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    Mathematical modelling of airflow during forced draft precooling operations : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Food Technology at Massey University, Palmerston North, New Zealand
    (Massey University, 2024-11-01) Tapia Zapata, Nicolas Ignacio
    By the year 2020, the kiwifruit industry represents approximately 37 % of the horticultural export industry sector in New Zealand. Thereof, the kiwifruit cold chain aim is to reduce losses due to poor temperature control and energy usage during refrigeration. By forced convection aided by fans in palletised kiwifruit, field heat is removed rapidly prior to storage, thus optimising shelflife of the produce. Previous Computer Fluid Dynamics (CFD) model determined the optimal operating point for palletised kiwifruit during forced-draft cooling. However, CFD requires complex simulation, in detriment to computational efficiency and solving time. Therefore, there is an imperative to provide innovative tools that optimise package design by iterating several designs and that is applicable to the local industry sector for cold chain optimisation. In this spirit, this projects aimed to development of a simplified approach for the prediction of airflow distribution of palletised kiwifruit during forced-draft cooling, that can be coupled with an alternative heat transfer model, thus providing a fast and robust package optimisation routine that can inform cooling performance of several package design and pallet configuration.
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    A systematic approach for developing and manufacturing fruit simulators : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Food Engineering, Massey University, Palmerston North, New Zealand
    (Massey University, 2023) Huang, Huijian
    Due to the high cost, variable nature and seasonal availability of fruit, conducting large scale experiments for research purposes is not easy. A fruit simulator is a physical tool that mimics the mechanistic features and properties of the targeted fruit; hence, it can be used as a replacement for the fruit in research experiments. This study focuses on developing simulators for heat transfer experiments, especially in horticultural produce precooling. A framework for developing the simulator was established based on the importance of each mechanistic feature. Depending on the application's needs, the simulator can mimic different length scale levels of the targeted fruit, such as the individual fruit, the bulk stacking of the fruit or sub-units of the fruit (e.g., a punnet/bag of table grapes). The scale level determines whether certain mechanistic features are important and affects the values of the thermal properties that must be matched. For example, a simulator that mimics a punnet of fruit with enclosed air pockets has an effective thermal conductivity and volumetric heat capacity that includes contributions from the thermal properties of the fruit and air, which provides more room for material selection. Based on this framework, a systematic approach for the simulator manufacture and material selection was developed. Three different simulators were developed based on the framework: kiwifruit, apple and table grape simulators. The comparison of a simulator and real fruit precooling trials showed good agreement, validating the approach and demonstrating the feasibility of using simulators in postharvest research. The kiwifruit simulator was validated at different experimental scale levels, from individual kiwifruit to multiple kiwifruit boxes containing numerous individual kiwifruit simulators (which reflected pallet scale precooling). During the simulator development, the concept of a time-scaled approach was identified and was explored. In theory, if the volumetric heat capacity of a simulator becomes smaller while the Bi of the simulator remains the same, the heating/cooling time of the simulator in an experiment will decrease proportionally according to the Fourier number (Fo). This approach was validated via the three simulators developed in this study. The validation of the simulators confirms the feasibility of this time-scaled concept. This approach has a significant advantage in reducing the experimental time and easing the material selection process for the simulator manufacture. In the table grape simulator development, a process of using CT scans of the bulk packaged system to study the bulk shape and effective properties of the fruit subunits (bags) were developed, where the bulk shape and effective thermal properties of a bag of table grape were determined based on the process. A set of bag shaped fruit simulators was then manufactured with equivalent bulk thermal conductivity and used to validate the bulk simulator approach by comparison of cooling rates with real fruit. Overall, this study has successfully developed a generalised heat transfer simulator development framework. In addition, this study validated the feasibility and applicability of the time-scaling approach, which could be helpful for any future experiments. Furthermore, this study has developed a process to use CT scanning to determine a bulk object's bulk shape and effective property. The outcomes of the work pave the way for carrying out postharvest and packaging optimisation experimental trials with reduced variability, greater ease and without seasonal constraints. The simulator development framework provides a basis for further expansion of these concepts into other applications beyond the heat transfer focus that they were developed for in this work.
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    Interpreting highly diverse dsRNA viral sequences from Picobirnaviridae within and among species for interspecies transmission inference : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Sciences at the School of Veterinary Science, Massey University, Manawatu, New Zealand
    (Massey University, 2021) Wierenga, Janelle
    Cross-species transmission of infectious diseases has been at the forefront of our current reality considering the COVID-19 global pandemic and its repercussions. Now more than ever, we realise that the factors involved in these transmissions between species is both simple, such as the impact of increased contact between wildlife and humans, and complicated, such as the impact of biodiversity loss. Our understanding of these influences, and the complexity, has progressed considerably in the last decade though we are still far from predicting epidemics and pandemics. We do, though, understand that many of these infectious diseases cross species barriers frequently, with some types of pathogens more likely to cross between species. Picobirnaviruses (genus Picobirnavirus, family Picobirnaviridae), a genus of double-stranded RNA (dsRNA) viruses, have been identified on almost every continent, though the pathogenic potential for these viruses is still debated. Picobirnaviruses are known to have massive genetic diversity. Picobirnaviruses were first identified in rabbits and then humans and since then have been reported in many mammalian species, birds, reptiles, along with wastewater, and potentially in protozoa; prokaryotes have been implicated as potential hosts, based on conserved ribosomal-binding motifs from prokaryotic messenger RNA. Although they are highly diverse, they have often been found to have very high similarity in different host species present at the same geographic site, raising the hypothesis that cross-species transmission has occurred. The study system from Uganda described in this thesis provides a setting for the possible transmission of infectious diseases between wildlife, humans and domestic livestock. I identified multiple potential pathogens to study cross-species transmission within this system and focused on Picobirnavirus. I identified multiple picobirnaviruses in humans, wildlife and domestic animals from Uganda and New Zealand, for comparison, by using metagenomic and targeted PCR amplicon sequencing. Initial phylogenetic analyses revealed some host clustering among the picobirnaviruses studied, but host and geographical clustering was not upheld when known picobirnaviruses from global databases were included. Furthermore, the use of near-complete and two genogroup-specific viral sequences did not reveal host or geographic clustering on phylogenetic analyses. I identified multiple picobirnaviruses within the same host, detecting up to eight distinct viral sequence types in the samples. Despite the wide-ranging within-host diversity of the viruses, nearly identical virus sequences were also identified in different hosts from the study. Given the high diversity, unclear host and geographic associations, and that picobirnaviruses may infect hosts from across the natural kingdoms, including bacteria and protozoa, I sought to identify picobirnaviruses from bacterial and protozoal samples, to try to determine the host range of the viruses. I discovered picobirnavirus RNA in purified Cryptosporidium oocysts from New Zealand, suggesting a possible alternative Protist host. However, using an alternative genetic code from invertebrate mitochondria removed within putative open reading frame stop codons from some picobirnavirus sequences, supporting other studies. Further analyses of the picobirnavirus sequences revealed alternative genetic code usage or motifs in the untranslated regions that could indicate the virus has a prokaryotic rather than a eukaryotic host—which have been commonly assumed to be the definitive hosts. The discovery that prokaryotes may also be considered hosts of picobirnaviruses, as well as the presence of homologous sequence between species of this highly diverse RNA virus genera, will influence our understanding of these vexatious and under-studied viruses.
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    Is the family pet a risk for multidrug resistant infections? : thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand
    (Massey University, 2019) Toombs-Ruane, Leah
    Risk factors for community-acquired urinary tract infections (UTI) caused by extended-spectrum beta-lactamase-(ESBL) and AmpC beta-lactamase-(ACBL) producing Enterobacteriaceae were investigated in a prospective case-control study conducted between August 2015 and September 2017. Both cases and controls were from the Auckland and Northland regions of New Zealand. A telephone questionnaire was delivered to participants, and the results analysed for putative risk factors for human infections. Analysis was performed using regression models, including factors around pet ownership and any other animal contact. Faecal samples were submitted from some households; this included samples from both people and companion animals. Isolates collected from index case urine samples and ESBL- or ACBL-producing faecal samples were sequenced and subsequently analysed through a bioinformatics pipeline. Pet ownership was not found to be a risk for human ESBL- or AmpC-producing infections in this study. Another important finding of this research was that E. coli ST-131 was the most commonly found bacteria associated with the UTI from people recruited into the case-control study. The strains of this sequence type were likely to have entered New Zealand in multiple introductions over the last 20 years. Transmission of ESBL-/ACBLproducing E. coli was also suspected to have occurred within households where a person had been recently infected with the same bacteria (in the form of a UTI) caused by an ESBL-/ACBL-producing Enterobacteriaceae. The results of this study as a whole indicate that while pets may not be a major risk for acquisition of ESBL/ACBL-producing bacteria, they are likely to play a role in the transmission of bacteria within homes and the community, and therefore warrant attention in future work.
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    An integrated modelling approach to inform package design for optimal cooling of horticultural produce : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Food Technology at Massey University, Palmerston North, New Zealand
    (Massey University, 2018) Olatunji, Jamal Rimkeit
    Forced-air cooling is a widely used pre-cooling process that enables the New Zealand horticultural industry, valued at over NZD $8B in 2016, to maintain the quality of perishable exports. In the typical systems used in New Zealand’s horticultural industry, forced-air cooling involves stacking fruit boxes into pallets, which are stacked together in a refrigerated room, and a fan is used to create a pressure drop through the pallets. This forces cold air through the packaging ventilation and over the fruit, facilitating heat transfer and rapidly cooling the product from the field heat (~20 °C) to the storage temperature (0-2 °C), thus prolonging shelf life and preserving fruit quality. Package design is linked with cooling performance, as the specifics of the ventilation (i.e. placement and size of vents in the boxes) results in different airflow patterns. Unfortunately, it is not well understood how to predict the performance of a hypothetical design, which is partly why in industry and academia there has been a focus on package design testing – where through experimental or computational means, the performance of a given design is thoroughly tested. Trial-and-error experimental work represents a steep materials cost, and construction and validation of detailed mathematical models can be a highly arduous and specialised task. It would therefore be beneficial to the New Zealand horticulture industry and academia to have a suite of methodologies that can simply and rapidly predict performance of a hypothetical package design. It was proposed that such methods are based upon mathematical modelling, with a focus on flexibility, computational efficiency, and automation. The goal is that such a model can be used to rapidly develop mathematical descriptions of a wide variety of products and cooling scenarios, and if integrated with optimisation routines, will allow swift iteration toward an optimised design.--Shortened abstract
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    The human antibody response to Giardia intestinalis : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University
    (Massey University, 1991) Chan, Judy Lai Peng
    Giardiasis is usually diagnosed in the laboratory by microscopic examination of faeces for the presence of cysts and / or trophozoites. However in principle, it is possible that Giardia infection could be diagnosed serologically. To investigate this possibility an Enzyme Immunoassay (EIA) was developed using Giardia-specific mouse serum as antibody. The efficiency of different Giardia antigen preparations to detect antibody in this test was investigated. The antigens included live trophozoites, frozen and thawed trophozoites, sonicated trophozoites, trophozoite membranes and cysts. Antibody titres were low and no marked differences were detected when the four different antigens were compared. However, since following a natural infection the immune response to surface proteins probably predominates, we concluded that live trophozoites or cysts represented the most appropriate antigens to use in an EIA test to detect Giardia-specific antibody in human serum. Live trophozoites adsorbed to polystyrene microtitre wells were removed by the washing procedure, thus giving an insensitive test and inconsistent results. This problem was overcome by precoating the microtitre wells with poly-I-lysine following which trophozoites and cysts adhered to the wells strongly enough to resist the washing procedures. The EIA test was optimised with Giardia­ specific mouse serum as antibody and the same system was used to detect antibody in human serum. lll IgG, IgM, and IgA antibody were assayed in "current infection", "convalescent" and "negative control" human sera. IgG antibody titres were slightly elevated in "convalescent" sera as compared to the other two groups. IgM antibody titres were slightly elevated m "current infection" sera and IgA antibody levels were not found to be elevated. Since IgM antibody is present early in an infection but does not persist, its presence or absence could, m principle, be used to distinguish a current from a previous infection of Giardia. However, only slightly elevated levels of Giardia-specific IgM antibody in "current infection" sera were detected in our tests so this approach to diagnosis will need further development if it is to be used for diagnostic purposes. Giardia IS not an invasive orgamsm and it is possible that some antigens may play a major role in eliciting an immune response in humans. Thus, potential Giardia antigens were investigated by "immunoblotting" total Giardia proteins with human sera from clinically diagnosed cases of giardiasis. It was found that the human antibody response to Giardia vanes between individuals and many Giardia proteins reacted with the Immune human sera. However, IgG antibody found m many of the serum samples reacted with a 200 kDa, 62 kDa and 42 kDa protein. IgA and IgM antibodies also reacted with a 62 kDa protein which may be similar to a 55 kDa structural protein (tubulin) found in Giardia.