title: Determining the risk of phosphite tolerance in Phytophthora species in New Zealand and the United States: a case study on the implications of long-term use of  phosphite to control Phytophthora cinnamomi in avocado (Persea americana)

authors: Hunter, Shannon Renee

subjects: Phytophthora

abstract: Phytophthora species cause many major plant disease epidemics worldwide, impacting horticulture, plant trade and production planting industries through the loss of plants and the costs arising from disease management. Phytophthora species have specialised structures which enhance their dispersal, survival and infection. These include motile swimming spores, caducous sporangia and resting spores. Nurseries and orchards use integrated management to control phytophthora diseases, including cultural practises, biological control, resistant host plants and chemical control. The use of fungicides is a very effective control method; however, Phytophthora species can develop resistance to fungicides after prolonged exposure. For example, phosphite tolerant isolates of Phytophthora cinnamomi have been found in avocado orchards in Australia and South Africa.
Phosphite is widely used in nurseries and orchards in New Zealand as a preventative and control treatment. The avocado industry largely relies on it for the control of avocado root rot caused by P. cinnamomi. Phosphite is most commonly applied to avocado trees using passive trunk injections but can also be applied as foliar sprays, soil drenches, high-pressure injections and capsule implants.
To assess phosphite tolerance of P. cinnamomi isolates from New Zealand avocado orchards, a high-throughput optical density (OD) assay was developed to measure mycelial growth inhibition in the presence of phosphite. The OD assay was used to screen 24 P. cinnamomi isolates from four orchards never treated with phosphite and 32 isolates from eight orchards treated with phosphite for 15 – 37 years. Four isolates had increased tolerance to phosphite and two were intermediately tolerant. These six isolates were from phosphite managed orchards and five were isolated from unhealthy trees.
To test if in vitro tolerance would be expressed in planta, three tolerant and three sensitive isolates were tested for their ability to colonise phosphite treated lupin (Lupinus angustifolius) roots. The tolerant isolates were more extensive colonisers of lupins treated with 5 and 10 g/L phosphite. In the presence of phosphite the tolerant isolates were able to produce more sporangia and release viable swimming zoospores more often.
Internationally important Phytophthora species from culture collections in New Zealand and the United States were assessed for sensitivity to phosphite and a subset of 32 isolates from the Berkeley collection was tested for mefenoxam sensitivity. The causal agent of kauri (Agathis australis) dieback, P. agathidicida, was found to be highly sensitive to phosphite while the possibly New Zealand native P. kernoviae, was found to be relatively tolerant. Intraspecific variation was found in lineages of P. ramorum, the causal agent of sudden oak death in the United States and the United Kingdom, NA2 was more tolerant than NA1. One P. megasperma isolate was more tolerant to mefenoxam compared to the other isolates tested. Of nine P. cinnamomi isolates from avocado orchards in southern California, one was relatively more tolerant to phosphite.
This study has shown phosphite tolerant isolates of P. cinnamomi have developed in phosphite managed avocado orchards in New Zealand and interspecific variation in sensitivity to fungicides is present across Phytophthora species in New Zealand and the United states.

text: Determining the risk of phosphite tolerance in Phytophthora species in New Zealand and the United States: a case study on the implications of long-term use of  phosphite to control Phytophthora cinnamomi in avocado (Persea americana) Phytophthora species cause many major plant disease epidemics worldwide, impacting horticulture, plant trade and production planting industries through the loss of plants and the costs arising from disease management. Phytophthora species have specialised structures which enhance their dispersal, survival and infection. These include motile swimming spores, caducous sporangia and resting spores. Nurseries and orchards use integrated management to control phytophthora diseases, including cultural practises, biological control, resistant host plants and chemical control. The use of fungicides is a very effective control method; however, Phytophthora species can develop resistance to fungicides after prolonged exposure. For example, phosphite tolerant isolates of Phytophthora cinnamomi have been found in avocado orchards in Australia and South Africa.
Phosphite is widely used in nurseries and orchards in New Zealand as a preventative and control treatment. The avocado industry largely relies on it for the control of avocado root rot caused by P. cinnamomi. Phosphite is most commonly applied to avocado trees using passive trunk injections but can also be applied as foliar sprays, soil drenches, high-pressure injections and capsule implants.
To assess phosphite tolerance of P. cinnamomi isolates from New Zealand avocado orchards, a high-throughput optical density (OD) assay was developed to measure mycelial growth inhibition in the presence of phosphite. The OD assay was used to screen 24 P. cinnamomi isolates from four orchards never treated with phosphite and 32 isolates from eight orchards treated with phosphite for 15 – 37 years. Four isolates had increased tolerance to phosphite and two were intermediately tolerant. These six isolates were from phosphite managed orchards and five were isolated from unhealthy trees.
To test if in vitro tolerance would be expressed in planta, three tolerant and three sensitive isolates were tested for their ability to colonise phosphite treated lupin (Lupinus angustifolius) roots. The tolerant isolates were more extensive colonisers of lupins treated with 5 and 10 g/L phosphite. In the presence of phosphite the tolerant isolates were able to produce more sporangia and release viable swimming zoospores more often.
Internationally important Phytophthora species from culture collections in New Zealand and the United States were assessed for sensitivity to phosphite and a subset of 32 isolates from the Berkeley collection was tested for mefenoxam sensitivity. The causal agent of kauri (Agathis australis) dieback, P. agathidicida, was found to be highly sensitive to phosphite while the possibly New Zealand native P. kernoviae, was found to be relatively tolerant. Intraspecific variation was found in lineages of P. ramorum, the causal agent of sudden oak death in the United States and the United Kingdom, NA2 was more tolerant than NA1. One P. megasperma isolate was more tolerant to mefenoxam compared to the other isolates tested. Of nine P. cinnamomi isolates from avocado orchards in southern California, one was relatively more tolerant to phosphite.
This study has shown phosphite tolerant isolates of P. cinnamomi have developed in phosphite managed avocado orchards in New Zealand and interspecific variation in sensitivity to fungicides is present across Phytophthora species in New Zealand and the United states.

year: 2018

title: “She Watches Over Her Household”: Wellbeing of mothers and children in motherled households

authors: Hunter, Rachel Lamdin

subjects: Wellbeing

abstract: Wellbeing is a term used in everyday conversation, and by health professionals, policy writers and analysts, economists and others, to sum up one’s ability to flourish and live a rewarding, fruitful life. Family is deemed a significant source and determinant of wellbeing. Here, people may expect to receive the love, nurturance, and belonging all humans need to thrive, as well as the most basic needs for food, shelter and warmth. The many forms of family in societies such asNew Zealand are of interest to those who posit that the conduct and wellbeing of mothers in families, is central to the flourishing of all within.
Some families are believed to hold better promise of wellbeing than others. Families with mothers at the helm, motherled households, are constructed in research and public discourse, and enacted in policy, as sites of social and economic peril. Studies abound in which women and children in motherled households are depicted as suffering social isolation, lacking moral support, and experiencing material poverty.
In this study I explore wellbeing in motherled households. My lived experience as nurse specialising in maternal, child and family health, and as a single mother for some time, is pertinent. Using Judi Marshall’s (1999) notion of life lived as the basis for inquiry, I grounded my study in a subjective, storied frame in which I troubled notions of wellbeing in families – notions which I had read in research, enacted in policy and practice, and questioned.
Berger and Luckmann (1966) theorised that what is understood as true or real, is a result of socially-fabricated claims to truth; that is, they posit the social construction of reality. I explore the conditions under which truths about families and motherhood are constructed, bolstered by research, enacted in and enacting institutionalised policy.
Institutionalised constructions of wellbeing and families constitute narratives writ large in research, policy and everyday conversation. I posit these as an example of the petrified grand narratives brought to my attention in the work of Boje (2008a). I read them now as monolithic, simplified and ultimately limited (and limiting) accounts of our humanity. The generation of living stories and their attendant many-voiced ante-narratives are seen as “bets on the future” (Boje, 2001), stories along the way to narrative. Antenarratives may interrupt or endorse a grand narrative. My thesis is a quest to story a version of those in motherled households which is rich and hopeful.
My noticing of contradictions in these grand narratives led me to seek conversations with mothers, and to share their stories in a reconstructed conversation. These mothers understood wellbeing in their motherled household as a deeply entwined and connected process. Women storied wellbeing in unique, individual, and evolving ways. These women valued their families as sites of purpose, wellbeing and intentionality, a version of family and wellbeing not told elsewhere.
Storytelling contributes to versions of mothering in which women and children flourish, foregrounding activist hopes for research about families. Reflexive storytelling approaches challenge those concerned with making a difference through research and policy formation, through individual practices and everyday conversation.

text: “She Watches Over Her Household”: Wellbeing of mothers and children in motherled households Wellbeing is a term used in everyday conversation, and by health professionals, policy writers and analysts, economists and others, to sum up one’s ability to flourish and live a rewarding, fruitful life. Family is deemed a significant source and determinant of wellbeing. Here, people may expect to receive the love, nurturance, and belonging all humans need to thrive, as well as the most basic needs for food, shelter and warmth. The many forms of family in societies such asNew Zealand are of interest to those who posit that the conduct and wellbeing of mothers in families, is central to the flourishing of all within.
Some families are believed to hold better promise of wellbeing than others. Families with mothers at the helm, motherled households, are constructed in research and public discourse, and enacted in policy, as sites of social and economic peril. Studies abound in which women and children in motherled households are depicted as suffering social isolation, lacking moral support, and experiencing material poverty.
In this study I explore wellbeing in motherled households. My lived experience as nurse specialising in maternal, child and family health, and as a single mother for some time, is pertinent. Using Judi Marshall’s (1999) notion of life lived as the basis for inquiry, I grounded my study in a subjective, storied frame in which I troubled notions of wellbeing in families – notions which I had read in research, enacted in policy and practice, and questioned.
Berger and Luckmann (1966) theorised that what is understood as true or real, is a result of socially-fabricated claims to truth; that is, they posit the social construction of reality. I explore the conditions under which truths about families and motherhood are constructed, bolstered by research, enacted in and enacting institutionalised policy.
Institutionalised constructions of wellbeing and families constitute narratives writ large in research, policy and everyday conversation. I posit these as an example of the petrified grand narratives brought to my attention in the work of Boje (2008a). I read them now as monolithic, simplified and ultimately limited (and limiting) accounts of our humanity. The generation of living stories and their attendant many-voiced ante-narratives are seen as “bets on the future” (Boje, 2001), stories along the way to narrative. Antenarratives may interrupt or endorse a grand narrative. My thesis is a quest to story a version of those in motherled households which is rich and hopeful.
My noticing of contradictions in these grand narratives led me to seek conversations with mothers, and to share their stories in a reconstructed conversation. These mothers understood wellbeing in their motherled household as a deeply entwined and connected process. Women storied wellbeing in unique, individual, and evolving ways. These women valued their families as sites of purpose, wellbeing and intentionality, a version of family and wellbeing not told elsewhere.
Storytelling contributes to versions of mothering in which women and children flourish, foregrounding activist hopes for research about families. Reflexive storytelling approaches challenge those concerned with making a difference through research and policy formation, through individual practices and everyday conversation.

year: 2017

title: Data and model bias in artificial intelligence for healthcare applications in New Zealand

authors: Yogarajan, Vithya

abstract: Introduction: Developments in Artificial Intelligence (AI) are adopted widely in healthcare. However, the introduction and use of AI may come with biases and disparities, resulting in concerns about healthcare access and outcomes for underrepresented indigenous populations. In New Zealand, Māori experience significant inequities in health compared to the non-Indigenous population. This research explores equity concepts and fairness measures concerning AI for healthcare in New Zealand. Methods: This research considers data and model bias in NZ-based electronic health records (EHRs). Two very distinct NZ datasets are used in this research, one obtained from one hospital and another from multiple GP practices, where clinicians obtain both datasets. To ensure research equality and fair inclusion of Māori, we combine expertise in Artificial Intelligence (AI), New Zealand clinical context, and te ao Māori. The mitigation of inequity needs to be addressed in data collection, model development, and model deployment. In this paper, we analyze data and algorithmic bias concerning data collection and model development, training and testing using health data collected by experts. We use fairness measures such as disparate impact scores, equal opportunities and equalized odds to analyze tabular data. Furthermore, token frequencies, statistical significance testing and fairness measures for word embeddings, such as WEAT and WEFE frameworks, are used to analyze bias in free-form medical text. The AI model predictions are also explained using SHAP and LIME. Results: This research analyzed fairness metrics for NZ EHRs while considering data and algorithmic bias. We show evidence of bias due to the changes made in algorithmic design. Furthermore, we observe unintentional bias due to the underlying pre-trained models used to represent text data. This research addresses some vital issues while opening up the need and opportunity for future research. Discussions: This research takes early steps toward developing a model of socially responsible and fair AI for New Zealand's population. We provided an overview of reproducible concepts that can be adopted toward any NZ population data. Furthermore, we discuss the gaps and future research avenues that will enable more focused development of fairness measures suitable for the New Zealand population's needs and social structure. One of the primary focuses of this research was ensuring fair inclusions. As such, we combine expertise in AI, clinical knowledge, and the representation of indigenous populations. This inclusion of experts will be vital moving forward, proving a stepping stone toward the integration of AI for better outcomes in healthcare.

text: Data and model bias in artificial intelligence for healthcare applications in New Zealand Introduction: Developments in Artificial Intelligence (AI) are adopted widely in healthcare. However, the introduction and use of AI may come with biases and disparities, resulting in concerns about healthcare access and outcomes for underrepresented indigenous populations. In New Zealand, Māori experience significant inequities in health compared to the non-Indigenous population. This research explores equity concepts and fairness measures concerning AI for healthcare in New Zealand. Methods: This research considers data and model bias in NZ-based electronic health records (EHRs). Two very distinct NZ datasets are used in this research, one obtained from one hospital and another from multiple GP practices, where clinicians obtain both datasets. To ensure research equality and fair inclusion of Māori, we combine expertise in Artificial Intelligence (AI), New Zealand clinical context, and te ao Māori. The mitigation of inequity needs to be addressed in data collection, model development, and model deployment. In this paper, we analyze data and algorithmic bias concerning data collection and model development, training and testing using health data collected by experts. We use fairness measures such as disparate impact scores, equal opportunities and equalized odds to analyze tabular data. Furthermore, token frequencies, statistical significance testing and fairness measures for word embeddings, such as WEAT and WEFE frameworks, are used to analyze bias in free-form medical text. The AI model predictions are also explained using SHAP and LIME. Results: This research analyzed fairness metrics for NZ EHRs while considering data and algorithmic bias. We show evidence of bias due to the changes made in algorithmic design. Furthermore, we observe unintentional bias due to the underlying pre-trained models used to represent text data. This research addresses some vital issues while opening up the need and opportunity for future research. Discussions: This research takes early steps toward developing a model of socially responsible and fair AI for New Zealand's population. We provided an overview of reproducible concepts that can be adopted toward any NZ population data. Furthermore, we discuss the gaps and future research avenues that will enable more focused development of fairness measures suitable for the New Zealand population's needs and social structure. One of the primary focuses of this research was ensuring fair inclusions. As such, we combine expertise in AI, clinical knowledge, and the representation of indigenous populations. This inclusion of experts will be vital moving forward, proving a stepping stone toward the integration of AI for better outcomes in healthcare.

year: 2022-12-22