title: Utilising risk analysis to predict post-earthquake functionality of critical healthcare facilities

authors: Boston, Megan

abstract: Hospitals, particularly emergency departments, are vital to a community’s resilience and earthquake recovery by providing emergent and ongoing critical care. Building standards and codes have higher structural requirements for hospital structures to help ensure continued functionality; nevertheless, hospitals are often damaged, evacuated or closed following design-level earthquakes. While post-earthquake hospital functionality has been the focus of recent research, it remains challenging to predict hospital functionality in a relevant and meaningful manner. Existing methods to quantify functionality are based on patient wait time, bed count, or available services. This work focuses on improving existing hospital functionality frameworks to predict various levels of hospital functionality using a combination of fault and event trees to provide a probabilistic prediction of different levels of functionality based on available services and bed counts for hospital emergency departments and whole hospitals. Fault and event trees were created using published data on hospital damage, evacuations, and operations following earthquakes and combined with international guidelines on hospital requirements and local hospital emergency procedures. The fault and event trees relate physical damage, staff shortages, and equipment failures to various hospital and emergency room functionality levels. Event trees provide a sequence of events (availability of critical staff, structural damage, and non-structural damage) leading to various levels of hospital functionality (full, partial, or not functional). Each event has an associated probability of occurring determined by a developed fault tree specific to that event failure. The methodology was validated using an additional hospital dataset to hindcast the functionality of the hospital facility. The hindcasted results match the published functionality data, indicating that this method provides a way to predict levels of functionality, which can indicate what types of services and space will be available for treatment following an earthquake.

text: Utilising risk analysis to predict post-earthquake functionality of critical healthcare facilities Hospitals, particularly emergency departments, are vital to a community’s resilience and earthquake recovery by providing emergent and ongoing critical care. Building standards and codes have higher structural requirements for hospital structures to help ensure continued functionality; nevertheless, hospitals are often damaged, evacuated or closed following design-level earthquakes. While post-earthquake hospital functionality has been the focus of recent research, it remains challenging to predict hospital functionality in a relevant and meaningful manner. Existing methods to quantify functionality are based on patient wait time, bed count, or available services. This work focuses on improving existing hospital functionality frameworks to predict various levels of hospital functionality using a combination of fault and event trees to provide a probabilistic prediction of different levels of functionality based on available services and bed counts for hospital emergency departments and whole hospitals. Fault and event trees were created using published data on hospital damage, evacuations, and operations following earthquakes and combined with international guidelines on hospital requirements and local hospital emergency procedures. The fault and event trees relate physical damage, staff shortages, and equipment failures to various hospital and emergency room functionality levels. Event trees provide a sequence of events (availability of critical staff, structural damage, and non-structural damage) leading to various levels of hospital functionality (full, partial, or not functional). Each event has an associated probability of occurring determined by a developed fault tree specific to that event failure. The methodology was validated using an additional hospital dataset to hindcast the functionality of the hospital facility. The hindcasted results match the published functionality data, indicating that this method provides a way to predict levels of functionality, which can indicate what types of services and space will be available for treatment following an earthquake.

year: 2024

title: The Role of Amino Acids and the Threonine-SAM Pathway in the Development of Bovine Inner Cell Mass and Pluripotency

authors: Najafzadeh, Vahid

subjects: amino acid

abstract: Pluripotent stem cells (PSCs) are the foundation of all cell types in the body including functional gametes. They are derived either from the inner cell mass (ICM) of preimplantation mouse and rat embryos, known as embryonic pluripotent stem cells (ePSCs) or embryonic stem cells (ESCs) or via reprogramming of somatic cells to their pluripotent state, known as induced pluripotent stem cells (iPSCs). PSCs are excellent tools for gene editing and accelerated breeding in livestock animals. So far, germline-competent PSCs have only been isolated in mice and rats. Bovine ESCs are yet to be isolated due to the inadequate understanding of the mechanisms involved in bovine pluripotency. This study aimed to investigate the metabolic aspects of bovine ICM development and pluripotency. 
In this study, amino acids were screened via a targeted depletion approach to determine if any amino acid was critical for bovine ICM development and pluripotency. Experiments were conducted on in vitro fertilised day (D) 5 preimplantation bovine embryos, individually cultured in chemically-defined, protein- and glutamine-free synthetic oviduct fluid with variations of essential (E) and non-essential (NE) amino acids (AAs) until D8. Depleting (Δ) one (threonine, methionine), two (threonine_methionine, cysteine_methionine, cysteine_threonine, isoleucine_leucine, isoleucine_lysine, leucine_lysine), three (cysteine_methionine_threonine, isoleucine_leucine_lysine) or six (histidine_phenylalanine_arginine_valine_tryptophan_tyrosine) EAAs did not affect ICM formation, even when NEAAs were also removed from Δthreonine and Δmethionine groups. However, depleting another six (cysteine_isoleucine_lysine_leucine_methionine_threonine), nine (+cysteine_methionine_threonine, +isoleucine_leucine_lysine), eleven EAAs (+threonine, +methionine) or all twelve EAAs impaired blastocyst development. In vitro fertilised D1 preimplantation mouse embryos cultured from D1-4 were also not affected by a Δthreonine culture condition.
The role of the threonine dehydrogenase (TDH)-mediated threonine-s-adenosylmethionine (SAM) pathway in bovine ICM development and pluripotency in bovine embryos and cells was also investigated. This metabolic pathway has been shown to play a critical role in sustaining mouse pluripotency. TDH expression was probed at mRNA and protein levels, and its activity was knocked down using chemical inhibitors quinazolinecarboxamide (Qc1) and 3-hydroxynorvaline (3-HNV). The effect of TDH inhibition on embryo development, cell numbers, lineage-specific marker gene expression, histone trimethylation and autophagy was studied. 
TDH was present in trophectoderm (TE), ICM and 6 day old (D6) ICM outgrowths but absent in D6 TE primary cultures. In bovine embryos, Qc1 reduced blastocyst grade 1-3 (B¹⁻³) and 
B¹⁻² embryo development 1.5- and 2-fold, respectively, compared to the dimethyl sulfoxide (DMSO) controls. Qc1 also reduced ICM and TE cell numbers ~2-fold. This cell loss was due to increased autophagy. Qc1-treated ICM and TE nuclei were explicitly hypermethylated at histone (H)3 lysine (K)4 trimethylation (me3), while H3K9me3 and H3K27me3 were not affected. Hypoblast (PDGRFα), pluripotency-associated epiblast (NANOG, FGF4, and SOX2) and TE (CDX2) markers were not altered in the Qc1 group compared to DMSO controls. Qc1 also severely compromised mouse embryos cultured from day 1-4. In bovine cells, Qc1 compromised fresh ICM, D6 ICM outgrowths and fresh TE cells but failed to impair D6 TE primary cultures. 3-HNV severely compromised bovine embryo development, D1 ICM outgrowths, D6 TE primary cultures and bovine embryonic fibroblast (BEF) cells. However, it unexpectedly severely impaired TDH-free skin fibroblasts in a Δthreonine culture condition. 
The results indicate that the effect of amino acid starvation on embryos is different from that on individual cells. The findings also suggest that TDH is vital for bovine embryonic development via regulating H3K4me3 levels. Moreover, the results denote that TDH becomes restricted to cultured ICM cells and disappears from TE primary cultures. This may indicate that TDH is essential for maintaining bovine pluripotency. 3-HNV was claimed to be a specific TDH enzyme inhibitor; However, this study showed that it compromises TDH-free cells in a Δthreonine culture condition, suggesting that it does not specifically impair cells and embryos via the TDH-mediated threonine-SAM pathway.

text: The Role of Amino Acids and the Threonine-SAM Pathway in the Development of Bovine Inner Cell Mass and Pluripotency Pluripotent stem cells (PSCs) are the foundation of all cell types in the body including functional gametes. They are derived either from the inner cell mass (ICM) of preimplantation mouse and rat embryos, known as embryonic pluripotent stem cells (ePSCs) or embryonic stem cells (ESCs) or via reprogramming of somatic cells to their pluripotent state, known as induced pluripotent stem cells (iPSCs). PSCs are excellent tools for gene editing and accelerated breeding in livestock animals. So far, germline-competent PSCs have only been isolated in mice and rats. Bovine ESCs are yet to be isolated due to the inadequate understanding of the mechanisms involved in bovine pluripotency. This study aimed to investigate the metabolic aspects of bovine ICM development and pluripotency. 
In this study, amino acids were screened via a targeted depletion approach to determine if any amino acid was critical for bovine ICM development and pluripotency. Experiments were conducted on in vitro fertilised day (D) 5 preimplantation bovine embryos, individually cultured in chemically-defined, protein- and glutamine-free synthetic oviduct fluid with variations of essential (E) and non-essential (NE) amino acids (AAs) until D8. Depleting (Δ) one (threonine, methionine), two (threonine_methionine, cysteine_methionine, cysteine_threonine, isoleucine_leucine, isoleucine_lysine, leucine_lysine), three (cysteine_methionine_threonine, isoleucine_leucine_lysine) or six (histidine_phenylalanine_arginine_valine_tryptophan_tyrosine) EAAs did not affect ICM formation, even when NEAAs were also removed from Δthreonine and Δmethionine groups. However, depleting another six (cysteine_isoleucine_lysine_leucine_methionine_threonine), nine (+cysteine_methionine_threonine, +isoleucine_leucine_lysine), eleven EAAs (+threonine, +methionine) or all twelve EAAs impaired blastocyst development. In vitro fertilised D1 preimplantation mouse embryos cultured from D1-4 were also not affected by a Δthreonine culture condition.
The role of the threonine dehydrogenase (TDH)-mediated threonine-s-adenosylmethionine (SAM) pathway in bovine ICM development and pluripotency in bovine embryos and cells was also investigated. This metabolic pathway has been shown to play a critical role in sustaining mouse pluripotency. TDH expression was probed at mRNA and protein levels, and its activity was knocked down using chemical inhibitors quinazolinecarboxamide (Qc1) and 3-hydroxynorvaline (3-HNV). The effect of TDH inhibition on embryo development, cell numbers, lineage-specific marker gene expression, histone trimethylation and autophagy was studied. 
TDH was present in trophectoderm (TE), ICM and 6 day old (D6) ICM outgrowths but absent in D6 TE primary cultures. In bovine embryos, Qc1 reduced blastocyst grade 1-3 (B¹⁻³) and 
B¹⁻² embryo development 1.5- and 2-fold, respectively, compared to the dimethyl sulfoxide (DMSO) controls. Qc1 also reduced ICM and TE cell numbers ~2-fold. This cell loss was due to increased autophagy. Qc1-treated ICM and TE nuclei were explicitly hypermethylated at histone (H)3 lysine (K)4 trimethylation (me3), while H3K9me3 and H3K27me3 were not affected. Hypoblast (PDGRFα), pluripotency-associated epiblast (NANOG, FGF4, and SOX2) and TE (CDX2) markers were not altered in the Qc1 group compared to DMSO controls. Qc1 also severely compromised mouse embryos cultured from day 1-4. In bovine cells, Qc1 compromised fresh ICM, D6 ICM outgrowths and fresh TE cells but failed to impair D6 TE primary cultures. 3-HNV severely compromised bovine embryo development, D1 ICM outgrowths, D6 TE primary cultures and bovine embryonic fibroblast (BEF) cells. However, it unexpectedly severely impaired TDH-free skin fibroblasts in a Δthreonine culture condition. 
The results indicate that the effect of amino acid starvation on embryos is different from that on individual cells. The findings also suggest that TDH is vital for bovine embryonic development via regulating H3K4me3 levels. Moreover, the results denote that TDH becomes restricted to cultured ICM cells and disappears from TE primary cultures. This may indicate that TDH is essential for maintaining bovine pluripotency. 3-HNV was claimed to be a specific TDH enzyme inhibitor; However, this study showed that it compromises TDH-free cells in a Δthreonine culture condition, suggesting that it does not specifically impair cells and embryos via the TDH-mediated threonine-SAM pathway.

year: 2018

title: Harakeke (Phormium tenax) ecology and historical management by Maori: The changing landscape in New Zealand

authors: Wehi, Priscilla M.

subjects: ethnobotany

abstract: Harakeke (Phormium tenax: Phormiaceae) is an important weaving resource for the indigenous Maori people of New Zealand. This research project investigates Maori knowledge of harakeke ecology and management practices prior to the early 20th century within the context of a study of relevant environmental parameters that limit its natural distribution. Ecological information referring to harakeke was analysed from interviews with elders and ancestral sayings (whakatauki). As well, documents from the late 181h to the early 20th century were examined, and environmental parameters for both harakeke and wharariki (Phormium cookianum) were quantified and analysed using correlative models. 
Interviews with 11 elders (from Waikato and Northland) identified key issues in harakeke management, including 'correct' harvesting procedures, use of natural harakeke stands, and specific use of different varieties. Planting practices varied regionally. Three different methods of excess harakeke disposal were reported, including burning. The 15 whakatauki analysed emphasise the interconnectedness of ecosystems, including pollinator-plant relationships for kaka and bellbirds. Four whakataukirefer to environmental tolerances for harakeke and two to the use of fire to stimulate harakeke growth. Others refer to competition between shoots, nutrient requirements, and the growth and multiplication of harakeke offsets. 
Numerous early reports indicate that harakeke has been cultivated throughout much of New Zealand, with cultivations ranging in size from a few bushes to at least several acres. Thirty six varieties were linked to specific weaving uses. Twenty varieties were cultivated, but ten prized fibre varieties were also harvested from natural stands. Numbers of recorded varieties varied between districts, with 31 recorded in Taranaki but only two recorded by name for Northland. Valued varieties, including raumoa and oue, were dispersed throughout the North Island. Mapping different varieties revealed a wide spatial spread for varieties such as rataroa and oue. Specific management techniques included seed germination as well as vegetative propagation. Early records of harakeke pests were not found. Records of harakeke irrigation and the use of fire indicate that Maori created suitable conditions for new cultivations or pii harakeke, which may also have prevented insect infestation. Cumulatively, there is evidence of extensive active management of harakeke. Wharariki and harakeke were found to have distinct environmental niches, with wharariki better able to withstand cooler temperatures, higher rainfall and greater frequency of ground frost than harakeke.
Predictive mapping of harakeke for the northern region of New Zealand shows a low probability of naturally occurring harakeke in much of the Northland and Waikato interior, and a high probability in coastal areas with warm temperatures. It seems likely that Maori transported harakeke into areas where it was unlikely to have occurred naturally and that some apparently 'natural' stands ofharakeke were created and maintained by Maori.
Maori cultivation, dispersal and active management of harakeke, as well as possible creation of wetland areas, emphasises the importance of harakeke as an economic resource prior to European colonisation, and indicates how the New Zealand landscape may have been transformed. Maori ecological knowledge can contribute new perspectives to restoration ecology and ecosystem research.

text: Harakeke (Phormium tenax) ecology and historical management by Maori: The changing landscape in New Zealand Harakeke (Phormium tenax: Phormiaceae) is an important weaving resource for the indigenous Maori people of New Zealand. This research project investigates Maori knowledge of harakeke ecology and management practices prior to the early 20th century within the context of a study of relevant environmental parameters that limit its natural distribution. Ecological information referring to harakeke was analysed from interviews with elders and ancestral sayings (whakatauki). As well, documents from the late 181h to the early 20th century were examined, and environmental parameters for both harakeke and wharariki (Phormium cookianum) were quantified and analysed using correlative models. 
Interviews with 11 elders (from Waikato and Northland) identified key issues in harakeke management, including 'correct' harvesting procedures, use of natural harakeke stands, and specific use of different varieties. Planting practices varied regionally. Three different methods of excess harakeke disposal were reported, including burning. The 15 whakatauki analysed emphasise the interconnectedness of ecosystems, including pollinator-plant relationships for kaka and bellbirds. Four whakataukirefer to environmental tolerances for harakeke and two to the use of fire to stimulate harakeke growth. Others refer to competition between shoots, nutrient requirements, and the growth and multiplication of harakeke offsets. 
Numerous early reports indicate that harakeke has been cultivated throughout much of New Zealand, with cultivations ranging in size from a few bushes to at least several acres. Thirty six varieties were linked to specific weaving uses. Twenty varieties were cultivated, but ten prized fibre varieties were also harvested from natural stands. Numbers of recorded varieties varied between districts, with 31 recorded in Taranaki but only two recorded by name for Northland. Valued varieties, including raumoa and oue, were dispersed throughout the North Island. Mapping different varieties revealed a wide spatial spread for varieties such as rataroa and oue. Specific management techniques included seed germination as well as vegetative propagation. Early records of harakeke pests were not found. Records of harakeke irrigation and the use of fire indicate that Maori created suitable conditions for new cultivations or pii harakeke, which may also have prevented insect infestation. Cumulatively, there is evidence of extensive active management of harakeke. Wharariki and harakeke were found to have distinct environmental niches, with wharariki better able to withstand cooler temperatures, higher rainfall and greater frequency of ground frost than harakeke.
Predictive mapping of harakeke for the northern region of New Zealand shows a low probability of naturally occurring harakeke in much of the Northland and Waikato interior, and a high probability in coastal areas with warm temperatures. It seems likely that Maori transported harakeke into areas where it was unlikely to have occurred naturally and that some apparently 'natural' stands ofharakeke were created and maintained by Maori.
Maori cultivation, dispersal and active management of harakeke, as well as possible creation of wetland areas, emphasises the importance of harakeke as an economic resource prior to European colonisation, and indicates how the New Zealand landscape may have been transformed. Maori ecological knowledge can contribute new perspectives to restoration ecology and ecosystem research.

year: 2005