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Elucidating the hidden infection dynamics between hairworms and their aquatic and terrestrial hosts
Full text linkParasitism, the act of acquiring nutrients at the expense of a host organism, has arguably become the most prevalent mode of life on this planet. Despite the remarkable diversity of parasite species, their life strategies can be grouped mainly into only six general categories. This is reflected by a convergent evolution in life cycle attributes and how parasites successfully transition from one development stage to the next. In parallel to the evolution of these general life strategies, many parasite lineages have been selected to adaptively increase the odds of successfully completing their life cycle through phenotypic changes in their hosts, a phenomenon known as host manipulation. Perhaps one of the best-known examples of parasites capable of host manipulation are freshwater hairworms (phylum Nematomorpha), which somehow cause their terrestrial host to enter water, for the parasite to exit and reproduce. Despite their notoriety, there is still much left to discover about this group of highly specialised organisms. In fact, I show that much of what is known about the host manipulation of hairworms has been largely misrepresented in both the popular media and the scientific literature. Therefore, due to the cryptic nature of parasite life cycles in general, understanding host-parasite interactions, including host manipulation, requires an in-depth investigation. This thesis aims to elucidate some of the hidden interactions between hairworms and their aquatic and terrestrial hosts in New Zealand. In the core chapters, I take the reader through the complex life cycle of hairworms to answer some of the broad research questions on the ecology and host-parasite interactions of this group. First, by observing naturally infected aquatic hosts, I show that the internal defence reactions of these hosts toward hairworm larvae and cysts are more complex than previously thought, casting doubt on the true lethality of aquatic host immunity towards hairworms. Then, I quantify the losses of hairworms in dead-end hosts from two communities of aquatic macroinvertebrates, showing that certain aquatic species can represent important population sinks for hairworms. Here, I reveal that, depending on the species, hairworms follow distinct host transmission routes to reach land, depending on where and when they are consumed by the aquatic hosts in the streams. In light of these challenges that hairworms face in the water, I present some evidence, from a controlled observational study, that they may in turn accelerate their transition to land by decreasing the development time of aquatic hosts, thus increasing the odds of successfully completing their life cycle. Finally, I show that different species of hairworm are capable of infecting a diverse range of terrestrial hosts through a survey of two communities of terrestrial arthropods in subalpine habitats, which suggests that hairworms may be less host-specific and more widespread than what is currently known in New Zealand. This thesis uncovers some of the complex and hidden interactions between hairworms and their aquatic and terrestrial hosts. Still, there remains much to explore of the ecology and infection dynamics of this fascinating, yet poorly understood group of parasites
OMS Health Professions Education Research Group Online Symposium 2021 Announcement
No full textIn 2021, the Otago Medical School - Health Professions Education Research Symposium will focus on fostering collaborative conversations about foundational knowledge, skills, and perspectives for conducting education research projects across our campuses using an online format. This document contains the invitation to participate, instructions for registering, and guidelines for submitting an abstract for discussion at the event
Detection and prediction of microsleeps from EEG via deep learning
Full text linkMicrosleeps are lapses in which there is a complete and unintentional sleep related loss of
consciousness up to 15 s. They are accompanied by partial to full eye closure and head nodding.
These, in turn, can lead to accidents resulting in fatal results not only to themselves but also people
around them. Thus, the detection and ideally prediction of microsleeps in subjects working in
high-hazard environment is imperative for the well-being of not only them but also for everyone
around in that environment.
Microsleeps are often subtle, and subjects are often unaware of them. They are also not
restricted to being sleep-deprived and often occur in situations in which the subjects are carrying
out monotonous tasks. For these reasons, detecting and predicting microsleeps pose a significant
challenge. There are several means to measure the brain activity of a subject during their routine,
like fMRI and EEG. The brain activities thus obtained are processed to obtain useful information
or features that can be used to identify microsleeps. This process of detecting and predicting
microsleeps needs to be automated to be deployed in real-time situations. Machine learning is a
field that aids this automation process. A recent development in the field of machine learning
is the Deep Neural Network (DNN), in which, unlike conventional Artificial Neural Networks
(ANN), more depth can be added to the neural layers to help the DNNs learn naturally with less
manual intervention.
The objective of this project was to use DNNs to detect and predict microsleeps during
sustained-attention tasks. DNN model(s) formed the basis of a system that can alert the subject
involved in such situations, helping them stay awake and focused on their tasks. Two previous
studies – Study A and C – were used in this work.
Deep learning (DL) approaches implemented for the detection and prediction of microsleeps
were Convolutional Autoencoder (CAE), Convolutional Neural Network (CNN), Long-Short
Term Memory (LSTM), and Bi-directional LSTM (BiLSTM). Several types of EEG representations,
specifically time-domain signal, log-power spectral 2D maps, and pseudo-3D
power-spectral maps, were fed to the deep learning models.
In Study A, EEG with vertical and horizontal EOG in parallel resulted in the best performance
for both microsleep state detection and prediction. The best performance yielded a phi = 0.53
(AUCROC = 0.97; AUCPR = 0.63) for microsleep state detection and a phi = 0.47 (AUCROC =0.95; AUCPR = 0.49) for microsleep state prediction with a prediction-time g = 1.0 s, respectively.
In comparison, EEG alone yielded a phi of 0.48 for microsleep state detection.
For microsleep onset detection (g = 0) and prediction (g = 1.0 s), the best performance
resulted in a phi = 0.10 (AUCROC = 0.94; AUCPR = 0.09) and a phi = 0.08 (AUCROC = 0.93;
AUCPR = 0.08), respectively.
For Study C, using the vertical EOG alone as input to the CNN-series network with weighted
cross-entropy as a classifier resulted in the overall-best performance for both microsleep state
and onset detection. The best performance yielded a phi = 0.32 (AUCROC = 0.77; AUCPR =
0.42) and a phi = 0.11 (AUCROC = 0.74; AUCPR = 0.06) for microsleep state detection and
microsleep state prediction with a prediction-time g = 1.0 s, respectively.
Our study and experimentation has provided the following insights.
• In a CNN, every network layer acts as a detection filter looking for the presence of features
or specific patterns. The CNN looks for simple features in the first few layers to very
complex, subtle, and abstract features in the later layers. This attribute of CNN has
aided in its learning of the complex and subtle nature of the microsleeps. It also resulted
in a superior end-to-end solution for detecting and predicting microsleeps states when
compared to using the features extracted by CNN and SVM and LDA classifiers.
• The addition of features extracted from EOG has significantly increased the performance
of both detection and prediction of microsleeps (both states and onsets).
• Initialising the CNN with CAE-based weights proved to yield a slightly better state
detection performance (phi: from 0.51 to 0.53) compared to initialising the CNN with
narrow-normal weights.
• When the CNN features were visualised, in Study A it was found that the CNN was
extracting features mainly from delta and theta bands to distinguish microsleeps from
responsives. It was also looking into differences in activity in the pre-frontal, parietal,
and occipital regions.
• n Study C, CNN was looking into the alpha and beta bands to distinguish microsleeps
from responsives. Spatially, CNN was looking into difference in activities from all regions
of the brain.
• Overall, the CNN did not perform superiorly when compared to traditional machine
learning approaches, when EEG alone was given as input, for microsleep detection and
prediction
“A New Shape of Reason”: Mapping Neuroatypical Minds in the Works of Virginia Woolf, Janet Frame, and Elizabeth Strout
Full text linkThe methodologies used to explore neuroatypical minds in fiction expose both the strengths and weaknesses of literary studies. How we interact with literature is often a microcosmic reflection of how we engage with the actual world and understanding the neuroatypical experience is essential to diversifying this engagement. Although literary studies are often the champion of empathy, critics who rely on outmoded theories may unwittingly ally themselves with antiquated ideas about neuroatypical minds and its experiential intersections with gender, class, and sexuality. In this thesis, I problematise several such methodologies used to approach neuroatypical functioning; in particular, psychoanalytic literary theory, which enacts the idiomatic separation of mind and body, the pathologizing of neuroatypicality, and reinforces the reductive timeline of diagnosis, treatment, and recovery. I argue for an empirically informed and multidisciplinary approach towards representations of mental processing in order to emphasise the rich potential literary studies has for the domain of cognitive study. My methodology is thus shaped by cognitive literary studies and based upon an ethos of equal exchange between the cognitive sciences and literary studies. Throughout this thesis, I engage with a variety of disciplines—including affect theory, disability studies, and memory studies—that offer insight into mental processing and evokes both the effable and ineffable qualities of the othered mind. The three texts I centre my discussion on are Mrs Dalloway (1925) by Virginia Woolf, Faces in the Water (1961) by Janet Frame, and My Name is Lucy Barton (2016) by Elizabeth Strout. All three novels articulate a subversive mode of representing neuroatypical minds that I suggest is further invigorated by a dialogue with the cognitive sciences. Following the diverse approach of my three authors, I demonstrate the need for a multidisciplinary methodology informed by epistemic care towards its neuroatypical subjects, and one that supports the urgent revision occurring in the relationship between artistic and scientific disciplines
Characterising the function of Tribbles Homolog 1 in breast cancer
No full textTribbles Homolog 1 (TRIB1) is a pseudokinase with a well characterised oncogenic capacity in acute myeloid leukaemia (AML). Although several transcriptomic studies have linked TRIB1 to the development and progression of several solid tumour types, including breast cancer, its role in the development of solid tumours is not well understood. This study aimed to evaluate the importance and mechanisms of action, of TRIB1 in breast cancer.
Using siRNA and shRNA TRIB1 knockdown across three different breast cancer cell lines, revealed TRIB1 as an important regulator of cell proliferation. The knockdown of TRIB1 expression and protein levels inhibited the growth of MCF7, HCC1419 and MDA-MB-231 breast cancer cell lines. Each of these cell lines was derived from a different subtype of breast cancer and express TRIB1 at different levels, suggesting a subtype-independent role of TRIB1 in breast cancer cell proliferation. TRIB1 knockdown in MCF7 cells also results in decreased c-MYC mRNA and protein levels. One potential mechanism for subtype-independent regulation of proliferation, may be the regulation of the oncogene c-MYC, thought to be critical in up to 70% of cancers, as the overexpression of c-MYC can drive cell proliferation. Therefore, while the mechanism of c-MYC regulation remains unknown, the suppression of c-MYC expression, by TRIB1 knockdown, is likely to have a significant impact on cell proliferation.
Two global analysis techniques were used to investigate the mechanisms underpinning the regulation of proliferation by TRIB1 in breast cancer. Quantitative Rapid Immunoprecipitation Mass Spectrometry of Endogenous proteins (qPLEX-RIME) was used to identify the TRB1 interactome in HCC1419 and MCF7 cells. The global changes in gene expression in response to TRIB1 knockdown in MCF7 cells were determined using RNAseq. The transcriptomic and proteomic datasets were analysed independently, and in conjunction, to elucidate the mechanisms underpinning the regulation of breast cancer cell proliferation.
Interrogation of the TRB1 interactome by qPLEX-RIME, showed the conservation of the TRB1-COP1 interaction from AML, but also revealed association with a wider range of ubiquitination machinery. Association with an expanded range of ubiquitin machinery indicates TRB1 is important in ubiquitin signalling in breast cancer, as in AML, but suggests it may play a wider role than previously described. The qPLEX-RIME also revealed novel TRB1 associations with a number of transcription factors and a range of epigenetic regulators, including the key heterochromatin proteins CBX1, CBX3 and CBX5. Newly identified association with key epigenetic regulators, such as the CBX proteins, suggest a novel function for TRB1 in epigenetic regulation, in particular the regulation of chromatin accessibility. TRB1 association with the transcription factor ZBTB7A, which is known to regulate chromatin accessibility in promoter regions, further suggests TRB1 may regulate transcription in breast cancer through the control of chromatin accessibility.
The RNAseq analysis of TRIB1 knockdown in MCF7 cells revealed the importance of TRIB1 across a range of proliferation associated processes. TRIB1 knockdown results in the down-regulation of cell cycle related signatures and the up-regulation of growth inhibiting signatures. TRIB1 knockdown also alters expression from specific transcription factors, including c-Myc, the oestrogen receptor and β-catenin. Wide reaching regulation of gene expression likely results in co-operative changes, allowing the regulation of proliferation across a range of genetic backgrounds. The direct integration of qPLEX-RIME and RNAseq analysis, through gene signatures, is supplemented with manual cross-referencing of observed gene expression changes with the known functions of TRB1 associated proteins. For instance integrated analysis allowed the importance of TRB1 associations with WNT/β-catenin regulators to FERMT2 and LRRFIP2 to be validated.
A biochemical approach to evaluate the mechanism underpinning key TRB1 associations is presented as a pilot study of how qPLEX-RIME associations can be further characterised. The identification of direct TRB1 interactors and the characterisation of the interaction mechanism is critical in understanding the functional mechanisms of TRB1 in breast cancer, and will aid long term, in the design of drugs to inhibit or promote critical proliferation regulating TRB1 associations.
In summary, TRIB1 has been shown to be important in the proliferation of a range of breast cancer cells and the regulation of a wide range of gene expression, including the expression of the potent oncogene c-MYC. The use of global approaches allowed the identification of a number of previously undocumented TRB1 associations, and enabled the identification of potential mechanisms for TRIB1 action in breast cancer. The integrated analysis of the qPLEX-RIME and RNAseq streamlined the identification of critical pathways and associations for further investigation. The work presented in this thesis identifies a number of novel functions of TRIB1 and provides a strong foundation for the continued investigation of TRIB1 in breast cancer
A guide to upcycle surplus bread into ginger beer soda
Full text link‘Upcycling’ some of the 29 million loaves of bread wasted annually in New Zealand into new food products is a fun concept that can help to raise awareness of food waste and divert unused bread away from landfills. In the previous “Homebrewers guide to upcycle unwanted bread into beer, Food Scientists at the University of Otago worked with Citizen Collective to substitute 50% of the malt with bread to produce an excellent tasting beer. To further expand the application of upcycled bread, we used the ‘sweet wort’, the sugary liquid extracted from the bread and malt during the brewing process, to make a non-alcoholic ginger beer soda. In this infographic, we provide you with a step-by-step guide to make a non-alcoholic ginger beer soda! For that extra citrusy zing, we recommend making the citrus syrup provided. So, we challenge you to utilise any leftover bread and make your own and in doing so, join the movement to reduce the number of loaves going to waste
Food availability for tamariki a rights-based approach
No full textBackground
The United Nations Convention on the Rights of the Child confirms a child's right to adequate food and the highest attainable standard of health. In New Zealand, tamariki (Māori children) experience inequitable rates of food insecurity and obesity, indicating their right to adequate food is not fully realised. Healthy food availability is a related component of the right to adequate food. Food availability is measured through the following concepts; the community nutrition environment that describes the location and type of food retail stores in a geographic area, and the consumer nutrition environment, which defines the conditions customers encounter in these stores including food availability and food marketing. The overall aim of this thesis was to measure food availability for tamariki within these nutrition environments and investigate policy options to increase healthy food availability informed by a rights-based approach.
Methods
This research was grounded within a Kaupapa Māori Research theoretical framework, utilising a mixed-method approach to address the research questions. Firstly, a narrative literature review identified influences that enable the availability of healthy food for tamariki. Findings were synthesised and analysed using Oranga Mokopuna – a rights-based approach consistent with Kaupapa Māori Research. Secondly, two studies examined the community and consumer nutrition environments for tamariki Māori, utilising image data from the Kids’Cam study. Finally, interviews were conducted with 15 key stakeholders to elicit their views on policy options to ensure the rights of tamariki to healthy food.
Results
The narrative literature review highlighted factors enabling healthy food availability for tamariki involve the fulfilment of their rights to 1) an environment that enables access to traditional foods and food practices; 2) be involved in decisions about their food environment; 3) the economic right to food; and, 4) the highest attainable standard of health (and, within this), to be protected from food marketing.
The community nutrition environment analysis on the journey to and from school for children with tamariki included within the sample showed food outlets were a feature of children’s environments. There were 444 journeys to school analysed. The camera captured image data for food outlets in 47.9% of journeys that had a component of active travel compared to 20.3% of journeys by vehicle. The most common food outlets were convenience stores, fast-food outlets and large supermarkets. Children were more likely to have image data for BMI unhealthy food outlets compared to BMI healthy food outlets and this was significantly impacted by the mode of travel, with those who spent time travelling actively either all or some of the journey being more likely; odds ratio 4.2 (95% CI 1.2 - 14.4) for mixed journeys, to have image data for a BMI unhealthy food outlet. In this study, children of all ethnicities were exposed to a higher density of unhealthy outlets compared to healthy food outlets. Of the 73 food and drink consumption occasions recorded, 94.5% were for discretionary food or drink.
Analysis of convenience stores' consumer nutrition environment showed that unhealthy foods dominated the food and drinks available to children in convenience stores at a rate of 8.3 to 1 (means, 300 non-core, and 36 core, respectively). Most of the 70 items purchased by children were non-core foods or drinks (94.6%), and all of the purchased food or beverages subsequently consumed by children was non-core.
The findings from key stakeholder interviews suggested that to ensure the right to adequate food and to healthy food availability for tamariki, there needs to be: a comprehensive policy response that supports children's rights; an end to child poverty; food provision and food policy in schools; local government policy to promote healthy food availability; and stronger Māori voices and values in decision-making.
Conclusions
In conclusion, this research suggests that tamariki live in an obesogenic environment and this effect is exacerbated by socioeconomic deprivation. This is a breach of the rights of tamariki and in fact of all children. The right to food for tamariki is linked to political and economic systems that reflect ongoing colonisation. A decolonising approach where Māori voices and values are central within NZ policies and policy-making processes related to food availability is urgently needed to give full expression to rights under Te Tiriti o Waitangi
The need to be (a) herd: Belonging as a motive for discrimination
No full textThree studies were conducted to examine the relationship between distinct forms of in-group favouritism and belonging. Studies 1 and 2 investigated the extent to which in-group favouring evaluations led to increased levels of belonging. Study 3 examined the extent to which the (a) difference in the amount of white noise allocation to in-group and out-group members led to increased levels of belonging and (b) threats to belonging (manipulated via Cyberball feedback) impacted on subsequent white noise allocations. Study 1 revealed that Christians that evaluated fellow Christians (i.e., in-group members ) more positively than they did Atheists (i.e., out-group members) reported elevated belonging levels. Study 2 showed that New Zealanders who evaluated fellow New Zealanders (i.e., in-group members) more positively than they did Americans (i.e., out-group members), demonstrated increased belonging levels. The findings of study 3 revealed that New Zealanders who were ostracised and who, therefore, reported decreased belonging levels, allocated increased levels of white noise to Americans (i.e., out-group members) following which they reported an increase in belonging levels. Partial correlation, across studies, revealed that the relationship between in-group favouritism and belonging levels was not a function of group esteem, personal self-esteem, or group identity (studies 1, 2 and 3) or motives like control and meaning (study 2). Taken together, these finding suggested that particular forms of in-group favouritism can result in higher levels of belonging and that threats to belonging can promote the display of negative forms of in-group favouritism
Consent, custom and international law in South Africa: What Australian lawmakers could learn
Full text linkThis article summarises a recent South African case, Baleni v Minister of Mineral Resources. It also analyses the Court’s reasoning to explore how a non-Australian common law state protects a traditional community’s customary laws and practices through legislation, a Constitutional Bill of Rights, and international law. Although a South African case, Baleni demonstrates how similar common law countries have adopted distinct approaches to protecting and treating traditional communities, from which Australian lawmakers could learn
Priming Effects of Female Pheromones on Reproductive Physiology in Gαo Knockout Male Mice
Full text linkPrimer effects are a type of communication, where pheromones affect the bodily functions of other individuals. Primer effects provide benefits for reproduction, as animals can prepare their bodies for mating successfully. For male mice, reproductive changes can take place when exposed to soiled female bedding containing female pheromones. These pheromones are detected by the vomeronasal organ (VNO), located within the nasal cavity. The VNO contains two neuron types, expressing either Gαi2 or Gαo G-proteins. By knocking-out Gαo neurons it is possible to determine whether these neurons are important in male mice to regulate responses to female pheromones. In this project, I observed that neurons within the VNO showed a large increase in activation after 1hr of female bedding exposure, irrespective of whether Gαo was deleted in the VNO. When mice were given chronic long-term bedding exposure over 10 weeks, then female bedding exposure, this resulted in fewer neurons being activated in the vomeronasal organ, compared to those without long-term bedding exposure, suggesting desensitization of the response. I observed no effect of long-term bedding exposure on sperm motility or testicular counts in either genotype, although deletion of Gαo in the VNO unexpectedly increased epididymal sperm counts. Over the ten-week experiment mice with Gαo deleted also lost more weight compared to wildtype mice. A decrease in body weight could suggest reproductive investment, as energy is being investing in sperm production and secreting pheromones to attract female mice. My results are partially inconsistent with previous studies because I did not observe primer effects on male reproductive physiology with long-term female bedding exposure in either genotype. Surprisingly I found evidence of greater reproductive investment in mice that do not express Gαo in the VNO. I hypothesize that this may be because they have not perceived male pheromones when caged with other males prior to the experiment. Male-male pheromonal communication suppresses reproductive function, and thus deletion of Gαo may inhibit these negative effects from occurring