title: The Effect of Cell Immobilization by Calcium Alginate on Bacterially Induced Calcium Carbonate Precipitation

authors: Seifan, Mostafa

subjects: bacteria

abstract: Microbially induced mineral precipitation is recognized as a widespread phenomenon in nature. A diverse range of minerals including carbonate, sulphides, silicates, and phosphates can be produced through biomineralization. Calcium carbonate (CaCO₃) is one of the most common substances used in various industries and is mostly extracted by mining. In recent years, production of CaCO₃ by bacteria has drawn much attention because it is an environmentally- and health-friendly pathway. Although CaCO₃ can be produced by some genera of bacteria through autotrophic and heterotrophic pathways, the possibility of producing CaCO₃ in different environmental conditions has remained a challenge to determine. In this study, calcium alginate was proposed as a protective carrier to increase the bacterial tolerance to extreme environmental conditions. The model showed that the highest concentration of CaCO₃ is achieved when the bacterial cells are immobilized in the calcium alginate beads fabricated using 1.38% w/v Na-alginate and 0.13 M CaCl₂.

text: The Effect of Cell Immobilization by Calcium Alginate on Bacterially Induced Calcium Carbonate Precipitation Microbially induced mineral precipitation is recognized as a widespread phenomenon in nature. A diverse range of minerals including carbonate, sulphides, silicates, and phosphates can be produced through biomineralization. Calcium carbonate (CaCO₃) is one of the most common substances used in various industries and is mostly extracted by mining. In recent years, production of CaCO₃ by bacteria has drawn much attention because it is an environmentally- and health-friendly pathway. Although CaCO₃ can be produced by some genera of bacteria through autotrophic and heterotrophic pathways, the possibility of producing CaCO₃ in different environmental conditions has remained a challenge to determine. In this study, calcium alginate was proposed as a protective carrier to increase the bacterial tolerance to extreme environmental conditions. The model showed that the highest concentration of CaCO₃ is achieved when the bacterial cells are immobilized in the calcium alginate beads fabricated using 1.38% w/v Na-alginate and 0.13 M CaCl₂.

year: 2017

title: Dynamics and precursor signs for phase transitions in neural systems

authors: Negahbani, Ehsan

subjects: nonlinear dynamics

abstract: This thesis investigates neural state transitions associated with sleep, seizure and anaesthesia. The aim is to address the question: How does a brain traverse the critical threshold between distinct cortical states, both healthy and pathological? Specifically we are interested in sub-threshold neural behaviour immediately prior to state transition. We use theoretical neural modelling (single spiking neurons, a network of these, and a mean-field continuum limit) and in vitro experiments to address this question.
Dynamically realistic equations of motion for thalamic relay neuron, reticular nuclei, cortical pyramidal and cortical interneuron in different vigilance states are developed, based on the Izhikevich spiking neuron model. A network of cortical neurons is assembled to examine the behaviour of the gamma-producing cortical network and its transition to lower frequencies due to effect of anaesthesia. Then a three-neuron model for the thalamocortical loop for sleep spindles is presented. Numerical simulations of these networks confirms spiking consistent with reported in vivo measurement results, and provides supporting evidence for precursor indicators of imminent phase transition due to occurrence of individual spindles.
To complement the spiking neuron networks, we study the Wilson–Cowan neural mass equations describing homogeneous cortical columns and a 1D spatial cluster of such columns. The abstract representation of cortical tissue by a pair of coupled integro-differential equations permits thorough linear stability, phase plane and bifurcation analyses. This model shows a rich set of spatial and temporal bifurcations marking the boundary to state transitions: saddle-node, Hopf, Turing, and mixed Hopf–Turing. Close to state transition, white-noise-induced subthreshold fluctuations show clear signs of critical slowing down with prolongation and strengthening of autocorrelations, both in time and space, irrespective of bifurcation type.
Attempts at in vitro capture of these predicted leading indicators form the last part of the thesis. We recorded local field potentials (LFPs) from cortical and hippocampal slices of mouse brain. State transition is marked by the emergence and cessation of spontaneous seizure-like events (SLEs) induced by bathing the slices in an artificial cerebral spinal fluid containing no magnesium ions. Phase-plane analysis of the LFP time-series suggests that distinct bifurcation classes can be responsible for state change to seizure. Increased variance and growth of spectral power at low frequencies (f < 15 Hz) was observed in LFP recordings prior to initiation of some SLEs. In addition we demonstrated prolongation of electrically evoked potentials in cortical tissue, while forwarding the slice to a seizing regime. The results offer the possibility of capturing leading temporal indicators prior to seizure generation, with potential consequences for understanding epileptogenesis.
Guided by dynamical systems theory this thesis captures evidence for precursor signs of phase transitions in neural systems using mathematical and computer-based modelling as well as in vitro experiments.

text: Dynamics and precursor signs for phase transitions in neural systems This thesis investigates neural state transitions associated with sleep, seizure and anaesthesia. The aim is to address the question: How does a brain traverse the critical threshold between distinct cortical states, both healthy and pathological? Specifically we are interested in sub-threshold neural behaviour immediately prior to state transition. We use theoretical neural modelling (single spiking neurons, a network of these, and a mean-field continuum limit) and in vitro experiments to address this question.
Dynamically realistic equations of motion for thalamic relay neuron, reticular nuclei, cortical pyramidal and cortical interneuron in different vigilance states are developed, based on the Izhikevich spiking neuron model. A network of cortical neurons is assembled to examine the behaviour of the gamma-producing cortical network and its transition to lower frequencies due to effect of anaesthesia. Then a three-neuron model for the thalamocortical loop for sleep spindles is presented. Numerical simulations of these networks confirms spiking consistent with reported in vivo measurement results, and provides supporting evidence for precursor indicators of imminent phase transition due to occurrence of individual spindles.
To complement the spiking neuron networks, we study the Wilson–Cowan neural mass equations describing homogeneous cortical columns and a 1D spatial cluster of such columns. The abstract representation of cortical tissue by a pair of coupled integro-differential equations permits thorough linear stability, phase plane and bifurcation analyses. This model shows a rich set of spatial and temporal bifurcations marking the boundary to state transitions: saddle-node, Hopf, Turing, and mixed Hopf–Turing. Close to state transition, white-noise-induced subthreshold fluctuations show clear signs of critical slowing down with prolongation and strengthening of autocorrelations, both in time and space, irrespective of bifurcation type.
Attempts at in vitro capture of these predicted leading indicators form the last part of the thesis. We recorded local field potentials (LFPs) from cortical and hippocampal slices of mouse brain. State transition is marked by the emergence and cessation of spontaneous seizure-like events (SLEs) induced by bathing the slices in an artificial cerebral spinal fluid containing no magnesium ions. Phase-plane analysis of the LFP time-series suggests that distinct bifurcation classes can be responsible for state change to seizure. Increased variance and growth of spectral power at low frequencies (f < 15 Hz) was observed in LFP recordings prior to initiation of some SLEs. In addition we demonstrated prolongation of electrically evoked potentials in cortical tissue, while forwarding the slice to a seizing regime. The results offer the possibility of capturing leading temporal indicators prior to seizure generation, with potential consequences for understanding epileptogenesis.
Guided by dynamical systems theory this thesis captures evidence for precursor signs of phase transitions in neural systems using mathematical and computer-based modelling as well as in vitro experiments.

year: 2014

title: Housing, mental health, and homelessness: Exploring lived experiences of homelessness to identify barriers to sustainable housing for vulnerable populations

authors: Cresswell, Caitlin Grace

subjects: Homelessness

abstract: Homelessness has become a much talked about topic in Aotearoa New Zealand in 2018 and the preceding years. This thesis explores the experiences of five people who have mental illness and have lived experience of homelessness in Aotearoa New Zealand, and two staff members who work closely with people who experience both mental illness and homelessness. The theoretical frameworks that inform this thesis are narrative research, social constructionism and humanistic psychology. Particular attention was paid to using theoretical frameworks and interview methods that suited Māori (the indigenous population of Aotearoa New Zealand) due to the inequities experienced by Māori in mental health and homelessness, and the majority of participants identifying as New Zealand Māori. Participants’ narratives were gathered using semi- structured interviews. This study argues the importance of a humanistic perspective being used for research on homelessness. In contrast to traditional psychology, humanistic psychology emphasises respecting individual participants’ voice and narratives about their personal experiences of homelessness while considering the environment that influence these narratives. The participants’ narratives reflected their desire to be viewed as more than their life circumstances and illness through the sharing of their life stories. While there has been growing public awareness about mental illness, stigma still exists about mental illness which influences social narratives and how people who have mental illness understand their experiences. I argue that people who are vulnerable to homelessness, like those who experience mental illness, should have better protection from homelessness. To achieve this, I argue that structural barriers to finding, gaining and sustaining housing need to be addressed,
iii
including the design of welfare and housing services. Additionally, there needs to be recognition that the solutions to homelessness are complex and require a whole of system approach to effectively address and prevent homelessness. Recognising the complex nature of homelessness and it’s solutions will help bring a focus to establishing predominantly preventative solutions while also providing emergency housing for people in need.

text: Housing, mental health, and homelessness: Exploring lived experiences of homelessness to identify barriers to sustainable housing for vulnerable populations Homelessness has become a much talked about topic in Aotearoa New Zealand in 2018 and the preceding years. This thesis explores the experiences of five people who have mental illness and have lived experience of homelessness in Aotearoa New Zealand, and two staff members who work closely with people who experience both mental illness and homelessness. The theoretical frameworks that inform this thesis are narrative research, social constructionism and humanistic psychology. Particular attention was paid to using theoretical frameworks and interview methods that suited Māori (the indigenous population of Aotearoa New Zealand) due to the inequities experienced by Māori in mental health and homelessness, and the majority of participants identifying as New Zealand Māori. Participants’ narratives were gathered using semi- structured interviews. This study argues the importance of a humanistic perspective being used for research on homelessness. In contrast to traditional psychology, humanistic psychology emphasises respecting individual participants’ voice and narratives about their personal experiences of homelessness while considering the environment that influence these narratives. The participants’ narratives reflected their desire to be viewed as more than their life circumstances and illness through the sharing of their life stories. While there has been growing public awareness about mental illness, stigma still exists about mental illness which influences social narratives and how people who have mental illness understand their experiences. I argue that people who are vulnerable to homelessness, like those who experience mental illness, should have better protection from homelessness. To achieve this, I argue that structural barriers to finding, gaining and sustaining housing need to be addressed,
iii
including the design of welfare and housing services. Additionally, there needs to be recognition that the solutions to homelessness are complex and require a whole of system approach to effectively address and prevent homelessness. Recognising the complex nature of homelessness and it’s solutions will help bring a focus to establishing predominantly preventative solutions while also providing emergency housing for people in need.

year: 2018