title: Development of a non-lethal biopsy technique for estimating total tetrodotoxin concentrations in the grey side-gilled sea slug Pleurobranchaea maculata

authors: Khor, Serena

subjects: Biopsy

abstract: High concentrations of tetrodotoxin (TTX) have been detected in some New Zealand populations of Pleurobranchaea maculata (grey side-gilled sea slug). Within toxic populations there is significant variability in TTX concentrations among individuals, with up to 60-fold differences measured. This variability has led to challenges when conducting controlled laboratory experiments. The current method for assessing TTX concentrations within P. maculata is lethal, thus multiple individuals must be harvested at each sampling point to produce statistically meaningful data. In this study a method was developed for taking approximately 200 mg tissue biopsies using a TemnoEvolution® 18G × 11 cm Biopsy Needle inserted transversely into the foot. Correlation between the TTX concentrations in the biopsy sample and total TTX levels and in individual tissues were assessed. Six P. maculata were biopsied twice (nine days apart) and each individual was frozen immediately following the second sampling. Tetrodotoxin concentrations in biopsy samples and in the gonad, stomach, mantle and the remaining combined tissues and fluids were measured using liquid chromatography-mass spectrometry. Based on the proportional weight of the organs/tissues a total TTX concentration for each individual was calculated. There were strong correlations between biopsy TTX concentrations and the total (r2 = 0.88), stomach (r2 = 0.92) and gonad (r2 = 0.83) TTX concentrations. This technique will enable more robust laboratory studies to be undertaken, thereby assisting in understanding TTX kinetics, ecological function and origin within P. maculata.

text: Development of a non-lethal biopsy technique for estimating total tetrodotoxin concentrations in the grey side-gilled sea slug Pleurobranchaea maculata High concentrations of tetrodotoxin (TTX) have been detected in some New Zealand populations of Pleurobranchaea maculata (grey side-gilled sea slug). Within toxic populations there is significant variability in TTX concentrations among individuals, with up to 60-fold differences measured. This variability has led to challenges when conducting controlled laboratory experiments. The current method for assessing TTX concentrations within P. maculata is lethal, thus multiple individuals must be harvested at each sampling point to produce statistically meaningful data. In this study a method was developed for taking approximately 200 mg tissue biopsies using a TemnoEvolution® 18G × 11 cm Biopsy Needle inserted transversely into the foot. Correlation between the TTX concentrations in the biopsy sample and total TTX levels and in individual tissues were assessed. Six P. maculata were biopsied twice (nine days apart) and each individual was frozen immediately following the second sampling. Tetrodotoxin concentrations in biopsy samples and in the gonad, stomach, mantle and the remaining combined tissues and fluids were measured using liquid chromatography-mass spectrometry. Based on the proportional weight of the organs/tissues a total TTX concentration for each individual was calculated. There were strong correlations between biopsy TTX concentrations and the total (r2 = 0.88), stomach (r2 = 0.92) and gonad (r2 = 0.83) TTX concentrations. This technique will enable more robust laboratory studies to be undertaken, thereby assisting in understanding TTX kinetics, ecological function and origin within P. maculata.

year: 2013

title: Investigation of jitter on full-field amplitude modulated continuous wave time-of-flight range imaging cameras

authors: Anthonys, Gehan

subjects: jitter

abstract: The time-of-flight (ToF) range imaging cameras indirectly measure the time taken from the modulation light source to the scene and back to the camera and it is this principle that is used in depth cameras to perform depth measurements. This thesis is focused on ToF cameras that are based on the amplitude modulated continuous wave (AMCW) lidar techniques which measure the phase difference between the emitted and reflected light signals. Due to their portable size, feasible design, low weight and low energy consumption, these cameras have high demand in many applications. Commercially available AMCW ToF cameras have relatively high noise levels due to electronic sources such as shot noise, reset noise, amplifier noise, crosstalk, analogue to digital converters quantization and multipath light interference. Many noise sources in these cameras such as harmonic contamination, non-linearity, multipath interferences and light scattering are well investigated. In contrast, the effect of electronic jitter as a noise source in ranging cameras is barely studied.

Jitter is defined to be any timing movement with reference to an ideal signal. An investigation of the effect of jitter on range imaging is important because timing errors potentially could cause errors in measuring phase, thus in range. The purpose of this research is to investigate the effect of jitter on range measurement in AMCW ToF range imaging. This is achieved by three main contributions: a development of a common algorithm for measurement of the jitter present in signals from depth cameras, secondly the proposal of a cost effective alternative method to measure jitter by using a software defined radio receiver, and finally an analysis of the influence of jitter on range measurement. 

Among the three contributions of this thesis, first, an algorithm for jitter extraction of a signal without access to a reference clock signal is proposed. The proposed algorithm is based upon Fourier analysis with signal processing techniques and it can be used for real time jitter extraction on a modulated signal with any kind of shape (sinusoidal, triangular, rectangular). The method is used to measure the amount of jitter in the light signals of two AMCW ToF range imaging cameras, namely, MESA Imaging SwissRanger 4000 and SoftKinetic DepthSense 325. Periodic and random jitter were found to be present in the light sources of both cameras with the MESA camera notably worse with random jitter of (159.6 +/- 0.1) ps RMS in amplitude.

Next, in a novel approach, an inexpensive software defined radio (SDR) USB dongle is used with the proposed algorithm to extract the jitter in the light signal of the above two ToF cameras. This is a cost effective alternative to the expensive real-time medium speed digital oscilloscope. However, it is shown that this method has some significant limitations, (1) it can measure the jitter only up to half of the intermediate-frequency obtained from the down shift of the amplified radio frequency with the local oscillator which is less than the Nyquist frequency of the dongle and (2) if the number of samples per cycle captured from this dongle is not sufficient then the jitter extraction  does not succeed since the signal is not properly (smoothly) represented.

Finally, the periodic and random jitter influence on range measurements made with AMCW range imaging cameras are studied. An analytical model for the periodic jitter on the range measurements under the heterodyne and homodyne operations in AMCW ToF range imaging cameras is obtained in the frequency domain. The analytical model is tested through simulated data with various parameters in the system. The product of angular modulation frequency of the camera and the amplitude of the periodic jitter is a characteristic parameter for the phase error due to the presence of periodic jitter. We found that for currently available AMCW cameras (modulation frequency less than 100 MHz), neither periodic nor random jitter has a measurable effect on range measurement. But with modulation frequency increases and integration period decreases likely in the near future, periodic jitter may have a measurable detection affect on ranging.

The influence of random jitter is also investigated by obtaining an analytical model based on stochastic calculus by using fundamental statistics and Fourier analysis. It is assumed that the random jitter  follows the Gaussian distribution. Monte Carlo simulation is performed on the model obtained for a 1 ms integration period. We found increasing the modulation frequency above approximately 400 MHz with random jitter of 140 ps has a measurable affect on ranging.

text: Investigation of jitter on full-field amplitude modulated continuous wave time-of-flight range imaging cameras The time-of-flight (ToF) range imaging cameras indirectly measure the time taken from the modulation light source to the scene and back to the camera and it is this principle that is used in depth cameras to perform depth measurements. This thesis is focused on ToF cameras that are based on the amplitude modulated continuous wave (AMCW) lidar techniques which measure the phase difference between the emitted and reflected light signals. Due to their portable size, feasible design, low weight and low energy consumption, these cameras have high demand in many applications. Commercially available AMCW ToF cameras have relatively high noise levels due to electronic sources such as shot noise, reset noise, amplifier noise, crosstalk, analogue to digital converters quantization and multipath light interference. Many noise sources in these cameras such as harmonic contamination, non-linearity, multipath interferences and light scattering are well investigated. In contrast, the effect of electronic jitter as a noise source in ranging cameras is barely studied.

Jitter is defined to be any timing movement with reference to an ideal signal. An investigation of the effect of jitter on range imaging is important because timing errors potentially could cause errors in measuring phase, thus in range. The purpose of this research is to investigate the effect of jitter on range measurement in AMCW ToF range imaging. This is achieved by three main contributions: a development of a common algorithm for measurement of the jitter present in signals from depth cameras, secondly the proposal of a cost effective alternative method to measure jitter by using a software defined radio receiver, and finally an analysis of the influence of jitter on range measurement. 

Among the three contributions of this thesis, first, an algorithm for jitter extraction of a signal without access to a reference clock signal is proposed. The proposed algorithm is based upon Fourier analysis with signal processing techniques and it can be used for real time jitter extraction on a modulated signal with any kind of shape (sinusoidal, triangular, rectangular). The method is used to measure the amount of jitter in the light signals of two AMCW ToF range imaging cameras, namely, MESA Imaging SwissRanger 4000 and SoftKinetic DepthSense 325. Periodic and random jitter were found to be present in the light sources of both cameras with the MESA camera notably worse with random jitter of (159.6 +/- 0.1) ps RMS in amplitude.

Next, in a novel approach, an inexpensive software defined radio (SDR) USB dongle is used with the proposed algorithm to extract the jitter in the light signal of the above two ToF cameras. This is a cost effective alternative to the expensive real-time medium speed digital oscilloscope. However, it is shown that this method has some significant limitations, (1) it can measure the jitter only up to half of the intermediate-frequency obtained from the down shift of the amplified radio frequency with the local oscillator which is less than the Nyquist frequency of the dongle and (2) if the number of samples per cycle captured from this dongle is not sufficient then the jitter extraction  does not succeed since the signal is not properly (smoothly) represented.

Finally, the periodic and random jitter influence on range measurements made with AMCW range imaging cameras are studied. An analytical model for the periodic jitter on the range measurements under the heterodyne and homodyne operations in AMCW ToF range imaging cameras is obtained in the frequency domain. The analytical model is tested through simulated data with various parameters in the system. The product of angular modulation frequency of the camera and the amplitude of the periodic jitter is a characteristic parameter for the phase error due to the presence of periodic jitter. We found that for currently available AMCW cameras (modulation frequency less than 100 MHz), neither periodic nor random jitter has a measurable effect on range measurement. But with modulation frequency increases and integration period decreases likely in the near future, periodic jitter may have a measurable detection affect on ranging.

The influence of random jitter is also investigated by obtaining an analytical model based on stochastic calculus by using fundamental statistics and Fourier analysis. It is assumed that the random jitter  follows the Gaussian distribution. Monte Carlo simulation is performed on the model obtained for a 1 ms integration period. We found increasing the modulation frequency above approximately 400 MHz with random jitter of 140 ps has a measurable affect on ranging.

year: 2021

title: For staff at the Eastern Institute of Technology, is Ōtātara a placeless geography? Or a geography of significance?

authors: Passey, Emma

subjects: Ōtātara

abstract: This thesis explores the experience of place for a group of tertiary employees in a regional area of New Zealand. Staff based at EIT Hawke’s Bay in Taradale, Napier can see the Ōtātara Pā Reserve from several vantage points on campus, and often visit because of its immediate proximity. Originally, joined and now adjacent, the cultural significance of this land for Māori over some centuries prior to Pākehā settlement, is still being uncovered. Through a series of interviews, the historical significance of this place is joined with the experiences of staff in being in this space. A range of meanings including belonging, attachment and sense of location were described by participants, showing the development over time of threads of connection for themselves, family, community and also staff members.

Ideas in the literature of place were considered including attachment to meaningful locations and landscape. A particular interest in the thesis was bringing this more general literature into focus for a New Zealand place, which has substantial Māori history connections including for participants of both Māori and Pākehā backgrounds. Several methodological issues were discussed within a series of interviews including cultural appropriateness and representation. The researchers transition from an English cultural upbringing, to developing and extending indigenous landscape knowledge, illustrates the changing recognition and involvement in an increasingly bi-cultural New Zealand, and demonstrates the implications of this in understanding place attachment.

Findings from this research were organised in three main chapters. The first, recounted historical material about Ōtātara, Māori and Pākehā times, exploring ideas of place and belonging. It also provided a natural anchor for the second and third chapters, which reported the findings of EIT staff enjoying being within, and feeling the presence of that history. Several themes emerged and were summarised as embodied landscape experiences, and the intriguing dimensions of social relationships and place for these tertiary staff.
Place is important across the social sciences as it is for other disciplines. It evokes on the one hand aspirations and ideals of an aesthetic and spiritual nature but at the same time, reminds human beings of their literal and biological being in time and space. The present study has contributed to this wider narrative by looking at one example and in one national bi-cultural setting.

The question posed at the start of the thesis considered whether EIT staff view Ōtātara as a place of significance or a geography which does not matter. The historical connections and physical closeness between EIT and Ōtātara, mean that the Institution and the landscape are inextricably linked. People are equally bonded to this place through culture and lived experiences. Often unconscious or incidental associations are handed down through the generations, within the organisation and throughout the wider community.
How we now occupy this place in a modern world, how we share the (hi)stories and become authors of new ones, will have a profound influence on the ways that staff continue to connect and develop feelings of belonging. Related to this, an idea about an institutional-wide hīkoi around the boundaries of the campus and Ōtātara is offered as an addendum. Our responsibility as educators is to signal to future generations that this is a landscape of significance ensuring that Ōtātara continues to be acknowledged as a taonga for EIT employees, and that it is nurtured in the same way as it nurtures us.

text: For staff at the Eastern Institute of Technology, is Ōtātara a placeless geography? Or a geography of significance? This thesis explores the experience of place for a group of tertiary employees in a regional area of New Zealand. Staff based at EIT Hawke’s Bay in Taradale, Napier can see the Ōtātara Pā Reserve from several vantage points on campus, and often visit because of its immediate proximity. Originally, joined and now adjacent, the cultural significance of this land for Māori over some centuries prior to Pākehā settlement, is still being uncovered. Through a series of interviews, the historical significance of this place is joined with the experiences of staff in being in this space. A range of meanings including belonging, attachment and sense of location were described by participants, showing the development over time of threads of connection for themselves, family, community and also staff members.

Ideas in the literature of place were considered including attachment to meaningful locations and landscape. A particular interest in the thesis was bringing this more general literature into focus for a New Zealand place, which has substantial Māori history connections including for participants of both Māori and Pākehā backgrounds. Several methodological issues were discussed within a series of interviews including cultural appropriateness and representation. The researchers transition from an English cultural upbringing, to developing and extending indigenous landscape knowledge, illustrates the changing recognition and involvement in an increasingly bi-cultural New Zealand, and demonstrates the implications of this in understanding place attachment.

Findings from this research were organised in three main chapters. The first, recounted historical material about Ōtātara, Māori and Pākehā times, exploring ideas of place and belonging. It also provided a natural anchor for the second and third chapters, which reported the findings of EIT staff enjoying being within, and feeling the presence of that history. Several themes emerged and were summarised as embodied landscape experiences, and the intriguing dimensions of social relationships and place for these tertiary staff.
Place is important across the social sciences as it is for other disciplines. It evokes on the one hand aspirations and ideals of an aesthetic and spiritual nature but at the same time, reminds human beings of their literal and biological being in time and space. The present study has contributed to this wider narrative by looking at one example and in one national bi-cultural setting.

The question posed at the start of the thesis considered whether EIT staff view Ōtātara as a place of significance or a geography which does not matter. The historical connections and physical closeness between EIT and Ōtātara, mean that the Institution and the landscape are inextricably linked. People are equally bonded to this place through culture and lived experiences. Often unconscious or incidental associations are handed down through the generations, within the organisation and throughout the wider community.
How we now occupy this place in a modern world, how we share the (hi)stories and become authors of new ones, will have a profound influence on the ways that staff continue to connect and develop feelings of belonging. Related to this, an idea about an institutional-wide hīkoi around the boundaries of the campus and Ōtātara is offered as an addendum. Our responsibility as educators is to signal to future generations that this is a landscape of significance ensuring that Ōtātara continues to be acknowledged as a taonga for EIT employees, and that it is nurtured in the same way as it nurtures us.

year: 2021