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Item Clinical utility of near-infrared spectroscopy in skeletal muscle : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (Sport and Exercise Science) at Massey University, Wellington, New Zealand(Massey University, 2021) Lucero, AdamIntroduction: Near infrared spectroscopy (NIRS) provides for non-invasive assessment of resting skeletal muscle hemodynamic and respiratory responses. However, the interday reliability of skeletal muscle blood flow (mBF) and oxygen consumption (mV̇O2) responses to stressors such as exercise in both healthy and clinical populations has not been established. Moreover, direct comparison of differing NIRS technologies is absent. The purpose of this thesis is three-fold 1) establish a standard protocol for the assessment of resting and exercise skeletal muscle hemodynamics for healthy and clinical populations, 2) compare the reliability of NIRS outcomes in continuous wave (cw) NIRS to the more robust frequency domain (fd) NIRS technology, and 3) assess validity against in-vitro skeletal muscle metabolic parameters. Methods: In the first study, a standard protocol developed to measure mBF, mV̇O2, and perfusion ([tHb]) in the vastus lateralis (VL) at rest and up to 30% of maximum voluntary contraction and mV̇O2 recovery rate constant (k) as an index of muscle oxidative capacity was conducted in twelve healthy adults and was repeated twice within 10 days to establish repeatability. The NIRS measures were conducted using a cw-NIRS device. Secondly, this protocol was repeated in 10, healthy males and 10 non-insulin dependent sedentary males with T2D for characterisation and comparison of outcomes derived from cw-NIRS versus fd-NIRS. Thirdly, cw-NIRS and whole-body oxygen consumption (V̇O2) were measured in 24 men with T2D while performing incremental ramp cycle exercise to volitional exhaustion; in addition, biopsies of the VL were collected. Results: In study 1, mBF and mV̇O2 proportionally increased with intensity (0.55 to 7.68 ml∙min-1∙100ml-1 and 0.05 to 1.86 mlO2∙min-1∙100g-1, respectively) up to 25% MVC where it began to plateau at 30% MVC. For studies 1 and 2, a mBF/mV̇O2 ratio of ~5 was consistent for all exercise stages. For both Healthy and T2D groups, patterns of change and values for mBF and mV̇O2 during exercise were not substantially different between devices and were moderate to highly reproducible (ICC: 0.72-0.98). The mean typical error for exercise mBF and mV̇O2 with 90% Confidence Intervals was 0.41 (0.31-0.59) and 0.38 (0.29-0.55) for ND and T2D, respectively. Substantial differences were seen in ND and T2D, respectively, between CW- and FD-NIRS values for perfusion. Thirdly, the [HHb] primary phase during dynamic exercise was substantially correlated to V̇O2peak while the secondary phase was substantially correlated to measures of mitochondrial function. Conclusion: NIRS can reliably assess mBF and mV̇O2 responses at rest and during low-moderate exercise. The popular cw-NIRS device performed comparably to the more robust fd-NIRS when assessing mBF and mVO2 in both healthy and T2D populations, but cw-NIRS tended to overestimate perfusion, likely due to assumptions of constant scattering. Finally, combining NIRS with external respiration during continuous exercise has potential in investigating barriers to glucose disposal and exercise tolerance in T2D. Taken together, NIRS is a valid tool for applications in research, clinical diagnosis, and therapeutic assessment of skeletal muscle hemodynamics, microvascular, and respiratory plasticity.Item An investigation on the stability of biochar-C in soils and its potential use to mitigate non-CO₂ greenhouse gases using near-infrared (NIR) spectroscopy : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Soil Science at Massey University, Manawatu, New Zealand(Massey University, 2020) Mahmud, Ainul FaizahThe global interest in using biochar for C sequestration-climate mitigation and soil improvement has driven rapid expansion in biochar research to understand its properties and application impacts. The potential for biochar application to increase soil organic carbon (SOC) stocks and its potential agronomic and additional environmental benefits, such as reducing soil nitrous oxide (N₂O) emission, are determined by its stability in the soil, which is dependent on its intrinsic properties and the soil conditions. The inherent properties of biochar are highly influenced by feedstock type and pyrolysis temperature hence, the use of various types of feedstock and pyrolysis technologies leads to uncertainties in predicting the effect of biochar addition to soils. Previous research has established a general assumption that biochar stability is strongly influenced by the type of feedstock used and maximum pyrolysis temperature. Research is required, however, to produce practical and reliable techniques that can be used to verify the reported maximum pyrolysis temperature, regardless of the type of feedstock used and predict the likely stability of the biochar. In addition to the pyrolysis process, the final particle size of the biochar and the method of incorporation into the soil may also influence the ability of the biochar to moderate soil properties and function. With previous research, there is general lack of attention given to these potentially influential parameters when assessing the impact of biochar application to soil. Therefore this thesis evaluates (i) the use of near-infrared (NIR) spectroscopy technique for predicting the maximum pyrolysis temperature of biochar as it is a well-known, non-destructive, and rapid technique for analyzing organic material; (ii) the effect of biochar application, with special attention to biochar particle size and depth of placement, on N₂O soil emission and SOC stocks; and (iii) the integrated use of NIR spectroscopy for SOC measurement. In the first study, we hypothesized that NIR spectroscopy can be used to predict the maximum pyrolysis temperature achieved during biochar production. Eighty-two carbonized materials produced from various feedstock types and pyrolysis conditions with the reported pyrolysis temperature ranged between 220 to 800 °C, were scanned using NIR spectrometer and were used as the calibration set. The NIR calibration model was built by correlating the NIR spectral data with the reported pyrolysis temperature using partial least squares regression (PLSR). A separate sample set (n=20) was compiled using laboratory-produced biochar made from pine wood at pyrolysis temperature ranged from 325 to 723 °C. The calibration model validated using (i) leave-one-out cross-validation (LOO-CV) and (ii) the prediction set, yielded good accuracy (LOO-CV: r²=0.80 and RMSECV:48.8 °C; prediction: r²=0.82 and RMSEP: 57.7 °C). Results obtained in this study have shown that NIR spectroscopy can be used to predict the maximum pyrolysis temperature of biochar and has the potential to be used as a monitoring tool for biochar production. In addition to the first study, the predictive ability of the NIR model was evaluated further. We hypothesized that the variation in feedstock types and pyrolysis processes may affect the predictive performance of the NIR model in predicting the maximum pyrolysis temperature of biochar. Therefore, three sample sets were generated from a total of 82 carbonized materials and its subsets (Set A: n=82; Set B: n=68; Set C: n= 48) and were used for developing three calibration models. The selection of samples for Set B and C was made by reducing the variability associated with production conditions and feedstock type i.e. Set B consist of samples produced by slow pyrolysis and using the same pyrolyzer unit, while for Set C (a subset of Set B), samples produced from “processed feedstocks” were excluded. A separate sample set (n=18) consists of samples produced from animal manure, crop residue, and woody materials were used as the prediction set. This biochar was produced using the slow pyrolysis technique in a laboratory or under relatively high production controlled conditions at temperature ranged from 250 to 550 °C. These calibration models were validated using (i) leave-one-out cross-validation (LOO-CV) and (ii) a prediction set, with the model based on set C gave the best prediction (R2: 0.941; RMSEP: 27.3 °C), followed by the model based on set A (R2: 0.896; RMSEP: 35.6 °C), and set B (R2: 0.928; RMSEP: 37.3 °C). These results indicate that feedstock types have a considerable effect on the performance of the NIR model while the effect of pyrolysis conditions was less pronounced. Thus, data variability from samples needs to be taken into account in developing the NIR calibration model for predicting the maximum pyrolysis temperature of biochar. Before studying the effect of biochar on N₂O soil emission and SOC stocks, the maximum pyrolysis temperature of biochar to be used in the experiment was predicted using the NIR spectroscopy technique. The estimated pyrolysis temperature – after scanning the 3-year old pine wood biochar and using the NIR model developed – was 500 °C, while the reported temperature was 550 °C. A controlled glasshouse study was conducted to investigate the effect of biochar particle size and the impact of soil inversion (through simulated mouldboard ploughing) on N₂O emissions from soils to which cattle urine was applied. We hypothesized that the application of biochar may (i) affect N₂O emissions through changes in soil physical properties, specifically soil aeration and water retention; and (ii) the effects of biochar addition on these properties may differ depending on their particle size (e.g., a larger particle size may increase soil aeration whereas a smaller particle size may clog pores), and their placement in soil (e.g., the incorporation of a large particle size-biochar at depth may promote water movement from the top layer and increase the overall drainage of the soil). Pine biochar (550 °C) with two different particle sizes (<2 mm and >4 mm) was mixed either into the top soil layer at the original 0–10 cm depth in the soil column or at 10–20 cm depth by inverting the top soil to simulate ploughing. Nitrous oxide emissions were monitored every two to three days, up to seven weeks during the summer trial, and measurements were repeated during the autumn trial. The use of large particle size biochar in the inverted soil had a significant impact on increasing the cumulative N₂O emissions in the autumn trial, possibly through changes in the water hydraulic conductivity of the soil column and increased water retention at the boundary between soil layers. Thus, the importance of the role of biochar particle size and the method of biochar placement on soil physical properties and the implications of these on N₂O emissions was highlighted. In the same glasshouse study, the effect of biochar particle size and depth of placement was further evaluated in relation to soil organic C. We hypothesized that (i) the large-particle size biochar may affect soil aeration and accelerate soil C decomposition rate with increased oxygen availability, and this effect is greater when biochar is incorporated at depth due to the more compacted soil at deeper layer with poorer aeration compared to the surface layer; and (ii) the NIR spectroscopy technique can be used to predict the SOC concentration and SOC stocks in biochar-amended soil. Carbon stocks were estimated using NIR spectroscopy coupled with partial least-squares regression analysis (NIR/PLSR) and direct organic C measurements using an elemental analyzer. The NIR spectra of the soil were acquired by scanning intact soil cores using the NIR spectrometer. By the end of the glasshouse trial (327 days), the large-particle size biochar applied at depth had induced significant soil C loss (9.20 Mg C ha⁻¹ (P < 0.05), possibly through the combination of enhanced soil aeration, and the interrupted C supply from new plant inputs at that depth due to soil inversion. This C loss did not occur in the treatment with the small-particle size biochar. Near-infrared (NIR) spectroscopy was able to predict the SOC concentration, however, the prediction accuracy may be negatively affected by an increasing biochar particle size and soil inversion, thus may affect the subsequent SOC estimates. The information obtained in this thesis will inform the future use of biochar and contribute to the knowledge of possible factors affecting soil N₂O emission from biochar-amended soil, the mineralization of native SOC, and the changes in SOC stocks over time, particularly in the pastoral soils of New Zealand. Also, based on this study, the use of NIR spectroscopy technique may potentially be integrated as part of the methodology for SOC estimation.Item Design of instrumentation for metabolic monitoring of the Adélie penguin : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Physics at Massey University(Massey University, 2000) Ryland, Paul StephenThe motivating question for the work described in this thesis was "How does the Adélie penguin cope with cold?" It was reasoned that the time-scale of temperature changes in Antarctica precluded all but metabolic and physiological responses. To determine these, a system capable of measuring and recording these biological variables in the penguins natural environment, was designed. A device, based on the principles of near infrared spectroscopy, was developed that could measure the relative oxygen saturation of haemoglobin and the reduction state of cytochrome oxidase as well as heart rate and blood volume. The completed device was housed in a black, waterproof, plastic container, measuring 65mm x 92mm x 25mm and weighing 132.7g. Co-ordination of measurements was achieved with operating system-like control software implemented in Motorola HC11 assembly code. Synchronous detection was used for signal acquisition and a pulse algorithm, implemented in assembly code, allowed real time pulse measurement from the input signals. Programs were written in Matlab and C++ to investigate the characteristics and limits of these techniques. Preliminary testing of the device on human subjects successfully showed changes in metabolic state as a result of physical activity. The results of field testing on Adélie penguins were unable to answer the original question due to a number of physical factors. However, the success of human trials suggests that, with modification and improvement, the device has potential as a valuable research instrument, applicable to a variety of other species.Item An investigation into the use of video image analysis (VIA) and visible-near infrared (NIR) spectroscopy for carcase evaluation : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand(Massey University, 2012) Craigie, Cameron RossIn order for the meat industry to move towards a carcase payment system that is more consumer-focused, there is a need to identify carcases that have a higher yield of superior eating quality meat. Through a series of experiments, this thesis investigates the relationships between video image analysis (VIA) variables and saleable meat yield (SMY%) of high-value cuts in beef carcases, and also the relationships between visible-near infrared (NIR) spectra and instrumental meat quality parameters in beef, lamb and venison of various breeds and genders. Results showed that VIA could effectively replace the visual classifier for classifying beef carcases according to the EUROP carcase classification system, and that both visual and VIA systems showed some promise for predicting the yield of high-value sirloin yield through the EUROP-grid information. Both VIA and visual systems could only account for approximately 57% of the variation in sirloin SMY%, but the relationship between SMY% and other possible VIA outputs such as lengths, widths and volumes remains largely uncharacterized. Instrumental measures of meat quality (shear force, pH and colour) of M. longissimus thoracis et lumborum (LTL) from 234 beef carcases and 208 Texel lambs showed that gender had a larger effect on meat quality than breed. Data from these two experiments was used to determine the relationship between NIR spectra and instrumental meat quality parameters in beef and lamb LTL. NIR showed promise for identifying beef with high ultimate pH values and lamb with high intramuscular fat percentages, but the prediction of shear force using NIR spectra in both beef and lamb was less accurate. The effects on meat quality of sex, breed, chilled aging and location within venison M. Longissimus lumborum, for samples from 79 farmed deer showed that all factors influenced venison meat quality, with aging time and gender having the largest effects. The relationships between NIR spectra and venison meat quality indicated that NIR spectra could be used to identify samples with high ultimate pH and high shear force values.