Establishing best practice for the classification of shark behaviour from bio-logging data

Understanding the behaviours of free-ranging animals over biologically meaningful time scales (e.g. diel, tidal, lunar, seasonal, annual) gives important insights into their ecology. Bio-logging tools allow the remote study of elusive or inaccessible animals by recording high resolution multi-channel movement data, however archival device recording duration is limited to relatively short temporal-scales by memory and battery capacity. Machine learning (ML) is becoming common for automatic classification of behaviours from large data sets. This thesis develops a framework for the programming of bio-loggers for the classification of shark behaviour through the optimisation of sampling frequency (Chapter 2) and the choice of movement sensor (Chapter 3). The effects of sampling frequency on behavioural classification were assessed using data published in a previous study collected from accelerometer equipped juvenile lemon sharks (Negaprion brevirostris) during captive trials in Bimini, Bahamas. The impacts of different combinations of movement sensors (accelerometer, magnetometer and gyroscope) were assessed using data collected from sub adult sicklefin lemon sharks (Negaprion acutidens). Sharks were equipped with multi-sensor devices recording acceleration, angular rotation and angular velocity during captive trials at St Joseph Atoll, Seychelles. Catalogues of discrete classes of behaviours (ethograms) were developed by observing sharks during captive trials. Behaviours (swim, rest, burst, chafe, headshake) were classified using a random forest ML algorithm with predictor variables extracted from the ground-truthed data. A range of sampling frequencies (30, 15, 10, 5, 3 and 1 Hz) and combinations of movement sensors were tested. For each dataset, a confusion matrix was determined from model predictions for calculation and comparison of evaluation metrics. Classifier performance was best described by the class or macro F- score, a measure of model performance, one indicating perfect classification and zero indicating no classification. As sampling frequency decreased, classifier performance decreased. Best overall classification was achieved at 30 Hz (F- score >0.790), although 5 Hz was appropriate for classification of swim and rest (>0.964). Behaviours characterised by complex movements (headshake, burst, chafe) were best classified at 30 Hz (0.535- 0.846). Classification of behaviours was best with a tri-sensor combination (0.597), although incorporating an additional sensor (magnetometer or gyroscope) resulted in little increase in classifier performance compared to using an accelerometer alone (0.590 compared to 0.535 respectively). These results demonstrate the ideal sampling frequencies and movement sensors for best-practice programming of bio-logging devices for classifying shark behaviour over extended durations. This thesis will inform future studies incorporating behaviour classification, enabling improved classifier performance and extending recording duration of bio-logging devices

A geomagnetic polarity timescale for the Carboniferous

The geomagnetic polarity pattern for the Carboniferous is incompletely known, but with the best resolved parts in the Serpukhovian and Bashkirian. Hence, data from both igneous and sedimentary units are also used in an additional polarity bias evaluation. In the Tournaisian to mid Visean interval polarity is mainly derived from palaeopole-type palaeomagnetic studies, allowing identification of polarity bias chrons. Seven polarity bias chrons exist in the Mississippian (MI1nB to MI4nB) with an additional 33 conventional magnetochrons and submagnetochrons (MI4r to MI9r). The Moscovian and Gzhelian polarity is best resolved in magnetostratigraphic studies from the Donets Basin and the southern Urals. Dispute about the reliability of these data is ill-founded, since an assessment of supporting data from palaeopole-type studies suggests that these datasets currently provide the best magnetic polarity data through the Pennsylvanian. Polarity bias assessment indicates a normal polarity bias zone in the Kasimovian. In the Pennsylvanian there are 27 conventional magnetochrons and submagnetochrons (PE1n to CI1r) and one normal polarity bias chron (PE8nB). The Kiaman Superchron begins in the mid Bashkirian, with clear data indicating brief normal polarity submagnetochrons within the Superchron. The magnetochron timescale is calibrated using 31 U-Pb zircon dates and a quantitative Bayesian-based age-scaling procedure

The conception of human nature in modern political thought : with special reference to the work of Charles Taylor

[From the introduction:]This thesis will analyse and advocate a 'contextualist' reading of human nature. By reference to the work of Charles Taylor it will be argued that Modern conceptions of human nature are (to echo Nietzsche) 'dead'. This is to attack the suggestion that a conception of human nature may be understood in an ahistorical, universalist, abstract or 'unencumbered' sense. A conception of human nature must, of necessity, it will be argued, be understood in a more dynamic and 'local' sense. It is the suggestion of this thesis that human nature must be understood in a sense akin to the existential notion of 'facticity', or as possessing a degree of 'determinacy'. While human nature is 'encumbered' by its 'situation' in time and geographical location it is not however wholly determined. An individual's existence is co-determined by individual choice, the individual's history, and by Nature. Human nature must be recognised to have a facticity, to exist at a certain point in history, in a certain country, to be encumbered by countless other emotional ties, friendships, and loyalties. This 'embedded' conception of human nature is delineated and explored through Taylor's conception of human nature as an 'interspatial epiphany', and is to be preferred to the unencumbered sense of interspatial epiphany that might be seen to be offered by some forms of existentialism. Such existentialist thought is not as astutely located or embedded as Taylor's thought, and suffers from what Taylor terms 'existential heroism', a focus on choice making rather than on the background of encumberment.While the notion of a universal conception of human nature must be abandoned, as the individual is now seen as 'located' temporally, and spatially, it is still possible to draw some (very) modest generalisations about the nature of individuals. This exploration proceeds by generating a 'thick description' of the selfs particular, but ultimately contingent, connections and affiliations. (Such a located description is seen as superior by Taylor, to thin, mechanistic, scientific and neurological descriptions of human agency.

Aggregation of growing crystals in suspension: II. Poiseuille flow crystalliser

We describe the design and operation of a Poiseuille Flow Crystalliser (PFC) that allows direct exploration of the effect of hydrodynamic and physico-chemical conditions on the aggregation of crystals growing in suspension. The PFC operates as a differential reactor where changes between inlet and outlet are small enough not to change the rate, but large enough to be measureable. Automatically measured changes in size distribution yield very clear quantitative evidence of aggregation. We use these data to explore the three open questions of Hounslow et al. (2013) and show how to average underlying point aggregation kinetics over a whole vessel and how to extract point data from average data. We introduce the critical aggregate size, D, as the particle size that at the average shear rate has a Mumtaz number, M=1, and so disruptive forces are in balance with the strength of growing bridges. In a study of rounded calcium oxalate monohydrate particles we show that values of D can readily be determined by fitting the change in size distribution in the PFC. We are able to discriminate among candidate models relating aggregation efficiency to M by means of an empirical fitting investigation and by directly determining the aggregation efficiency – both averaged and un-averaged for the vessel. We conclude that aggregate rupture happens under simple tension and that the effective average size of two colliding particles is their geometric mean. D2 is predicted and observed to be directly proportional to the ratio of crystal growth rate to flow rate squared. We demonstrate that no attractive or repulsive inter-particle forces are active in aiding or retarding aggregation in this system. The constant of proportionality from these results allows the material property controlling aggregation – the product of yield strength and a geometric factor with dimensions of length – to be determined as L⁎σY=1.35±0.01 Nm−1

The denatured state of N-PGK is compact and predominantly disordered

The Organisation of the structure present in the chemically denatured N-terminal domain of phosphoglycerate kinase (N-PGK) has been determined by paramagnetic relaxation enhancements (PREs) to define the conformational landscape accessible to the domain. Below 2.0 M guanidine hydrochloride (GuHCl), a species of N-PGK (denoted I-b) is detected, distinct from those previously characterised by kinetic experiments [folded (F), kinetic intermediate (I-k) and denatured (D)]. The transition to I-b is never completed at equilibrium, because F predominates below 1.0 M GuHCl. Therefore, the ability of PREs to report on transient or low population species has been exploited to characterise I-b. Five single cysteine variants of N-PGK were labelled with the nitroxide electron spin-label MTSL [(1-oxyl-2,2,5,5-tetramethyl-3-pyrroline-3-methyl)methanesulfonate] and the denaturant dependences of the relaxation properties of the amide NMR signals between 1.2 and 3.6 M GuHCl were determined. Significant PREs for I-b were obtained, but these were distributed almost uniformly throughout the sequence. Furthermore, the PREs indicate that no specific short tertiary contacts persist. The data indicate a collapsed state with no coherent three-dimensional structure, but with a restricted radius beyond which the protein chain rarely reaches. The NMR characteristics Of I-b indicate that it forms from the fully denatured state within 100 mu s, and therefore a rapid collapse is the initial stage of folding of N-PGK from its chemically denatured state. By extrapolation, I-b is the predominant form of the denatured state under native conditions, and the non-specifically collapsed structure implies that many non-native contacts and chain reversals form early in protein folding and must be broken prior to attaining the native state topology. (C) 2008 Elsevier Ltd. All rights reserved

Magnetostratigraphy of the Lower Triassic beds from Chaohu(China) and its implications for the Induan–Olenekian stage boundary.

A magnetostratigraphic study was performed on the lower 44 m of the West Pingdingshan section near Chaohu city, (Anhui province, China) in order to provide a magnetic polarity scale for the early Triassic. Data from 295 paleomagnetic samples is integrated with a detailed biostratigraphy and lithostratigraphy. The tilt-corrected mean direction from the West Pingdingshan section, passes the reversal and fold tests. The overall mean direction after tilt correction is D=299.9º, I=18.3º (κ=305.2, α95=1.9, N=19). The inferred paleolatitude of the sampling sites (31.6ºN, 117.8ºE) is about 9.4º, consistent with the stable South China block (SCB), though the declinations indicate some 101o counter-clockwise rotations with respect to the stable SCB since the Early Triassic. Low-field anisotropy of magnetic susceptibility indicates evidence of weak strain. The lower part of the Yinkeng Formation is dominated by reversed polarity, with four normal polarity magnetozones (WP2n to WP5n), with evidence of some thinner (<0.5 m thick) normal magnetozones. The continuous magnetostratigraphy from the Yinkeng Formation, provides additional high-resolution details of the polarity pattern through the later parts of the Induan into the lowest Olenekian. The magnetostratigraphic and biostratigraphic data shows the conodont marker for the base of the Olenekian (first presence of Neospathodus waageni) is shortly prior to the base of normal magnetozone WP5n. This provides a secondary marker for mapping the base of the Olenekian into successions without conodonts. This section provides the only well-integrated study from a Tethyan section across this boundary, but problems remain in definitively relating this boundary into Boreal sections with magnetostratigraphy

Population balance modelling for a flow induced phase inversion based granulation in a two-dimensional rotating agglomerator

A novel two-dimensional rotating agglomerator was developed to carry out the flow induced phase inversion (FIPI) based granulation. The process in this agglomerator shows that a continuous paste flow (mixed with liquid binder and primary particles) is extruded into the interstice of two relatively rotating disks, as the paste becomes solidified due to the loss of heat to the disks, it is then broken into granules by the shearing force imposed by the rotating disk. Experimental measurements have shown that the size of these granules is enlarged along the positive radial direction of the disks. It is also found that these granules contain approximately the same quantity of binder in terms of its volume fraction. The paper thus proposes a population balance (PB) model to describe the growth of the granules by considering a size independent agglomeration kernel. The PB simulated results are found to be well capable of describing the change of the particle size distribution (PSD) of the granules in the radial direction. This study also proposes a velocity profile for the paste flow and attempts to establish a quantitative relationship between the granulation rate and the deformation rate as this would help us understand the mechanism of the agglomeration. It is hoped that this study would be used to improve the design of the agglomerator and to assure the control of the process and the granular product quality

A geomagnetic polarity timescale for the Permian, calibrated to stage boundaries

The reverse polarity Kiaman Superchron has strong evidence for at least three, or prob ably four, normal magnetochrons during the early Permian. Normal magnetochrons are during the early Asselian (base CI1r.1n at 297.94+0.33 Ma), late Artinskian (CI2n at 281.24+2.3 Ma), mid-Kungurian (CI3n at 275.86+2.0 Ma) and Roadian (CI3r.an at 269.54+1.6 Ma). The mixed-polarity Illawarra Superchron begins in the early Wordian at 266.66+0.76 Ma. The Wordian– Capitanian interval is biased to normal polarity, but the basal Wuchiapingian begins the beginning of a significant reverse polarity magnetochron LP0r, with an overlying mixed-polarity interval through the later Lopingian. No significant magnetostratigraphic data gaps exist in the Permian geomagnetic polarity record. The early Cisuralian magnetochrons are calibrated to a succession of fusulinid zones, the later Cisuralian and Guadalupian to a conodont and fusulinid biostratigraphy, and Lopingian magnetochrons to conodont zonations. Age calibration of the magnetochrons is obtained through a Bayesian approach using 35 radiometric dates, and 95% confidence intervals on the ages and chron durations are obtained. The dating control points are most numerous in the Gzhelian–Asselian, Wordian and Changhsingian intervals. This significant advance should provide a framework for better correlation and dating of the marine and non-marine Permia