A method for quantifying reflex responses from intra-muscular and surface electromyogram

Measuring human reflex responses from electromyogram (EMG) traces in an accurate, repeatable and reliable way with a high degree of specificity has traditionally been a difficult task. This paper describes a new method that can be used to quantify reflex responses from both surface and intra-muscular EMG. This technique extends the classical cumulative sum (CUSUM) calculations by defining precise points for the calculation of latencies, durations and strengths to facilitate automatic reflex detection and permit the strength of a reflex to be defined in absolute units. The effect of varying the pre-stimulus time, the number of trials averaged and the amount of filtering used on the identification and classification of reflex parameters are also investigated. Furthermore, the effect of noise on these values, and how to remove it, is discussed. The new method, which is an expansion of the CUSUM analysis, is compared and contrasted with the more common threshold-crossing method in two different muscles: masseter and first dorsal interosseous (FDI), in experiments utilizing both mechanical and electrical stimulation. There are a number of advantages to using the new method; not only does the modified CUSUM method detect reflexes earlier than threshold-crossing methods but also the strength and duration are less susceptible to averaging and filtering parameters while giving a better indication of the reflex size. The data suggests that a pre-stimulus analysis period of at least 100 ms be used to correctly identify the variability inherent in EMG traces. It is also concluded that for subtle reflexes, 50 stimuli should be the minimum number used when spike trigger averaging is employed as lower numbers are associated with much greater pre-stimulus variability. Zero-phase filtering the rectified averaged EMG traces is recommended as this makes it easier to identify significant changes in the electrical activity of the muscle in question. In addition, noise estimation and removal from averaged rectified EMG recordings yields results that are a more accurate representation of the synaptic activity of the motor units in question.

The role of receptor dimerization domain residues in growth hormone signaling

While there is a considerable amount of evidence that signal transduction by the growth hormone (GH) receptor requires receptor homodimerization, there has been no systematic study of the role of receptor dimerization domain residues in this process. In conjunction with the distances derived from the crystal structure of the hGH-hGH receptor (extracellular domain) complex, we have used a luciferase-based c-fos promoter reporter assay in transiently transfected Chinese hamster ovary (CHO) cells, and stable receptor expressing CHO cell populations to define the dimerization domain residues needed for effective signaling. In addition to alanine substitution, we have used both aspartate and lysine substitutions to allow us to provide evidence for proximity relations through charge complementation. Introduced cysteine substitutions were also used, but unlike the erythropoietin receptor, these were unable to generate constitutively active receptor. We conclude that serine 145, histidine 150, aspartate 152, tyrosine 200, and serine 201, but not leucine 146 or threonine 147 are required for effective signal transduction through the dimerization domain. This information may be valuable in designing small molecule antagonists of GH and other cytokines that block dimerization by binding to the dimerization domain.

Standardization of H-reflex analyses

Variability in the H-reflex can make it difficult to identify significant changes using traditional pooled analysis techniques. This study was undertaken to introduce a normalisation approach to calculate both the relative size and the relative stimulus intensity required to elicit the H-reflex response so that comparisons can be made not only with results obtained during different experimental session but also between different subjects. This normalisation process fits the size of the measured M-responses and H-reflexes over the entire stimulus range with model curves to better facilitate the calculation of important parameters. This approach allows normalisation of not only the size of the response but also the relative stimulus intensity required to elicit the response. This eases the comparison of the reflex responses under various situations, and is capable of bringing out any genuine differences in the reflex in a reliable manner not previously possible. This study illustrates that comparison of the reflex between days is problematic, even in the same subject, as both the reflex size and the relative stimulus intensity required to obtain this reflex changed in all subjects. We suggest that H-reflex studies need to use normalisation not only for size of the reflex but also for the stimulus intensity, and also that all experiments for a single subject should be performed in the same session or during the same day using some level of background muscle activity in the muscle concerned as the variability of the muscle at rest was found to be larger.

Genetic, functional, and histopathological evaluation of two C-terminal BRCA1 missense variants

BACKGROUND

The vast majority of BRCA1 missense sequence variants remain uncharacterized for their possible effect on protein expression and function, and therefore are unclassified in terms of their pathogenicity. BRCA1 plays diverse cellular roles and it is unlikely that any single functional assay will accurately reflect the total cellular implications of missense mutations in this gene.

OBJECTIVE

To elucidate the effect of two BRCA1 variants, 5236G>C (G1706A) and 5242C>A (A1708E) on BRCA1 function, and to survey the relative usefulness of several assays to direct the characterisation of other unclassified variants in BRCA genes.

METHODS AND RESULTS

Data from a range of bioinformatic, genetic, and histopathological analyses, and in vitro functional assays indicated that the 1708E variant was associated with the disruption of different cellular functions of BRCA1. In transient transfection experiments in T47D and 293T cells, the 1708E product was mislocalised to the cytoplasm and induced centrosome amplification in 293T cells. The 1708E variant also failed to transactivate transcription of reporter constructs in mammalian transcriptional transactivation assays. In contrast, the 1706A variant displayed a phenotype comparable to wildtype BRCA1 in these assays. Consistent with functional data, tumours from 1708E carriers showed typical BRCA1 pathology, while tumour material from 1706A carriers displayed few histopathological features associated with BRCA1 related tumours.

CONCLUSIONS

A comprehensive range of genetic, bioinformatic, and functional analyses have been combined for the characterisation of BRCA1 unclassified sequence variants. Consistent with the functional analyses, the combined odds of causality calculated for the 1706A variant after multifactorial likelihood analysis (1:142) indicates a definitive classification of this variant as "benign". In contrast, functional assays of the 1708E variant indicate that it is pathogenic, possibly through subcellular mislocalisation. However, the combined odds of 262:1 in favour of causality of this variant does not meet the minimal ratio of 1000:1 for classification as pathogenic, and A1708E remains formally designated as unclassified. Our findings highlight the importance of comprehensive genetic information, together with detailed functional analysis for the definitive categorisation of unclassified sequence variants. This combination of analyses may have direct application to the characterisation of other unclassified variants in BRCA1 and BRCA2.

A growth hormone agonist produced by targeted mutagenesis at binding site 1. Evidence that site 1 regulates bioactivity

Growth hormone (GH) is believed to signal by dimerizing its receptor through two binding sites on the hormone. Previous attempts to increase the biopotency of GH by increasing its site 1 affinity have been unsuccessful, which has led to a bias toward engineering site 2 interactions in the quest for creation of super agonists. Here we report that increasing site 1 affinity can markedly increase proliferative bioactivity in FDC-P1 cells expressing full-length GHR. In contrast, we find three site 1 mutants with affinities for site one similar to or greater than wild type GH, which have markedly decreased bioactivity. Through crystal structure analysis of the receptor interactive regions of these GH analogues, we are able to suggest why previous mutagenesis on human GH failed to improve biopotency, and thus provide a new avenue for GH and cytokine agonist design.

The role of periodontal mechanoreceptors in mastication

The aim of this review is to discuss what is known about the reflex control of the human masticatory system by the periodontal mechanoreceptors and to put forward a method for standardised investigation. To deliver mechanical stimulus in a reproducible way, the following precautions are suggested: the stimulus should be brought into secure contact with the area of stimulation, and slack between the probe and the area to be stimulated should be taken up by the application of a preload. It is also important to ensure that there is minimal simultaneous activation of receptor systems other than the periodontal mechanoreceptors. It is also necessary to standardise the method for recording and analysing the response.

Establishment of paediatric biochemical reference intervals

Background: The standard method for the determination of reference values in a population by testing a number of healthy volunteers is difficult within the paediatric age group; this study explores an alternative approach.

Methods: Biochemical blood test results collected by the Woman's and Children's Hospital over a 1 year period were used and the data selected to ensure, as far as possible, that the results were from patients who were 'healthy'. This was achieved using various selection criteria, such as the exclusion of patients with more than one test episode. Some of the data were skewed, making standard statistical approaches difficult. In such cases, transformations were used to ensure that the resulting information had a distribution that was approximately Gaussian.

Results: Data from different biochemical tests covering both genders and ages in the range 0-18 years were collected; this included more than 250 000 laboratory test results. After elimination of non-representative data and tests with insufficient results, there were approximately 23 500 results covering almost 3000 individuals and 16 different biochemical tests. There were no results from very young children (< 1 year) after the data selection process; hence the derivation of reference values from that age group was not possible.

Conclusions: This approach permitted better delineation of reference intervals for common biochemical tests performed on paediatric patients than is currently readily available. In addition, some important benchmarks for transformation of medical data have been found.

Signal transduction by the growth hormone receptor

It has been proposed that dimerization of identical receptor subunits by growth hormone (GH) is the mechanism of signal transduction across the cell membrane. We present here data with analogs of porcine GH (pGH), with GH receptors (GHR) mutated in the dimerization domain and with monoclonal antibodies to the GHR which indicate that dimerization is necessary but not sufficient for transduction. We also report nuclear uptake of GH both in vivo and in vitro, along with nuclear localization of the receptor and GH-binding protein (GHBP). This suggests that GH acts directly at the nucleus, and one possible target for this action is a rapid increase in transcription of C/EBP delta seen in 3T3-F442A cells in response to GH. This tyrosine kinase-dependent event may be an archetype for induction of other immediate early gene transcription factors which then interact to determine the programming of the subsequent transcriptional response to GH.

Photoreceptor processing improves salience facilitating small target detection in cluttered scenes

Target detection amidst clutter is a challenging task for both natural and artificial vision, yet one solved at the level of neurons in the 3rd optic ganglion of insects. These neurons are capable of responding to the motion of small objects, even against complex moving backgrounds. While the basic physiology has been investigated, little is known about how these cells are able to reject background motion while robustly responding to such small stimuli. By recording intracellularly from fly photoreceptors stimulated with natural image sequences containing a target viewed against a complex moving background, we show that the process of target detection begins at the earliest stages of vision. The temporal processing by photoreceptors alone, in the absence of any spatial interactions, improved the discrimination of targets (essentially a spatial task) by around 70%. This enhancement of target salience can be explained by elaborate models of photoreceptor temporal non-linear dynamics. The application of the functional principals outlined in this work could be utilized in areas such as robotics and surveillance, medical imaging, or astronomy, anywhere it is necessary to detect a small item from a cluttered surround.

Response of human jaw muscles to axial stimulation of the incisor

The role of periodontal mechanoreceptors (PMRs) in the reflex control of the jaw muscles has thus far been mainly derived from animal studies. To date, the work that has been done on humans has been limited and confined to orthogonal stimulation of the labial surface of the tooth. The purpose of this study was to investigate the response of the masseter and digastric muscles in humans to controlled axial stimulation of the upper left central incisor, both before and during a local anaesthetic block of the PMRs. Ten neurologically normal young adult females were tested, each on two separate occasions to confirm the reproducibility of the results. It was found that the reflex response in the masseter was modulated by the rate of rise of the stimulus used and, to a lesser degree, the level of background muscle activity. There was little detectable change in the activity of the digastric muscle under the tested conditions and what was found could be attributed to cross-talk with the masseter. The reflex responses obtained were significantly different between subjects; however retesting the same subject on a different occasion yielded similar results. The results indicate that the most common response of the masseter muscle to brisk axial stimulation of the incisor is a reflex inhibition at 20 ms, followed by a late excitation at 44 ms. However, it is possible that this late excitation could be due to delayed action potentials and hence be artefactual. As the application of a local anaesthetic block removed or significantly reduced both of these responses, it was concluded that they originated from the PMRs. Unlike during orthogonal stimulation, slowly rising stimuli did not produce any excitatory reflex activity. This indicated a difference in jaw reflexes to forces applied in different directions, possibly due to the activation of different receptor types when stimulating the tooth in either the orthogonal or axial directions.

Periodontal anaesthesia reduces common 8 Hz input to masseters during isometric biting

During isometric contractions of the jaw muscles, oscillations in the rectified masseteric EMG record that are coherent with the mandibular force output are evident at ~8 Hz. We have investigated the load dependence of these oscillations under both force and EMG feedback conditions and the extent to which these oscillations are coupled bilaterally in the jaw muscles. We further investigated the extent to which afferent information arising from the periodontium during biting influenced the extent of ~8 Hz EMG tremor and the bilateral coupling between masseters at this frequency. Using coherence analysis we have shown that a significant load-independent coupling of EMG between the closing muscles of the jaw occurs at ~8 Hz as a result of common ~8 Hz input to the masseters. This common input is significantly reduced when afferent information from the periodontium is blocked. These results suggest that afferent information arising from the periodontium enhances the expression of peripheral tremulous activity, which may be important for optimising the response of the jaw to changes in forces occurring between the teeth.

A device for investigating neuromuscular control in the human masticatory system

A new apparatus has been developed to study the control of mastication in humans. The subject places his/her teeth on fixed upper and mobile lower bite plates; the device then enables opening and closing movements of the lower jaw against a controlled resistance. It is also possible to vary the number of teeth in contact with the device during an experiment from the entire dental arcade to a single tooth. The specially designed lower bite plate is dynamic and allows for both rotation and translation of the lower jaw during movement, thus, permitting the natural curvilinear trajectory of the jaw. The lower bite plate can follow chewing initiated by the subject without resisting the movement ('no force' mode) via a dedicated microprocessor controlled compensation mechanism. Another function of the device is to inject a constant predetermined load onto the lower bite plate so that the subject 'chews' against a fixed resistance simulating rapidly yielding food bolus ('fixed force' mode). The device can be programmed to increase or decrease the force during the closing or opening phase of chewing by feeding the position information into the force compensation system so both position and force change in parallel, hence, simulating a bite onto a non-yielding, or sticky, food bolus ('normal chewing' mode). By use of a jaw position compensation mechanism, the device can actively move the lower jaw, following any imposed position pattern ('position controlled' mode). The chewing simulator also has a mode that holds the position at a fixed level and allows the force to change ('position hold' mode). Furthermore, the device can inject additional rapid or slow forces or displacements onto the lower bite plate in order to elicit reflexes so that the response of jaw muscles to such stimuli can be examined at various jaw positions, force levels, phases of motion and velocities. The different modes of the apparatus can be used to study the operation and feedback control of human mastication; in particular whether modulations in jaw muscle activity and reflexes are due to changes in force, velocity, position, chewing cycle phase or a combination of these factors.

Response of human jaw muscles to axial stimulation of a molar tooth

The reflexes of the main jaw-closer muscles (masseter and anterior temporalis) on both sides of the jaw were investigated using surface electromyography to observe reflex activity following mechanical stimulation of the 1st right upper-molar tooth at various forces under a number of levels of jaw-muscle activity. As with analogous studies performed on the incisor, three distinct reflex events were identified in the EMG before the earliest conscious subject reaction: early excitation, inhibition and late excitation. However, contrary to observations found during studies on the incisor, excitation, not inhibition was the primary reflex response. The application of a local anaesthetic block around the stimulated molar showed that the primary agents in eliciting the observed reflexes were not contained within the periodontium of the stimulated tooth. A diminished representation of periodontal mechanoreceptors around the molar teeth and more elaborate root structures, hence a more solid connection to the jaw and consequently less tooth movement, were deemed the likely reason for the distinction between the reflex responses of the incisal and molar regions. In addition to the reflex studies, the minimum reaction time of a number of subjects was determined to permit the distinction of a reflex event and an event that could be a conscious subject reaction. It was found that the reaction time of the temporalis muscles was significantly shorter than those of the masseter, while no significant difference was found between the left and right sides. Overall, the data showed that the presence or absence of background muscle activity and subject variability were the main causes of changes in the reflex response, provided the level of the stimulus was greater than 3 N. The application of local anaesthetic had no impact on the reflexes evoked.

Evidence for involvement of the carboxy terminus of helix 1 of growth hormone in receptor binding: use of charge reversal mutagenesis to account for calcium dependence of binding and for design of higher affinity analogues

In this study we have demonstrated that the C-terminus of helix 1 of porcine GH (pGH) is a receptor-interactive region, thus extending the current binding site model of GH. This was achieved by introducing charge reversal mutations into this region of pGH, which influenced receptor affinity and Ca2+ dependence of binding. The first mutant (R34E pGH, conversion of Arg 34 to Glu) introduced a putative Ca2+ binding site which is present in human GH (hGH) [Barnard et al. (1989) J. Theor. Biol. 140, 355-367] and sits opposite E220 of receptor subunit 1. This mutant exhibited increased Ca2+ dependence of receptor binding but even at optimal Ca2+ did not display higher than wild-type affinity. Introduction of a second Ca2+ binding site adjacent to the first by a second charge reversal (K30E R34E pGH) further increased Ca2+ dependence of binding and also increased affinity for the rabbit GH receptor (2.4 +/- 0.4)-fold relative to wild-type pGH at optimal Ca2+. Equilibrium dialysis and Scatchard analysis of binding of 45Ca2+ to pGH and K30E R34E pGH revealed two Ca2+ binding sites on wild-type pGH and an additional two Ca2+ binding sites on the K30E R34E pGH mutant (Kd 0.5-0.8 mM), as predicted. A third partial charge reversal mutant in the fourth helix (H170D) also led to enhanced Ca2+ dependence of binding, supporting our proposal that E34 and D170 are responsible for the Ca2+ dependence of hGH binding to the rabbit GH receptor. Examination of the crystal structure shows that E34 and D170 are in close proximity and would interact repulsively with a cluster of acidic residues on the receptor consisting of E126, E127, and E220 unless neutralized by Ca2+ or an introduced basic residue. Accordingly, charge reversal at the adjacent pGH residue E33 (E33K pGH) led to a Ca2+ independent (3.0 +/- 0.4)-fold increase in affinity of binding. As well as extending the binding site model of GH, these studies provide a mechanistic explanation for the unique Ca2+ dependence of hGH binding to the rabbit GH receptor. They also indicate that charge reversal can be used to design higher affinity GH analogues and could assist in the mapping of interactive regions in ligand-receptor complexes generally.

Implementation of an elaborated neuromorphic model of a biological photoreceptor

We describe here an elaborated neuromorphic model based on the photoreceptors of flies and realised in both software simulation and hardware using discrete circuit components. The design of the model is based on optimisations and further elaborations to the mathematical model initially developed by van Hateren and Snippe that has been shown to accurately simulate biological responses in simulations under both steady-state and limited dynamic conditions. The model includes an adaptive time constant, nonlinear adaptive gain control, logarithmic saturation and a nonlinear adaptive frequency response mechanism. It consists of a linear phototransduction stage, a dynamic filter stage, two divisive feedback loops and a static nonlinearity. In order to test the biological accuracy of the model, impulses and step responses were used to test and evaluate the steady-state characteristics of both the biological (fly) and artificial (new neuromorphic model) photoreceptors. These tests showed that the model has faithfully captured most of the essential characteristics of the insect photoreceptor cells. The model showed a decreasing response to impulsive stimuli when the background intensity was increased, indicating that the circuit adapted to background luminance in order to improve the overall operating range and better encode the contrast of the stimulus rather than luminance. The model also showed the same change in its frequency response characteristics as the biological photoreceptors over a luminance range of 70,000 cd/m(2), with the corner frequency of the circuit ranging from 10 to 90 Hz depending on the current state of adaptation. Complex naturalistic experiments have also further proven the robustness of the model to perform in real-world scenario. The model showed great correlation to the biological photoreceptors with an r (2) value exceeding 0.83. Our model could act as an excellent platform for future experiments that could be carried out in scenarios where in vivo intracellular recording from biological photoreceptors would be impractical or impossible, or as a front-end for an artificial imaging system.

A Survey of Underwater Acoustic Data Classification Methods Using Deep Learning for Shoreline Surveillance

This paper presents a comprehensive overview of current deep-learning methods for automatic object classification of underwater sonar data for shoreline surveillance, concentrating mostly on the classification of vessels from passive sonar data and the identification of objects of interest from active sonar (such as minelike objects, human figures or debris of wrecked ships). Not only is the contribution of this work to provide a systematic description of the state of the art of this field, but also to identify five main ingredients in its current development: the application of deep-learning methods using convolutional layers alone; deep-learning methods that apply biologically inspired feature-extraction filters as a preprocessing step; classification of data from frequency and time–frequency analysis; methods using machine learning to extract features from original signals; and transfer learning methods. This paper also describes some of the most important datasets cited in the literature and discusses data-augmentation techniques. The latter are used for coping with the scarcity of annotated sonar datasets from real maritime missions.

Mandibular physiological tremor is reduced by increasing-force ramp contractions and periodontal anaesthesia

We have previously shown that the application of anaesthesia to periodontal mechanoreceptors (PMRs) dramatically reduces the 6-12 Hz physiological tremor (PT) in the human mandible during constant isometric contractions where visual feedback is provided. This current study shows that during a ramp contraction where force is slowly increased, the amplitude of mandibular PT is almost five times smaller on average than when the same force ramp is performed in reverse, i.e. force is slowly decreased. This smaller tremor is associated with a higher mean firing rate of motor units (MUs) as measured by the sub-30 Hz peak in the multi-unit power spectrum. The decrease in the amplitude of PT following PMR anaesthetisation is associated in some instances with a similar increase in the overall firing rate; however this change does not match the diminution of tremor. The authors postulate that the decrease in mandibular PT during increasing force ramps may be due to a change in the mean firing rate of the MUs. The change in tremor seen during PMR anaesthetisation may in part be due to a similar mechanism; however other factors must also contribute to this.

Detecting Small Size and Minimal Thermal Signature Targets in Infrared Imagery Using Biologically Inspired Vision

Thermal infrared imaging provides an effective sensing modality for detecting small moving objects at long range. Typical challenges that limit the efficiency and robustness of the detection performance include sensor noise, minimal target contrast and cluttered backgrounds. These issues become more challenging when the targets are of small physical size and present minimal thermal signatures. In this paper, we experimentally show that a four-stage biologically inspired vision (BIV) model of the flying insect visual system have an excellent ability to overcome these challenges simultaneously. The early two stages of the model suppress spatio-temporal clutter and enhance spatial target contrast while compressing the signal in a computationally manageable bandwidth. The later two stages provide target motion enhancement and sub-pixel motion detection capabilities. To show the superiority of the BIV target detector over existing traditional detection methods, we perform extensive experiments and performance comparisons using high bit-depth, real-world infrared image sequences of small size and minimal thermal signature targets at long ranges. Our results show that the BIV target detector significantly outperformed 10 conventional spatial-only and spatiotemporal methods for infrared small target detection. The BIV target detector resulted in over 25 dB improvement in the median signal-to-clutter-ratio over the raw input and achieved 43% better detection rate than the best performing existing method.

EMG, force and discharge rate analysis of human jaw reflexes in response to axial stimulation of the incisor

Reflex studies utilising controlled stimulation along the long axis of human incisors are relatively new, and the effects that various stimulus parameters have on the elicited reflexes are not fully understood. Twelve subjects were recruited to determine the effects that contraction level, stimulus force and amount of constant force applied between stimuli have on the reflex response of the masseter muscle. Multi-unit intramuscular electromyogram (EMG) was recorded alongside surface EMG to determine whether any differences existed between the two. Furthermore, cumulative peri-stimulus "dischargegrams" were constructed to determine whether events seen in the EMG corresponded to changes in the discharge rates of the underlying motor units. Axial stimulation of the incisor induced a response in the EMG comprising of peak-trough-peak, with the trough being the most dominant. The bite force record showed only a reduction (relaxation) in response to the stimulation. The most significant experimental factor affecting the reflex occurrence and strength was the stimulus force. Although the latency, duration and occurrence rates were not significantly different, the strength of the responses was greater in intramuscular recordings compared with the surface recordings. Discharge rate analysis showed that approximately two-thirds of the late peaks detected in the EMG did not correspond to an increase in the discharge rates of the underlying units; hence they were due to the clustering of action potentials following the trough and not to a change in the membrane potential of the motoneurone. It was also found that the duration of the trough, as seen by the reduced cumulative discharge rate of the underlying units, was longer than indicated by the EMG.

Jaw movement alters the reaction of human jaw muscles to incisor stimulation

The changes in the minimum time to consciously react (reaction time) and the order of jaw muscle recruitment to precisely controlled axial stimulation of the incisors during controlled jaw movements are not known. To this end, ten subjects were recruited to investigate the reaction time of bilateral temporalis and masseter muscles and bite force. Stimuli were delivered axially to the upper central incisors during active jaw closing and opening, and under static conditions. The results showed that the reaction time was increased an average of 35% during both jaw opening and closing movements when compared with static jaw conditions. The left temporalis was recruited approximately 10 ms before the right temporalis, whereas no significant side differences were found between the masseter muscles. The masseter muscles were recruited an average of 20 ms before the temporalis muscles during jaw closing, but no difference existed during opening. Under static conditions the reaction time in the bite force was approximately 16 ms longer than the left temporalis, but was not significantly different from the reaction time of any of the other muscles, indicating that, under the static conditions tested, the left temporalis was more often responsible for initiation of the mechanical reactions in the jaw. Because of active compensation, no force measurements were made during jaw movement. This study is a prerequisite for investigations into the modulation of reflexes during jaw movement, because a response to a stimulus commencing after the minimum reaction time may not be entirely reflex in origin.

Developing a Machine-Learning 'Smart' PCR Thermocycler, Part 1: Construction of a Theoretical Framework

The use of PCR is widespread in biological fields. Some fields, such as forensic biology, push PCR to its limits as DNA profiling may be required in short timeframes, may be produced from minute amounts of starting material, and may be required to perform in the presence of inhibitory compounds. Due to the extreme high-throughput of samples using PCR in forensic science, any small improvement in the ability of PCR to address these challenges can have dramatic effects for the community. At least part of the improvement in PCR performance could potentially come by altering PCR cycling conditions. These alterations could be general, in that they are applied to all samples, or they could be tailored to individual samples for maximum targeted effect. Further to this, there may be the ability to respond in real time to the conditions of PCR for a sample and make cycling parameters change on the fly. Such a goal would require both a means to track the conditions of the PCR in real time, and the knowledge of how cycling parameters should be altered, given the current conditions. In Part 1 of our work, we carry out the theoretical groundwork for the ambitious goal of creating a smart PCR system that can respond appropriately to features within individual samples in real time. We approach this task using an open qPCR instrument to provide real-time feedback and machine learning to identify what a successful PCR 'looks like' at different stages of the process. We describe the fundamental steps to set up a real-time feedback system, devise a method of controlling PCR cycling conditions from cycle to cycle, and to develop a system of defining PCR goals, scoring the performance of the system towards achieving those goals. We then present three proof-of-concept studies that prove the feasibility of this overall method. In a later Part 2 of our work, we demonstrate the performance of the theory outlined in this paper on a large-scale PCR cycling condition alteration experiment. The aim is to utilise machine learning so that throughout the process of PCR automatic adjustments can be made to best alter cycling conditions towards a user-defined goal. The realisation of smart PCR systems will have large-scale ramifications for biological fields that utilise PCR.

Evaluation of Automated Object-Detection Algorithms for Koala Detection in Infrared Aerial Imagery

Effective detection techniques are important for wildlife monitoring and conservation applications and are especially helpful for species that live in complex environments, such as arboreal animals like koalas (Phascolarctos cinereus). The implementation of infrared cameras and drones has demonstrated encouraging outcomes, regardless of whether the detection was performed by human observers or automated algorithms. In the case of koala detection in eucalyptus plantations, there is a risk to spotters during forestry operations. In addition, fatigue and tedium associated with the difficult and repetitive task of checking every tree means automated detection options are particularly desirable. However, obtaining high detection rates with minimal false alarms remains a challenging task, particularly when there is low contrast between the animals and their surroundings. Koalas are also small and often partially or fully occluded by canopy, tree stems, or branches, or the background is highly complex. Biologically inspired vision systems are known for their superior ability in suppressing clutter and enhancing the contrast of dim objects of interest against their surroundings. This paper introduces a biologically inspired detection algorithm to locate koalas in eucalyptus plantations and evaluates its performance against ten other detection techniques, including both image processing and neural-network-based approaches. The nature of koala occlusion by canopy cover in these plantations was also examined using a combination of simulated and real data. The results show that the biologically inspired approach significantly outperformed the competing neural-network- and computer-vision-based approaches by over 27%. The analysis of simulated and real data shows that koala occlusion by tree stems and canopy can have a significant impact on the potential detection of koalas, with koalas being fully occluded in up to 40% of images in which koalas were known to be present. Our analysis shows the koala's heat signature is more likely to be occluded when it is close to the centre of the image (i.e., it is directly under a drone) and less likely to be occluded off the zenith. This has implications for flight considerations. This paper also describes a new accurate ground-truth dataset of aerial high-dynamic-range infrared imagery containing instances of koala heat signatures. This dataset is made publicly available to support the research community.