, MinT, MaxT, T4, CT, LT and LN) at t = 0 s, 5 s and 10 s and dynamic measures on two OST indices (T4 at 3 s onward and MaxT at 5 s onward) were found to be valuable in detecting DED. The temperature metrics (static and dynamic) were identified for further investigation. Thereafter, the diagnostic ability of the temperature metrics were evaluated singly and as combinations in terms of their area under the curve (AUC), Youden index and discrimination power. Receiver operating characteristic curves were plotted for each metric. Best detectors for DED were found to be the T4 temperature metrics: particularly T4-5 and T4-10 (i.e. absolute temperature of the extreme nasal conjunctiva at 5 s and 10 s). Values of T4-5 of < 34.8 °C were found to give sensitivity and specificity of 87.1% and 50.8% respectively and values of T4-10 of < 34.6 °C were found to give sensitivity and specificity of 77.6% and 61.9% respectively. The two temperature metrics had highest Youden index as compared to other metrics and were shown to be useful in view of AUC > 70% but of limited performance in view of their discrimination power. Nevertheless, measuring T4-5 and T4-10 was found to be comparable to other conventional methods for DED. T4-10 was better than T4-5 in view of higher AUC and Youden index. None of the tested dynamic metrics was good detector for DED and combining metrics were not able to increase the diagnostic ability. The last part of this thesis was to validate the effectiveness of some common conventional dry eye tests, to study their correlation with T4 temperature metrics and derive the best composite/combined tests for DED. Sixty two DED patients and 82 controls were studied. The conventional clinical tests examined were: symptom evaluation using McMonnies dry eye questionnaire (Mscore) and symptom count (Scount), fluorescein break-up time (FBUT) and corneal epithelial staining (CES), non-invasive break-up time (NIBUT) and tear meniscus height (TMH). Mscore and Scount was the best detectors for DED, followed by FBUT and CES. Discordance between signs and symptoms for DED was further confirmed. Combining CES with T4-10 (series) can be future objective tests for DED. Further research is warranted, particularly to (1) validate the ability of T4-10 as a stand-alone test for DED and (2) work out an algorithm and validate the diagnostic ability of the recommended combined test (CES and T4-10) using newly recruited subjects.

The human foot is a biomechanical marvel which forms the distal link in the lower limb kinematic chain. With its small polyarticular construct and flexibility, it supports the body and provides balance during walking. The first metatarsophalangeal joint (MTPJ) is a vital joint in the forefoot for normal load transmission and energy efficient locomotion. Albeit a lot in literature about this joint, paucity still exists in the biomechanical aspects. Also, there is a speculation in the biomechanical world that the time integral component of pressure recorded from the plantar pressure measuring devices maybe representative of the shear force recorded from force platforms. The aim of the current study was to quantify the kinematics of the first MTPJ in three dimensions and the pedobarographic data under the first MTPJ during each sub-phase of stance in the gait cycle of normal subjects and to assess the correlation between the shear force from the force plate of the motion capture system with the variables from the barefoot plantar pressure measuring device. Similar quantification will be undertaken for the patients with isolated hallux rigidus. After obtaining ethical approval, 40 normal subjects (80 feet) and 6 patients with varying grades of hallux rigidus were recruited for the study. The equipment used to collect data included the Vicon® motion analysis system, AMTI® force plate and the emed® plantar pressure measuring device. Various checks were performed to establish the reliability of the system setup. Four trials from each foot were taken. Of the 320 total trials from the normal subjects, the trial numbers varied for specific tasks as some trials which were suitable for testing one objective might not be suitable for testing the other. One of the patients’ data could not be used as the data quality was below par due to issues with marker tracking. The correlation between the shear force from the force plate and the anthropometric measurements/parameters from the plantar pressure measuring device was performed using the statistical regression model. The Vicon® data of the whole stance phase revealed that the first MTPJ’s sagittal plane motion ranged from 9° of plantarflexion to 53° of dorsiflexion. In the coronal plane, the maximum pronation was 34° and supination was 31°. In the transverse plane, the maximum varus was 11° and the valgus was 24°. There were two dorsiflexion peaks; one at the Initial contact and the other at Pre-swing. The joint moved from supination to pronation and varus to valgus during the progression of stance phase from Initial contact to Pre-swing. Considering the emed®-m, there were four basic parameters namely the force, area, peak pressure and maximum mean pressure from which the other parameters were derived. Only the basic parameters accounted for the sub-phases of stance and it came to light that the force under the first MTPJ was maximum in the terminal stance (22.1%). For the whole stance phase, the first MTPJ contributed about 11% of the contact area, 14.5% of the mean area, 24% of the maximum force, 56% of the peak pressure, 63% of maximum mean pressure, 44% of Pressure-time integral, 14% of Force-time integral and 14% of mean force. The correlation equation with reasonable number of dependent variables obtained by the statistical regression model could account for only 46% of the shear force. Among the paired correlation equations with single dependent variable, the one with the mean force was the best and even this could only account for 31.1% of the shear force. Albeit 3 patients were having similar radiological grading of the pathology and 2 others falling into another grade, their objective data were diverse and couldn’t be grouped together. The normal kinematics of the first MTPJ and the pedobarographic data under the first MTPJ were quantified during each subphase of stance. Attempt to use one system alone instead of two to calculate the shear force did not provide satisfactory results. The patients’ data questions the use of radiology alone in deciding the management plan which is a common scenario in the current clinical setting.

Many of those artefacts with which we are so familiar – including, for example, works of music, photographs, novels, essays, films, television adverts, and graphic designs – share a common ontological nature. I argue in this thesis that they are all repeatable, and set out to provide an ontological account of these entities that explains the phenomenon of repeatability. In a fruitful meeting of aesthetics and metaphysics, a great deal has been written recently on the ontological nature of musical works. More encompassing enquiries have sought to understand the ontology of artworks in general. I will be responding to and engaging with this body of literature insofar as it also offers accounts of the entities I describe as repeatable. However, my approach gives metaphysical concerns and the phenomenon of repeatability primacy over aesthetic concerns.Here I argue that repeatable artefacts fall into the ontological category of kinds. I develop an account of repeatable artefacts as kinds that has two key components. Firstly, on my view kinds are physical rather than abstract. Secondly, I argue that repeatable artefacts, as kinds, have essences that are purely relational and historical. The thesis begins with a discussion of method. The methodological issue has grown in prominence in recent years, as theorists have sought some higher level arbitration on the expanding number of theories and approaches being offered in response to ontological puzzles. Drawing on the work of Amie Thomasson, I defend a methodology according to which we should develop an ontological account using careful conceptual analysis that assesses our intuitions about the application of referring terms. This commitment to conceptual analysis is then defended from misunderstandings and objections. I apply this method in giving an ontological explanation for the phenomenon of repeatability. I argue that repeatable artefacts are kinds. Kinds are strongly individuated by their essences, which are the conditions that must be satisfied for the kind to be instanced. I then develop an account of kinds as physical multiply located entities, that exist when and where they have instances. This stands in contrast to the prevailing view according to which kinds are abstract. I then set out to give an account of the essences of paradigmatic repeatable artefacts. I argue that this can be done if we are willing to reject the default view according to which essences are at least partly structural, and replace it with an account of purely relational and historical essences. The essences of many paradigmatic repeatable artefacts, I claim, involve causal historical processes of copying.

Clinicians are becoming increasingly aware of the effect of various pathologies on the characteristics of saccadic eye movements. As such, an efficient and non-invasive means of measuring eye-movement in a clinical environment is of interest to many. The aim of this thesis is to investigate the clinical application of a non-invasive eye movement recording technique as a part of a clinical examination. Eye movements were measured using an IRIS 6500 infrared limbal eye tracker, which we customized for the direct recording of oblique eye movements as well as horizontal and vertical. Firstly, the eye-tracker itself was assessed. Visually normal observers made saccadic eye movements to a 10' stimulus in eight directions of gaze. Primary (ANOVA) and secondary analyses (mean error less than 5%) resulted in acceptance that averaging four measurements would give a representative measurement of saccadic latency, peak velocity, amplitude and duration. Test-retest results indicated that this technique gives statistically (± 1.96*STDEVDifference) repeatable responses. Several factors that could potentially influence clinically based measures of eye-movements were examined. These included, the effect of ageing, viewing distances, dioptric blur and cataract. The results showed that saccadic latency and duration are significantly (p < 0.05) longer in older (60-89 years) observers compared to younger (20-39 years). Peak velocity and amplitude were not significantly affected by the age of the observer. All saccadic parameters (SP) were significantly affected by direction (Chapter 5). The compact nature of this eye movement methodology is obtainable since there is no significant effect on viewing distance (300 cm vs. 49 cm) (Chapter 6). There is also no significant effect of dioptric blur (up to +LOODS) on any of the four SP. In contrast, a higher level of defocus (+3.O ODS) has a larger probability of interfering with the measurements of peak velocity and duration (Chapter 7). Saccadic eye-movements were also recorded whilst normally sighted subjects wore cataract simulation goggles. The results suggested that the presence of dense cataract introduces significant increases in saccadic latencies and durations. No effect was found on the peak velocities and amplitudes. The effect of amblyopia on SP was also investigated in order to examine if this methodology is able to detect normal from abnormal responses (i.e. increased saccadic latencies). This set of data (Chapter9 ) showed that using IRIS 6500, longer than normal latencies may be recorded from the amblyopic eye but no consistent effect was found for the other SP (peak velocity, amplitude, duration). Overall, the results of this thesis demonstrate that the IRIS 6500 eye-tracker has many desirable elements (it is non-invasive; comfortable for the observers and gives repeatable and precise results in an acceptable time) that would potentially make it a useful clinical tool as a part of a routine examination.

Abstract: This work was concerned with the construction and testing of anion exchange membrane water electrolysis (AEMWE) cells to study the effect of electrolyte feed method. Each cell used a catalyst-coated membrane (CCM) fabricated in-house by inkjet printing catalyst layers onto Aemion+ membranes using a Fujifilm Dimatix DMP-2850 printer. Inkjet printing allowed for precise control in the deposition of catalyst layer materials, but necessitated that printable inks containing catalyst nanopowder (platinum supported on carbon and iridium oxide) and ionomer (Aemion+ AP2-HNN5-00-X) be formulated. To develop ink formulae, a procedure was followed that began by selecting a base of propylene glycol and isopropanol with a dynamic viscosity and surface tension close to that required for printing. The ionomer solution was then added, and the mixture was re-characterized to ensure it still had the required rheology. Any necessary adjustments were made and the catalyst powder was finally added. This process resulted in inks that were successfully printed without the need to produce multiple complete inks, reducing the waste of expensive catalyst and ionomer. Initial in-situ AEMWE cell tests were run to ensure that cell performance was repeatable. Five cells were tested, achieving this goal as the last four all performed similarly. Cell construction was altered between some of these cells, most notably the type of Aemion+ membrane was changed, i.e., increasing the thickness from 50 to 75 µm and altering the reinforcement type, the cathode porous transport layer (PTL) was changed from carbon to nickel, and the bipolar plate material was changed from titanium to nickel 400 alloy. These changes slightly improved cell performance by reducing the ohmic losses caused by resistance within the cells. Cells were tested by feeding 1 M potassium hydroxide (KOH) and compared to literature. The performance of the cells was similar to state of the art CCM cells using Aemion+, achieving a current density of 900 mA/cm2 at 2 V. Once good, repeatable cell performance was achieved, the same cell construction was used for the study on electrolyte feed method. Four cells were used to study the effect of feeding aqueous 1 M potassium hydroxide solution to both electrodes, just the cathode, and just the anode was done for the first time in AEMWE cells. A reference electrode was also connected to the cell membrane using a strip of membrane passed out the side of the cell. Challenges were encountered with the experimental setup that resulted in some inconsistent measurements from the reference electrode, caused by cell operation. Despite this, it did allow for separate anode and cathode overpotentials to be measured. The cells tested in this work performed similarly with two-electrode and anode-only feed, resulting in 900 mA/cm2 at 2 V, whereas cathode-only feed achieve the lower 550 mA/cm2 at 2 V. Six hour constant-current stability tests also resulted in increased degradation for cathode-only feed. The change was due to poor anode performance, as the separate electrode potentials obtained using the reference electrode showed an increase in anode overpotential in this feed configuration. The lack of electrolyte in the anode catalyst layer possibly resulted in increased ionic resistance as the electrolyte normally supports this, or a loss of reactant hydroxide that would normally be supplied by the electrolyte.

Background Texel sheep are known for their double-muscling phenotype and extraordinary meat production (Miar et al., 2014). Satellite cells are essential for this desired muscle growth. MicroRNAs can silence target genes by binding to the target messenger RNA (mRNA) (Horak et alk., 2016). Antagomirs are miRNA inhibitors and are used for loss of function studies. MiR-22-3p is known for inhibiting skeletal muscle growth and directly targets HDAC4, TGFBR1, PAX7 mRNA expression. Computed Tomography (CT) imaging is now growing in popularity in the animal science field to record changes in muscle characteristics. Materials and Methods Texel x Suffolk lambs (n=4) were given an antagomiR-22-3p intramuscular injection for 3 consecutive days in the longissimus muscle compared to sham. The lambs were CT scanned pre-treatment and then for 4 weeks. Samples were obtained from LM and used to isolate cells, measure miRNA and mRNA expression, and proximate composition. A standardized CT image analysis protocol was used to determine the transverse sectional area and mean density (Hounsfield units, HU) for the antagomiR (left) and sham (right) sides of the LM. Results AntagomiR-22-3p treatment down-regulated miR-22-3p compared to sham. HDAC4 and TGFBR1, both mRNA targets of miR-22-3p, were up-regulated compared to the sham. PAX7 did not differ in this study between sham and trt sides (p=0.9094). For the CT imaging, the ribeye area (REA) size was not found to be statistically significant between miR and sham. In the CT measurements for intra-observer repeatability, there were no Coefficient of Variation (CV) values outside the “good” range. For inter-observer repeatability, 80% of the observers did not statistically differ from each other for the left area, 73.34% for the left corrected density, 66.67% for the right area, and 73.34% for the right corrected density measurement. Conclusions AntagomiR-22-3p seemed to silence miR-22-3p, and the effect appeared to be the greatest at two weeks instead of four weeks. Muscle growth was not shown over time using the CT images, but the methodology is deemed repeatable.

Abstract: Concussions are one of the most common injuries in sport and can result in detrimental long-term health effects. To reduce the severity of concussion and head injury, protective headgear has been implemented and is continually evaluated to minimize head kinematics after impact. For investigation of head dynamic behavior in impact and to conduct helmet certification testing, surrogate anthropomorphic test device head and neck models are used. Although there is evidence of head-neck-body coupling in impacts, most testing methods use isolated surrogate head-neck assemblies that ignore or provide no justification for the simulated torso mass on resultant head behavior in impacts. The objective of this thesis was to quantify the head kinematic and upper neck kinetic differences in head impacts using an isolated head-neck system fixed to a translating linear rail and a head-neck assembly fixed to a dummy torso. A secondary objective was to overview the repeatability of a novel surrogate neck model when fixed to a translating linear rail. One Hybrid III neck and three copies of a novel surrogate neck (Phase III neck) were fixed to a Hybrid III headform fit with a NOCSAE certified football helmet and subjected to two sets of impacts; 1) fixed to a translating platform on a linear rail and, 2) fixed to a Hybrid III dummy torso. Direct head impacts were conducted with a pendulum impactor at 4.0 m/s to frontal, lateral, and front boss locations. The impact metrics investigated were head center of gravity linear acceleration, angular acceleration, angular velocity, and upper neck impact and peak force, and upper neck impact and peak moment. The Phase III neck showed acceptable within-neck and between-neck repeatability based on the coefficient of variation of repeatability, coefficient of variation of reproducibility, and normalized absolute difference values. Normalized absolute difference values of >20% between the surrogate necks and the Hybrid III neck and significantly different ANOVA results indicate the surrogate neck and the Hybrid III neck produce differing head kinematics during impact. Significant differences were found in almost all impact metrics between the system with the head-neck assembly fixed to a translating linear rail (head-neck-rail system) and a head-neck assembly fixed to a Hybrid III dummy torso (head-neck-torso system). An independent samples, two-tailed t-test, a Welch t-test, or a Mann-Whitney U Test were used to analyze the seven impact metrics from impacts with four surrogate necks. Out of a combination of 28 impact metric comparisons, 75% (21 of 28), 71.4% (20 of 28), and 50% (14 of 28) of impact metrics were higher for the head-neck-torso system compared to the head-neck-rail system in frontal, lateral, and front boss impact locations, respectively. Linear acceleration was the only impact metric that was higher for the head-neck-torso system for all four surrogate necks in all three impact locations. The results from this investigation suggest that torso mass influences the head center of gravity kinematics and the upper neck kinetics. However, it remains unknown which approach is the better approximation of human head dynamics from a head impact in sport, and further investigation is needed to determine which method is more appropriate for use in helmet testing to ensure the most accurate methods are used to increase player safety. Additionally, significant differences between the head kinematics and upper neck kinetics from the Hybrid III neck and the Phase III neck emphasizes the demand for the continued development and biofidelity assessment of surrogate neck models such as the Phase III neck to compare against the Hybrid III neck, to ultimately assist researchers in improving injury assessment effectiveness.

Optical spectroscopy technology has evolved significantly, from its use in research to detectnew materials to its use in the medical field to diagnose diseases. Applications of this technology have been used in wearables that provide insights to promote health and wellness. Rockley Photonics has prototyped a novel wearable via a miniaturized laser system, and the characterization of the laser output power is important for algorithm development. The functional data of interest includes repeated measurements across multiple laser systems operating at various current and temperature ranges. The ability to develop a repeatable and reliable test system is crucial, and thus this paper aims to apply statistical methods to propose a framework in developing models for power prediction. Prototype laser systems (N=5) were tested using a standard procedure and laser output power was characterized to understand significant test factors. Preliminary findings suggest that operator and repeated measurement factors are not significant to the output power and that models can be developed on an individual laser channel bases using an ordinary least squares (OLS) model with third order current effects. The application of using the same base model for individual lasers on each tested device is important for continued development of algorithms to be used to detect various biomarkers in the health sensing space.

Parkinson's disease (PD) is a progressive neurodegenerative disorder affecting both motor and non-motor neural circuits. Common frontline treatment includes dopamine agonists, but long-term levodopa use can cause dyskinesias and lower quality of life. Deep brain stimulation (DBS) is a second-line therapy to treat motor symptoms caused by movement disorders. Overall, the project aimed to better understand how DBS affects brain networks to improve patient outcomes. The repeatability of resting state functional magnetic resonance imaging (rs-fMRI) data was evaluated in patients with DBS and stimulation-induced longitudinal and immediate changes in brain activity and connectivity were related to symptom improvement. It was hypothesized that functional connectivity (FC) and variability would decrease with sub-thalamic nucleus (STN) or globus pallidus (GPi) DBS over time, and that these changes would be associated with symptom improvement. The two oldest patients with the highest MDS-UPDRS raw scores exhibited superior repeatability, while those with the worst MDS-UPDRS raw scores displayed lower repeatability. The Wilcoxon sign rank test's rejection of the null hypothesis suggested challenges in achieving group-level repeatability due to motion artifacts. Adjusting degrees of freedom may mitigate this issue. The study found a decrease in connectivity within thalamic regions, supplementary motor area and cerebellum Crus I and Crus II from pre-op to post-op, indicating neuroplastic changes in the brain. The variability metrics examined the brain's network adaptability, with an overall decrease in variability in the post-op DBS off and on conditions.

Abstract: Individual variation provides the material for natural selection to act upon, influencing ecological and evolutionary processes. Much phenotypic variation in traits, such as behaviour and life-history, have a moderate to high heritable component, suggesting that these traits may have adaptive potential and are genetically influenced. Yet, investigating the genetic basis of complex traits remains limited to few natural systems – partly due to the difficulty of sampling phenotypes in the wild, a lack of existing genomic resources, and detailed pedigree information – and remains a great challenge in biology today. Advances in DNA sequencing technologies now permit investigations into the evolutionary potential of traits as well as the genetic architecture underlying phenotypic variation in the wild. In this dissertation, I examine the genetic basis of maternal performance traits in free-ranging grey seals (Halichoerus grypus), a long-lived, iteroparous species that has rebounded following a long history of overexploitation. First, I performed a literature review and meta-analysis to examine trends in analytical molecular approaches used to elucidate the genetic basis of animal behaviour. Analyzing nearly 150 studies focused on candidate gene, quantitative trait locus mapping, and genome-wide association analyses, I discovered evidence of limited taxonomic breadth in the literature. I highlighted commonly studied candidate genes and behaviours, and further reported global genetic effect sizes for each approach undertaken. Second, I determined the existence of an animal personality signal along the shy-bold continuum in the Sable Island National Park Preserve (Nova Scotia, Canada) population of female grey seals. Using behavioural data collected over a nine-year period (2008-2016), I showed that boldness is highly repeatable both between and within years. Boldness was influenced by maternal age, such that younger females were generally less bold than older, more experienced females providing some support for the life-history trade-off hypothesis. Seal pups produced by bolder females were on average ~2 kg heavier than pups of shy females. Third, I used a candidate gene approach to investigate relationships between genetic variants and repeated measures of boldness, offspring weaning mass, and lactation duration in grey seals. I isolated and re-sequenced five candidate genes commonly screened in primates, rodents, and passerines. Here, I found genetic effects of the serotonin transporter (SERT) and dopamine receptor D4 (DRD4) genes on boldness and offspring weaning mass. Genotypes explained 6.52-13.66% of total trait variation. Lastly, using a reduced representation DNA sequencing method, I obtained genome-wide genotypic data for over 450 female grey seals and determined that eight maternal traits, representing morphological, life-history, and behavioural traits, had low to moderate heritability (h2 = 0.08-0.38). Genome-wide association analyses did not reveal any loci that were significantly associated with the traits examined, suggesting these traits are polygenic. Altogether, this thesis integrated molecular genetic methodologies and statistical approaches with a longitudinal field program, and presented support for the adaptive potential of fitness-related traits in Sable Island grey seals. Results further provided insights into factors and mechanisms underlying maternal performance variation in this ecologically important marine predator. Though challenges exist in investigating the genetic basis of quantitative traits, such analyses give insight into the evolutionary dynamics and capacity for adaptation in natural populations, especially relevant as biodiversity is exposed to novel selection pressures and changing environmental conditions.

Abstract: Head impacts, both concussive and sub-concussive, are common in sports and can lead to adverse side effects. Since head kinematics are thought to correlate with brain injury, the implementation of protective headgear aimed to mitigate kinematics of the head during impacts. While fatal brain injuries have been reduced, concussions and other long-term effects of repetitive head impacts are still prevalent in football players at all levels. Physical surrogate models of the human head and neck are often used to assess impact severity in sports and infer the risk of brain injury, and in helmet certifications to explore the efficacy of helmets. The surrogate models can be instrumented with accelerometers to measure resultant head kinematics. Since the neck is thought to partially govern head kinematics during impact, the surrogate necks must demonstrate several performance characteristics to produce accurate results. Commercially available necks have acceptable repeatability and reproducibility, but they were not developed for the direct, multiplane loading in sports. As such, a novel prototype surrogate neck was developed for omni-directional direct head impacts. The objective of this work was to assess the repeatability and reproducibility of the neck. Three copies of the prototype surrogate neck and one Hybrid III neck were attached to the same Hybrid III head and repeatedly impacted at 3.5 m/s using a pendulum impactor. Both the helmeted and the unhelmeted head were impacted at the front and the front boss locations. The within-neck coefficient of variation (CVW) of the prototype surrogate neck kinematics for all impact conditions was 10% or less, which satisfies standard requirements for surrogates and is comparable to work on several standardized surrogate models. While differences between the three prototype surrogate necks were generally statistically significant, the normalized absolute differences between the neck copies were usually less than 10% and less than 20% in all cases except one. Most head and neck certifications for current standardized models provide corridors that allow a range of ±10% on mean peak kinematics to be considered within specification - the normalized absolute differences of the prototype surrogate neck kinematics fall within that range. Further, the normalized absolute differences for other neck models were similar to what was calculated for the prototype surrogate neck. The reproducibility coefficient of variation (CVB) values for the prototype surrogate necks were less than 15% for all kinematics and usually 10% or less, which is considered acceptable and is comparable to the reproducibility of commercially available surrogate models. The prototype surrogate neck had CVW values equivalent to the Hybrid III, but definitive conclusions cannot be made as to whether the kinematics differ. The Hybrid III kinematics were significantly different from the prototype surrogate neck kinematics for unprotected impacts, and the normalized absolute differences were greater than the differences calculated between the three copies of the prototype surrogate neck. In contrast, the helmeted impacts resulted in kinematics that were less significantly different between the Hybrid III and the prototype surrogate neck, with the normalized absolute differences commensurate in magnitude for the Hybrid III comparison and the prototype surrogate neck reproducibility assessment. However, the Hybrid III neck almost always had kinematics consistently greater than or less than all three of the prototype surrogate necks. Thus, the signs on the kinematics allow observation of actual differences between necks. In summary, the prototype surrogate neck fit to a Hybrid III head and subject to multi-directional direct head impacts resulted in repeatable and reproducible kinematics. Although more testing is needed to quantify differences between the prototype surrogate neck and the Hybrid III, the prototype surrogate neck may be an effective tool for sports impact assessments.

Background: Ocular surface characteristics in children have not been as well investigated as in adults. Children’s digital device usage is rapidly increasing, and smartphones are the most commonly used device. The ocular surface impacts are unknown in children. In adults, use of digital devices induces ocular symptoms, adversely impacts blinking, and disrupts ocular surface homeostasis. Although blinking is integral to a healthy ocular surface, this is yet to be characterised in children, including the effects of digital devices. This thesis aims to characterise the ocular surface of children including blinking and to examine the impact of smartphone use on ocular surface homeostasis in children. Methods: The literature on ocular surface (symptoms, clinical indices, tear film function, blinking) of healthy children was reviewed and a meta-analysis of tear film stability and tear secretion was conducted. Cross-sectional studies of healthy school-aged children were conducted to examine the utility of commonly used adult-validated dry eye symptom questionnaires (SANDE, OSDI, NRS, OCI, DEQ-5, IOSS), and to characterise ocular surface clinical indices. This included blinking which was measured in situ using a novel eye tracking headset (Pupil Labs GmbH, Germany). The impact of one hour smartphone gaming on the ocular surface (including symptoms and blink parameters) of this paediatric population was examined with an intervention study. Blinking was also examined in situ under different conditions and tasks (reading from hard copy and on digital devices, conversation, walking) using the eye tracking headset in healthy adults. Repeatability of blink measurements (blink rate and interblink interval) in adults using the eye tracking headset was determined. Results: Ocular symptoms, tear film function and blinking were sparsely reported in children. The pooled mean by tear stability measurement methods in the meta-analysis were higher than previously reported in healthy adults while the pooled mean for tear secretion by methods were within the expected normal range for adults. Six existing dry eye questionnaires could be successfully used in paediatric eye care, and their repeatability was mostly comparable to that reported previously in adults. More time and assistance were at times required for younger children and specific terms such as ‘gritty’ and ‘foreign body sensation’ were not always well understood by younger children. The DEQ-5 and IOSS are recommended for use in younger age children. Blinking was associated with greater tear volume and worse meibomian gland expressibility but not digital device use, age, sex, or symptoms in children. One hour smartphone gaming led to increased symptoms of dryness, discomfort, and tiredness but did not impact tear film function. Blinking was rapidly reduced by a third within the first minute of gaming and this effect remained unchanged throughout one hour of gaming (p

This research examined the effects of acclimation to lowered salinity, elevated temperature, and hypoxia on aerobic metabolism of the Gulf killifish, Fundulus grandis, a common estuarine resident of the Gulf of Mexico. Standard metabolic rate (SMR), maximum metabolic rate (MMR), absolute aerobic scope (AAS), and critical oxygen tension (Pcrit) were each influenced by one or more acclimation treatments. Assessing the consistency of these traits measured in the same individuals over time, all were found to be significantly repeatable with no indication that the repeatability of any traits was affected by acclimation conditions. Significant correlations were found between SMR and Pcrit (positively correlated), between SMR and AAS (negatively correlated), between MMR and AAS (positive), and between AAS and Pcrit (negative). This study, therefore, documents the effects of acclimation on these traits, their repeatability, and correlations among them. It further suggests that repeatability of these traits is not context dependent.

Females can vary in their mate choice decisions and this variability can play a key role in evolution by sexual selection. Variability in female preferences can affect the intensity and direction of selection on male sexual traits, as well as explain variation in male reproductive success. I looked at how consistency of female preference can vary for a male sexual trait, song length, and then examined context-dependent situations that may contribute to variation in female preferences. In Chapter 2, I assessed repeatability – a measure of among-individual variation – in preference for male song length in female American goldfinches (Spinus tristis). I found no repeatability in preference for song length but did find an overall preference for shorter songs. I suggest that context, including the social environment, may be important in altering the expression of female preferences. In Chapter 3, I assessed how the choices of other females influence female preference. Mate choice copying, in which female preference for a male increases if he has been observed with other females, has been observed in several non-monogamous birds. However, it is unclear whether mate choice copying occurs in socially monogamous species where there are direct benefits from choosing an unmated male. I found evidence for mate choice copying and suggest that copying occurs when choosing extrapair mates. In Chapter 4, I examine how social relationships among females influence copying. A female may be more likely to copy another female if they are familiar with one another due to shared environments and experiences. I found that females are more likely to copy familiar rather than unfamiliar females, which has not been shown in this context. The latter two chapters show that social context is a source of variation that can cause a female to alter her preferences. This suggests an important potential role of female-female social relationships on male reproductive success and the evolution of male characteristics.

Pavement macrotexture has been shown to influence a range of safety and comfort issues including wet weather friction, splash and spray, ambient and in-vehicle noise, tire wear, and rolling resistance. While devices and general guidance exist to measure macrotexture, the wide-scale collection and use of macrotexture is neither mandated nor is it typically employed in the United States. This work seeks to improve upon the methods used to calibrate, collect, pre-process, and distill macrotexture data into useful information that can be utilized by pavement managers. This is accomplished by 1. developing a methodology to evaluate and compare candidate data collection devices; 2. plans and procedures to evaluate the accuracy of high-speed network data collection devices with reference surfaces and measurements; 3. the development of a method to remove erroneous data from emerging 3-D macrotexture sensors; 4. development of a model to describe the change in macrotexture as a function of traffic; 5.finally, distillation of the final collected pavement surface profiles into parameters for the prediction of important pavement surface properties aforementioned. Various high-speed macrotexture measurement devices were shown to have good repeatability (between 0.06 to 0.09mm MPD) and interchangeability of single-spot laser dfevices was demonstrated via a limits of agreement analysis. The operational factors of speed and acceleration were shown to affect the resulting MPD of several devices and guidelines are given for vehicle speed and sensor exposure settings. Devices with single spot and line lasers were shown to reproduce reference waveforms on manufactured surfaces within predefined tolerances. A model was developed that predicts future macrotexture levels (as measured by RMS) for pavements prone to bleeding due to rich asphalt content. Finally, several previously published macrotexture parameters along with a suite of novel parameters were evaluated for their effectiveness in the prediction of wet weather friction and certain types of road noise. Many of the parameters evaluated outperformed the current metrics of MPD and RMS.

The purpose of this thesis was to assess the repeatability and reproducibility of two high-speed macrotexture measuring systems. The first portion of the study collected macrotexture measurements using the two high-speed systems on the Virginia Smart Road facility and validated the reproducibility of the mean profile depth (MPD) measurements with reference CT Meter measurements. The various data sets were then compared with each other. The objective was to determine whether the two systems are collecting repeatable and reproducible data. The analysis showed that the two high-speed systems investigated have good repeatability (0.105 mm for the Ames and 0.113 mm for the SCRIM) when measuring the average MPD of the sections investigated. The two systems produce measurements that are highly-correlated (Ames R2 = 0.9591 and SCRIM R2 = 0.9157) with the reference ones obtained with the CT Meter. While the Ames systems, with the data processed using the Virginia Tech filter, measures MPD values that are very close to those of the CT Meter, with a virtually zero systematic bias. The SCRIM obtains slightly lower readings. The differences are thought to be due to the filtering of the raw pavement elevation measurements used by the SCRIM processing software to eliminate dropout and spikes in the laser measurements.

The brain is a very vulnerable organ and damage to it is often followed by severe implications such as long-term disabilities and it may even lead to death. Cerebral oximetry by near-infrared spectroscopy (NIRS) has repeatedly been cited as promis- ing technology, potentially enabling clinicians to prevent these outcomes. Preterm neonates are likely to suffer from complications leading to brain damage and may thus benefit strongly from NIRS monitoring. Although a number of commercial NIRS oximeters are clinically approved, the method has not yet been widely established. Two of the major reasons for this are poor precision of instruments and that tissue oxygen haemoglobin saturation (StO 2 ) obtained from different oximeters and sensors are incomparable. This thesis addresses these two problems and provides solutions. OxyPrem was developed with the objective to provide an instrument with increased precision to clinicians. Two versions, OxyPrem v1.2 and v1.3, are introduced in this thesis and their performance is validated in vivo and in vitro. Both sensors are based on symmetric arrangement of light sources and detectors and employ a self-calibrating algorithm. OxyPrem v1.2 performed excellently in vivo in a precision assessment on the forearm of adults (repeatability = within-subject standard deviation (S w ) = 1.7 %). Repeata- bility in preterm neonates was S w = 3.3% which is still good, taking into account that S w in neonates is typically higher than in adults. An improved version of the instrument, OxyPrem v1.3, was assessed in vivo in neonates as well. The study demonstrated S w as good as 2.8 %. Simultaneous mea- surements with another OxyPrem v1.3 sensor and a pulse oximeter revealed unstable physiology in some neonates. In a second analysis without these confounding sub- jects, S w improved drastically to 1.9 % which is amongst the best precision values ever achieved for NIRS oximeters. To overcome the lack of comparability of different oximeters and sensors, we have performed several studies with liquid phantoms simulating optical properties of neona- tal brain tissue. We first conducted experiments with a simple, homogeneous phantom and then refined the set-up to model a more realistic two-layer geometry resembling skull and brain. Our studies showed substantially different StO 2 readings provided by different oximeters which, however, were mostly linearly related. With the improved set-up, we characterized a large number of commercially available oximeters and sen- sors and provided coefficients for their pairwise linear relation. The method showed good repeatability and helps establishing comparability. As neonates are a very heterogeneous group, we investigated the effect that a varia- tion in total haemoglobin concentration (c tHb ) has on StO 2 readings by NIRS oxime- ters. We found strong influence of c tHb on StO 2 while only OxyPrem v1.3 proved to be largely immune to this effect, which causes substantial uncertainty to readings of other instruments. As the presented phantom set-up is very versatile, we additionally investigated sev- eral other effects with slight adaptations. These showed that StO 2 readings were un- affected by a thin superficial layer, while sensitivity decreased substantially for a layer with 16 mm thickness. In another experiment, we did not observe a change in StO 2 readings for very thin clear layers such as oil on the skin of neonates, whereas thicker layers must be avoided. Partial placement of sensors on top of hair and birth marks may seriously flaw StO 2 of sensors without symmetric source-detector arrangement and self-calibrating algorithm. In summary, this thesis provides solutions to two of the problems mentioned most often in association with cerebral oxygenation monitoring by NIRS. We have intro- duced OxyPrem v1.2 and v1.3 and demonstrated superior precision of the instruments in vivo. OxyPrem v1.3 proved to be largely immune to variation in c tHb , which reduces this considerable uncertainty in StO 2 readings to a minimum. By a series of in vitro experiments with liquid phantoms we were able to establish comparability of different instruments and systematically assessed several types of influences to StO 2 readings.

A reliable and robust laboratory method is essential for the forensic analysis of deoxyribonucleic acid (DNA), particularly for low-template samples. Electropherogram peak heights are important to the identification of STR alleles, and these peak heights are prone to error. Since error can be introduced into the process during sample preparation, quantification, amplification, or analysis, validation studies are performed in an attempt to characterize the signal variation associated with the process. While current practices assess aspects of a method, such as sensitivity and reproducibility, the effects of daily laboratory alterations are often not considered. Additionally, samples used in a validation study may be prepared using serial dilutions. Therefore, understanding the extent to which error is propagated through the series and the effect it has on the results could help improve validation practices. This work aimed to assess the effect daily laboratory modifications have on the signal in a forensic electropherogram. Specifically, the variability in signal when different capillary and amplification kit lots were used was evaluated against the variability observed when a single sample was either injected or amplified multiple times. The variability was determined via the examination of peak heights, peak height ratios, stutter, and drop-out. The effect of serially diluting samples was examined via an in silico model of the dilution process, polymerase chain reaction (PCR), and capillary injection. The peak heights from simulated serially diluted samples using the concentration of a stock DNA were compared to the peak heights from simulated samples that were quantified after the dilution series was generated and prior to amplification. The different capillary lots and amplifications were found to result in greater variation compared to the multiple injections. Additionally, when the stutter percentages obtained from using multiple kit lots were compared to those obtained using the same kit lot, differences in stutter percentage deviations resulted in different stutter thresholds. Drop-out rates were also different between the samples amplified with one kit versus the same samples amplified with multiple kit lots. Therefore, at a minimum, multiple amplifications should be run on multiple capillary lots during validation. Further, if available, the use of multiple kit lots is recommended, particularly in cases where stutter thresholds or drop-out models are used during interpretation. Creating validation samples via serial dilutions was also found to increase the variation observed in peak height in the simulated samples, suggesting that samples should be quantified post-dilution. In addition to characterizing the variability of several components of DNA analysis, an alternative quantification method was investigated in order to decrease the overall variability associated with the quantification process. This work sought to develop an electrochemical biosensor using a single-stranded DNA (ssDNA) probe chemically adsorbed to a gold electrode. This would allow for the direct quantification of DNA and eliminate the need for qPCR and fluorescent-based oligonucleotide detection systems. The DNA probe was successfully adsorbed to the surface of the gold disk electrode, hybridized to a single-stranded complementary DNA sequence, and detected using square wave voltammetry. Additionally, the ability to control the amount of DNA chemisorbed to the electrode surface was investigated by varying the incubation time in the probe solution. The measured current increased as the incubation time increased from 15 minutes to one hour, after which it plateaued. The use of an electrochemical biosensor is a promising alternative to qPCR for the quantification of DNA, with one hour being the optimal incubation time in the probe solution.

Body condition is expected to reflect individual quality because high quality individuals should be better at acquiring and using resources, resulting in higher fitness. However, the hypothesis that condition indices are meaningful indicators of individual quality has been questioned. I monitored a population of crimson finches (Neochmia phaeton) for reproductive success and survival over four breeding seasons. My study population is well suited for this research because individuals forage in common areas and do not hold territories such that variation in condition between individuals is not confounded by differences in habitat quality. Because little is known about crimson finches in the wild, I first describe their breeding biology and life-history traits (Chapter I). Next, I sampled them for commonly used condition indices including mass adjusted for body size, muscle and fat scores, packed cell volume, hemoglobin concentration, total plasma protein, and heterophil to lymphocyte ratio. I describe the variation in these indices and find that many vary by sex and breeding stage, and to a lesser extent by year, age and time of day, concluding that these covariates need to be controlled for when examining intraspecific variation in condition (Chapter II). If condition indices reflect inherent individual quality, then condition indices should be (a) repeatable within individuals, and (b) predictors of realized fitness. I test these two predictions in Chapters III and IV, respectively, and I find that condition indices are repeatable within individuals over short, but not long, time periods and that some indices predict reproductive success, while others do not, and that none predict survival. Both findings only partially support the hypothesis that condition indices are meaningful indicators of individual quality, raising concerns over this common interpretation. In Chapter V, I glean insights from the ecological and poultry science literature and discuss further complications with the use of condition indices as proxies for individual quality and fitness. I conclude that condition indices indicate how well an individual is currently acquiring resources as well as its likely physiological state over the next few months, but that they do not reflect individual quality and are not reliable proxies for fitness.

Our ability to consistently predict which taxa will become invasive and where, and understanding of the drivers of this variation is limited. A better understanding of how variation in traits within species and biotic and abiotic conditions within regions influence patterns of invasion is needed to improve our understanding of the processes underlying invasions and our ability to manage alien species. The taxonomic unit used to assess alien invasiveness is usually the species. There is considerable intraspecific variation in plant traits, but the extent to which these differences can affect invasiveness is unknown. I tested the hypothesis that most of the variation in plant performance among taxa would reside at the species level (relative to subspecies and varieties). I quantified variation in performance among taxa of alien Brassica with data from a seed sowing experiment comprising 24 taxonomically stratified varieties (six subspecies, three species) used to parameterise hierarchical models. Around 30 times more variation resided among varieties within species than among species. Differences in the viability rates of the sown seeds explained some of the differences in performance. My results show that intraspecific taxa of alien species can vary significantly in performance and suggest novel genotypes may pose a different invasion risk to that currently established for the species. Weed risk assessment protocols could be modified to include varietal traits such as seed viability in assessments. The availability of seeds and bare ground both influence whether plant populations establish, but the degree to which they influence persistence is less well known. The taxonomic level at which most variation in alien performance resides may shift under different regimes of seed and site availability. I quantified the effects of relaxing seed and site limitation on the performance of a taxonomically stratified selection of 12 varieties of alien Brassica, and looked for shifts in the taxonomic level at which most variation in performance resided. Seeds were sown at two densities (400 seeds/m⁻² and 4000 seeds/m⁻²), and with and without pre-sowing soil disturbance. Both a higher sowing density and pre-sowing disturbance increased Brassica emergence, but only disturbance increased survivorship, and neither resulted in significantly higher population growth rates. Most variation in performance among taxonomic levels resided at the varietal level regardless of seed density or disturbance. While high seed density and disturbance can increase seedling recruitment, unless aliens can pass subsequent ecological filters persistence is unlikely. Alien plant populations often become extinct due to demographic and environmental stochasticity, unsuitable traits, and Allee affects. Such aliens may appear to be naturalised if new populations are founded by dispersed or immigrant propagules. Differentiating between transient and persistent populations is crucial to our understanding and management of invasions. I recorded feral alien Brassica populations in three annual surveys, along with measures of seed sources, site and management characteristics that may influence the probability of presence and survival. I identified correlates of population presence and survival, and quantified the probability of population survival from year to year. Brassica would likely not persist in the landscape beyond ten years without anthropogenic seed input. Only around 40% of populations survived two or more years after foundation, but new populations focused around transportation routes and seed companies compensated for extinctions. Stochasticity and trait-site mismatch were causes of population extinction. Adventive aliens may be controlled by managing propagule sources; accounting for population extinctions is important to accurately assess distributions from cumulative presence data. Further research is required to identify which traits drive variation in plant performance and invasiveness within species. In addition we need to be able to identify taxa which are most likely to contain substantial intraspecific variation in these traits. Applying the precautionary principle would suggest that the same restrictions should apply to the importation of new plant varieties, subspecies and genotypes as are applied to the importation of new plant species.

Optical signals of the peripheral retina control eye growth and associated myopia more than previously believed. Traditional thought held that the fovea must play the largest role in progression of refractive error because of its integral role in vision. However, recent research shows that the peripheral retina may be involved. In Rhesus monkeys, peripheral form deprivation and optically induced hyperopia lead to increased axial elongation and myopia. Furthermore, emmetropization occurs when the peripheral cue is removed, even after ablation of the central retina. Human myopes have relative hyperopic blur in the periphery, whereas emmetropes and hyperopes exhibit emmetropia or myopia in the retinal periphery. In fact, relative peripheral hyperopia precedes myopia onset by two years in children. This peripheral hyperopic blur may be a signal for myopic eye growth. Tracking the 3-dimensional shape of the eye through peripheral measurements could provide clues about how peripheral blur increases axial elongation. Understanding these optical signals and pathways could be valuable in ultimately determining how to manage or prevent myopia.Research has focused on methods to stymie eye growth by inducing peripheral myopic defocus. It is therefore important to determine whether any change in peripheral eye length is greater than that which can be expected by measurement error alone. This study aims to determine the inter-occasion repeatability of peripheral axial length measurements using the IOLMaster in order to learn more about the growth of peripheral eye.To assess the repeatability of the IOLMaster in measuring peripheral eye length, we performed five measurements of both non-cycloplegic and cycloplegic (two drops of 1% tropicamide) axial length in primary gaze and at gazes 20 degrees nasal, temporal, superior, and inferior. The same examiner repeated the measurements one week (± 2 days) later to assess how similar the measurements were from one week to the next, assuming that no significant eye growth would happen in that span of time.A total of 30 subjects completed the study. The 95% limits of agreement (LoA) for the cycloplegic repeatability at each location were: central (-0.05, +0.07), nasal (-0.24, +0.23), temporal (-0.14, +0.12), superior (-0.11, +0.11), and inferior (-0.11, +0.11). The 95% LoA for the non-cycloplegic repeatability at each location were: central (-0.07, +0.06), nasal (-0.17, +0.17), temporal (-0.11, +0.09), superior (-0.27, +0.23), and inferior (-0.15, +0.13). In general, nasal measurements were the least repeatable of the peripheral locations. Neither cycloplegic nor non-cycloplegic measurements consistently provided better repeatability at all locations. However, cycloplegic measurements provide shorter eye lengths than non-cycloplegic measurements (p < 0.001). If peripheral eye length is to be measured over time, operators of the IOLMaster must be consistent in whether or not they use cycloplegic drops. Users of the IOLMaster can be confident that any change of 0.25 mm in peripheral eye length is due to a real change in the eye and not due to measurement error. Repeatability of the IOLMaster is quite good for tracking peripheral eye growth.

Objectives: Phase 1) Establish echocardiographic reference intervals for measurements of the normal canine right heart. Phase 2) Describe the repeatability of normal right heart echocardiographic measurements. Phase 3) Describe the repeatability of right heart echocardiographic measurements which predict pulmonary artery pressure. Materials and Methods: Phase 1) 45 healthy adult dogs. Dogs underwent one echocardiographic examination by the same operator. Phase 2) 6 randomly selected dogs from the pool of Phase 1 dogs. Dogs underwent repeated echocardiograms by two operators. Phase 3) 4 client-owned dogs. Dogs underwent repeated echocardiographic examination by two operators. Results: Phase 1) The linear relationship between dimension and transformed body weight was highly variable. For linear dimensions, most of the scaling exponents were close to the theoretical value of 1/3. For area measurements, most of the scaling exponents were close to 2/3. Phase 2) Of the 168 within-day, between-day and between-operator coefficients of variation (CV) generated, 154 (91.7%) were below 15% and 135 (80.4%) were less than 10%. Phase 3) Of the 100 within-day, between-day and between-operator CVs generated, 72 (72%) were below 20% and 46 (46%) were below 10%. Conclusions: The right heart can be measured with relatively low repeatability. Measurement of the tricuspid regurgitation velocity should be the first priority when attempting to predict pulmonary artery pressure. If tricuspid regurgitation is not present, the use of transpulmonic acceleration time (AT) and the ratio of transpulmonic acceleration-to-ejection time (AT:ET) to indirectly assess pulmonary artery pressure is recommended.

Many PCR-based methods for microbial source tracking (MST) have been developed and validated within research laboratories, but require inter-laboratory validation before implementation. As part of the State of California Source Identification Protocol Project (SIPP), a blinded set of challenge filters were analyzed by three to five laboratories with a suite of PCR-based methods utilizing standardized methods. Repeatability (within lab agreement) and reproducibility (between lab agreement) of results were assessed by multiple metrics and compared to previously observed values for other environmental methods. Repeatability and reproducibility were found to be generally comparable to previously observed values for other methods (Median CV .001-.033 and .020-.106, respectively). Variance component analysis showed contribution of laboratory to total variability to be larger but of similar magnitude to inherent intra-laboratory variability among laboratories using standardized methods. Results among laboratories using non-standardized protocols for the same methods were also observed to have >2 log differences at times. These findings verify the repeatability and reproducibility of these MST methods and highlight the need for standardization of protocols and consumables prior to implementation of larger scale microbial source tracking studies involving multiple laboratories.

Background: Accuracy of a measurement is a cornerstone in research in order to make robust conclusions about the research hypothesis. Objective: To examine whether the number of items (questions) and the number of responses of consumption included in nutritional assessment tools influence their repeatability. Methods: During 2009, 400 participants (250 from Greece, 37±13 yrs, 34% males and 150 participants from Spain, 39±17 yrs, 41% males) completed a diet index with 11-items and binary (yes/no) responses, a diet-index with 11-items and 6-scale responses, a 36-item and a 76-item food frequency questionnaire (FFQ) with 6-scale responses. Participants completed these tools, twice, within 15-days period. Spearman-Brown (rsb), Kendall’s tau coefficients and the Bland-Altman method were applied to answer the research hypothesis. Results: The highest repeatability coefficient was observed for the 11-items with binary responses index (rsb=0.948, p0.23); whereas the aforementioned tools had significantly higher repeatability coefficients as compared with the 76-item FFQ (p=0.002). Sub-group analyses by gender, education, smoking and clinical status, confirmed the aforementioned results. Conclusion: Repeatability has been revealed for all food frequency assessment tools used, irrespective of the number of items or the number of responses included.

It is the responsibility of pavement engineers to design pavements that provide safe and smooth riding surfaces over their entire life cycle. Each year many people around the world lose their lives in vehicle crashes, which are one of the leading causes of death in the United States (US). One of the contributing factors in many of these crashes is inappropriate friction between tires and the pavement. To minimize the impact of this factor, state Departments of Transportation (DOTs) must monitor the friction of their pavement networks systematically and regularly. Several devices are used around the world for measuring friction. Locked-wheel skid trailers are the predominant technology for roadways in the U.S. However, Continues Friction Measuring Equipment (CFME) is emerging as a practical alternative, especially for network-level monitoring. This type of technology has been used for monitoring runway friction for many years and is starting to be used also for measuring roadway friction. This thesis evaluates the different operational characteristics of CFME to provide guidelines for highway agencies interested in using this technology for supporting their friction management programs. It follows a manuscript format and is composed of two papers. The first part of the thesis presents a methodology to objectively synchronize and compare CFME measurements using cross-correlation. This methodology allows for comparing the “shape” of the friction profiles, instead of only the average friction values. The methodology is used for synchronizing friction measurements and assessing the repeatability and reproducibility of the CFME using friction measurements taken on a wide range of surfaces at the Virginia Smart Road. The proposed approach provides highway agencies with a rigorous method to process CFME measurements. The second part of the thesis evaluates the impact of several operational characteristics on the CFME measurements using a field experiment. The results of the experiment confirmed that the measurements are significantly affected by (1) the direction of testing while testing on sections of road with a significant grade, (2) water film thickness, and (3) testing speed. The experiment showed that measurements taken downhill on a 6% grade were significantly higher than those taken uphill. The analysis also verified that, consistent with previous studies, the measured friction decreases with higher water depth and testing speeds. It also showed that the change of friction with speed is approximately linear over the range of speeds used in the experiment. In general, the thesis results suggest that CFME can provide repeatable and reproducible friction profiles that can be used to support friction management programs and other asset management business functions. However, care should be taken with regard to the operational conditions during testing since the measurements are affected by several factors. Further research is needed to (1) quantify the effect of these, and potentially other, operational factors; and (2) establish standard testing condition and approaches for correcting measurements taken under other conditions.

The purpose of this study was to determine the short-term repeatability of average airflow in children, ages 4.0 – 5.11 years. Thirty participants with healthy voices and normal hearing sustained the vowel /a/ for 5 seconds at their comfortable frequency and intensity for 3 consecutive productions during 2 separate trials, using the Phonatory Aerodynamic System. The trials were separated by performance of additional acoustic tasks. Results indicated that average airflow measurements were repeatable in young children with no significant difference in average airflow values.

The purpose of this study was to evaluate the validity and repeatability of crystalline lens thickness measurements obtained by anterior segment optical coherence tomography (OCT). Optical coherence tomography utilizes infrared light and partial-coherence interferometry to produce a two-dimensional scan of the internal ocular structures in vivo. Changes in crystalline lens thickness are important to monitor for refractive error development, cataract progression, and anterior chamber alterations. Our goal was to develop an effective method of measuring the thickness of the crystalline lens with the Visante anterior segment OCT, to assess OCT repeatability, and to evaluate OCT validity as compared to A-scan ultrasonography. Forty-seven normal children (mean age ± SD = 11.06 +/- 2.30 years) had their crystalline lens thickness measured with the Visante anterior segment OCT (Carl Zeiss Meditec, Dublin, CA) and with conventional A-scan ultrasonography (Humphrey 820). The subjects’ right corneas were anesthetized, and their right eyes were cyclopleged. Five A-scan ultrasonography measurements and three Visante OCT measurements were made per eye. Thirty-eight subjects had measurements at a second visit where three additional Visante OCT measurements were made. The mean of the differences between the Visante OCT and A-scan ultrasonography was –0.045 mm (p = 0.017), indicating that the average measurement of crystalline lens thickness was thinner with the Visante OCT. The 95% limits of agreement were from –0.29 to 0.20 mm. When validity was assessed using only Visante OCT images that contained the corneal reflex, the mean of the differences was 0.019 mm (p = 0.11) with 95% limits of agreement from –0.091 to 0.13 mm. For the repeatability of the Visante OCT, the mean of the differences between visit one and visit two was –0.008 mm (p = 0.25) with 95% limits of agreement from -0.088 to 0.072 mm. Repeatability improved when reassessed using only images that contained the corneal reflex; the mean of the differences for these images was –0.0001 mm (p = 0.97) with 95% limits of agreement from –0.030 to 0.030 mm. In comparison to A-scan ultrasonography, a statistically significant difference was observed only when images that did not contain the corneal reflex were included in the analysis. When assessing inter-visit repeatability, a statistically significant difference was not found in either case, but the limits of agreement were narrower when repeatability was assessed using only the images containing a corneal reflex.The Visante OCT is a non-contact instrument that is simple to use, and it provides valid crystalline lens thickness measurements with excellent repeatability. Validity and repeatability were optimized when the Visante OCT images contain the corneal reflex.

The purpose of this study was to compare baseline aerodynamic measurements of voice to measurements repeated after a 10-minute break and a one week break. Average airflow and estimated subglottal pressure measurements were gathered from females between 18 and 24 years of age with healthy voices. Each participant’s frequency and intensity was held constant during each testing session. Results indicated that aerodynamic measurements of average airflow and estimated subglottal pressure were repeatable, as there were no significant differences between mean measurements taken during each testing session. The results of this study provided support for the clinical use of average airflow and estimated subglottal pressure for voice assessments and treatment data.

A validated gas chromatography-mass spectrometry (GC-MS) detection method for the quantitative analysis of sterol oxidation products (SOPs) in serum is described. After a lipid extraction procedure with chloroform-methanol, a cold saponification and purification by solid phase extraction, oxysterols were derivatized to form trimethyl-sylil-ethers which were subjected to GC-MS analysis. Calibration curves for cholesterol oxidation products showed determination coefficient (R(2)) of 1.0, with low values for the coefficient of variation of the response factors (< 1%). Detection and quantification limits were below 5 ng/mL and 10 ng/mL, respectively. Recovery data were between 77.65% and 110.29% (CV < 10% for all compounds). Good results were obtained for within- and between-day repeatability, with values below 10%. In conclusion, the method performed is suitable for the determination and quantification of SOPs in serum.

Road smoothness is one of the most important road functional characteristics because it affects ride quality, operation cost, and vehicle dynamic load. There are many types of devices that measure the road profile, which is often used to compute different smoothness indices. The development of performance-based specifications and pavement warranties that use ride quality as a performance measure has increased the need for accurate measurement of pavement smoothness. For this reason, researchers have compared and evaluated the performance of available profilers and several profiler accuracy criteria have been proposed. However, there is not a definite answer on the ability of available profilers to accurately measure the actual road profile as well as the various smoothness indices. A recent profiler round-up compared the performance of 68 profilers on five test sections at Virginia Smart Road. The equipment evaluated included high-speed, light-weight, and walking-speed profilers, in addition to the reference device (rod and level). The test sites included two sites with traditional hot-mix asphalt (HMA) surfaces, one with a coarse-textured HMA surface, one on a continuously reinforced concrete pavement (CRCP), and one on a jointed plain concrete pavement (JCP). This investigation used a sample of the data collected during the experiment to compare the profiles and International Roughness Index (IRI) measured by each type of equipment with each other and with the reference. These comparisons allowed determination of the accuracy and repeatability capabilities of the existing equipment, evaluation of the appropriateness of various profiler accuracy criteria, and recommendations of usage criteria for different applications. The main conclusion of this investigation is that there are profilers available that can produce the level of accuracy (repeatability and bias) required for construction quality control and assurance. However, the analysis also showed that the accuracy varies significantly even with the same type of device. None of the inertial profilers evaluated met the current IRI bias standard requirements on all five test sites. On average, the profilers evaluated produced more accurate results on the conventional smooth pavement than on the coarse textured pavements. The cross-correlation method appears to have some advantages over the conventional point-to-point statistics method for comparing the measured profiles. On the sites investigated, good cross-correlation among the measured and reference profiles assured acceptable IRI accuracy. Finally, analysis based on Power Spectral Density and gain method showed that the profiler gain errors are nonuniformly distributed and that errors at different wavelengths have variable effects on the IRI bias.

The purpose of this study was to investigate the repeatability and efficacy of Evoked Otoacoustic Emissions (EOAE) screenings performed by non-audiology professionals using the AuDX universal newborn hearing screening device by Bio-logic. After a brief instructional program, student clinicians and a certified audiologist performed screenings on each of five subjects. Results from student clinicians were compared to one another for repeatability. Clinician results were then compared to results obtained by the audiologist for reliability. Research from this study showed no significant difference in results obtained from non-audiology clinicians and those obtained by a certified clinical audiologist.

Blood oxygen level dependent (BOLD) functional magnetic resonance imaging (FMRI) was implemented at 1.5 Tesla to characterize visual cortex activation patterns in human amblyopia. The dissertation consists of three main components. First, the voxel-wise repeatability of visual cortex FMRI results was assessed using a mixed-effects ANOVA group analysis. Two stimuli were presented monocularly and binocularly to ten subjects in two independent scanning sessions. Visual cortex activation maps were found to be repeatable regardless of the stimulus type or eye stimulated. The second study investigated interocular differences in the level and extent of activation in amblyopic and normal subjects. Five amblyopes and six normals were recruited. Stimuli included a homogeneous flickering field (8 Hz) and counterphasing (8 Hz) vertical sinusoidal gratings at 0.5, 1 and 2 cpd. Amblyopes exhibited a larger (P

In 1984 a Merino wether trial at Matakanui station, Omakau, Central Otago, was set up to demonstrate the production possible from well-bred Merino wethers. Thirty teams of ten sheep from a variety of environmental and genetic backgrounds took part in the trial. Prizes were awarded for the highest returns per head, highest average clean fleece weight and highest liveweight off shears. Data from 1984, 1985 and 1986 which included fibre diameter, clean fleece weight, greasy fleece weight, clean scoured yield, liveweight and staple length were analysed in relation to within and between group phenotypic variation, repeatabilities and phenotypic correlations. The efficiency of wool growth was also calculated. The design of the trial was critically reviewed. Highly significant (p

This dissertation addresses the problem of which arrays should be used for experimentation in environments with low repeatability error. This problem is relevant because engineers increasingly are using rapid prototyping, repeated simulations, finite element analysis, computational fluid methods, and other highly repeatable methods. Many engineers incorrectly believe that two-level or sometimes three-level orthogonal arrays are their only economical option. This dissertation concludes that a new class of search arrays is the most appropriate choice in environments with low repeatability error. In general, the recommended arrays offer a substantial reduction in the number of runs needed to permit interactions and other non-linear effects to be modeled. For example, with less than one-third the number of runs, the methods achieved greater accuracy than modeling based on the 3$\sp3$ factorial array (L$\sb{27}$) when applied to the design of a plastic seal (Chapter 1V), as measured in integrated squared error. We demonstrate in Chapters I and II that, if the repeatability error is low and the appropriate arrays are used, then runs beyond the number required to estimate all coefficients are useful for two purposes only: (1) to select the best candidate model and (2) to detect whether none of the candidate models is acceptable. Further, we show that only limited numbers of runs are required for these purposes. Chapter III presents search arrays that exploit a common cost structure to permit a substantial reduction in the engineering time required for experimenting using finite element analysis. The array is applied to the design of D-shaped shafts. The resulting engineering design is expected to be useful for automotive heating, ventilating, and cooling (HVAC) applications. Chapter IV provides a case study of the development of a tongue and groove design for an HVAC application. The chapter also compares the application of one of the arrays and procedures from Chapters I and II with alternative approaches. In Chapter V, we explain how the problems formulated in Chapter I are sometimes so small that they can be solved by complete enumeration and discuss symmetry operations of the type used in the case study in Chapter IV.