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There are two theories of how the neocortex processes sound. The feature detection theory posits that cortical neurons process sound to extract its features, whereas, in the decoding theory, cortical neurons are viewed as the decoders of “sound objects”: specific spectrotemporal patterns. In this thesis, I assess both theories in a set of longitudinal experiments with simple and complex sounds presented to awake and isoflurane-anesthetized mice. For the feature detection theory, the auditory cortex (AC) maps of tone frequency and frequency modulation (FM) rate are updated. In these maps, new areas and topographic gradients are discovered. The maps are stable across a recording period and reproducible between brain states. Moreover, a region in the primary AC encodes for the FM direction, crucial in the perception of complex sounds. Finally, fast FM rate topographic areas are the most involved in processing MVocs. For the prediction theory, both AC and the dorsal neocortex (DC) were considered. First, network analysis revealed that AC and DC work together to process sounds, with the interaction level determined by acoustic complexity and brain state. Second, a classification analysis showed that both cortices are informative of the stimuli, with AC twice as informative as DC. Isoflurane-anesthesia maintains the informative power of AC but vanishes the power of DC, except for simple sounds. Lastly, a regression analysis between sounds and behavior (predictors) and the cortical activity (response) was performed to assess the power of stimuli to explain the cortical activity. The sound stimuli could explain AC and DC activity up to 68% and 32%, respectively. The higher explanation power of sound is observed for more complex sounds in the awake state. To conclude, despite the simplicity of the feature detection theory, the detection theory provides a superior understanding of the neocortical functions in auditory processing.

Traditionally, behavioural research of Alzheimer disease animal models involved specialized experiments that require dedicated apparatus and presence of experimenter. However, experiment apparatus and the interaction between animals and experimenters can influence the behaviours of the animals, and result in difficulty in reproducibility. One recent innovation is to study behaviours of Alzheimer disease mouse model in their homecages. This thesis presents an experiment using automated homecages to observe the homecage behaviours of 5xFAD mouse models over 26 weeks. By measuring daily activity level, circadian rhythm and excursion behaviours, the experiment successfully produces measurements consistent with prior knowledge and provides some further insight in the behaviours of the mouse model. This thesis validates the approach using homecage behaviours as a paradigm for AD animal research.

Analysis of bovine movement and behavior is crucial in detecting their motor disorders and maintaining their welfare. Quantitative gait analysis methods have been designed to facilitate this task, but the on-site subjective assessment of the gait pattern remains prominent and depends on human expertise. Gait pattern could be assessed in feedlot cattle using AI as a substitute for the absence of human diagnosis, but creating an AI diagnosis procedure requires substantial behavioral information for training the AI tool. One solution for obtaining behavioral information is to use AI-assisted tools for diagnosis based on recordings of cattle movement. In this study, we created a three-dimensional digital representation of walking cattle to generate the required information and compare its applicability to that of the actual gait patterns. We used video recordings of cattle walking and trotting, and then used them as reference to create three-dimensional pose representations. Then, we introduced variations to these representations by altering specific aspects of the original walking cow model and its environment. We then tested the combined representations against the real data to see if they can prove useful in training a deep neural network for detecting gait pattern and features. This method can compensate for the scarcity of behavioral data, provide information to create mathematical representations of specific behaviors and be used for the development of smart-phone-based diagnosis systems.

Analysis of bovine movement and behavior is crucial in detecting their motor disorders and maintaining their welfare. Quantitative gait analysis methods have been designed to facilitate this task, but the on-site subjective assessment of the gait pattern remains prominent and depends on human expertise. Gait pattern could be assessed in feedlot cattle using AI as a substitute for the absence of human diagnosis, but creating an AI diagnosis procedure requires substantial behavioral information for training the AI tool. One solution for obtaining behavioral information is to use AI-assisted tools for diagnosis based on recordings of cattle movement. In this study, we created a three-dimensional digital representation of walking cattle to generate the required information and compare its applicability to that of the actual gait patterns. We used video recordings of cattle walking and trotting, and then used them as reference to create three-dimensional pose representations. Then, we introduced variations to these representations by altering specific aspects of the original walking cow model and its environment. We then tested the combined representations against the real data to see if they can prove useful in training a deep neural network for detecting gait pattern and features. This method can compensate for the scarcity of behavioral data, provide information to create mathematical representations of specific behaviors and be used for the development of smart-phone-based diagnosis systems.

Traditionally, behavioural research of Alzheimer disease animal models involved specialized experiments that require dedicated apparatus and presence of experimenter. However, experiment apparatus and the interaction between animals and experimenters can influence the behaviours of the animals, and result in difficulty in reproducibility. One recent innovation is to study behaviours of Alzheimer disease mouse model in their homecages. This thesis presents an experiment using automated homecages to observe the homecage behaviours of 5xFAD mouse models over 26 weeks. By measuring daily activity level, circadian rhythm and excursion behaviours, the experiment successfully produces measurements consistent with prior knowledge and provides some further insight in the behaviours of the mouse model. This thesis validates the approach using homecage behaviours as a paradigm for AD animal research.

Analysis of bovine movement and behavior is crucial in detecting their motor disorders and maintaining their welfare. Quantitative gait analysis methods have been designed to facilitate this task, but the on-site subjective assessment of the gait pattern remains prominent and depends on human expertise. Gait pattern could be assessed in feedlot cattle using AI as a substitute for the absence of human diagnosis, but creating an AI diagnosis procedure requires substantial behavioral information for training the AI tool. One solution for obtaining behavioral information is to use AI-assisted tools for diagnosis based on recordings of cattle movement. In this study, we created a three-dimensional digital representation of walking cattle to generate the required information and compare its applicability to that of the actual gait patterns. We used video recordings of cattle walking and trotting, and then used them as reference to create three-dimensional pose representations. Then, we introduced variations to these representations by altering specific aspects of the original walking cow model and its environment. We then tested the combined representations against the real data to see if they can prove useful in training a deep neural network for detecting gait pattern and features. This method can compensate for the scarcity of behavioral data, provide information to create mathematical representations of specific behaviors and be used for the development of smart-phone-based diagnosis systems.

From the waking hours into the depths of sleep, the hippocampus and the neocortex engage in an enigmatic dialogue on that which occurs, that which had occurred and that which could occur eventually. Together, this information weaves the memories of our past and the knowledge of our world. Yet, if one attempts to eavesdrop on this conversation, they would be perplexed to discover that the details that would give rise to such sophisticated structures could mostly be diluted into the mapping of space. What invisible bonds may tie space and memory in the brain, this present thesis offers no answers for. What it does offer, instead, are more enigmas to be fancied over and more confusions to be resolved: (1) The neural representation of space is found across multiple regions of the dorsal cortex and necessitates an intact hippocampus to form; (2) During offline periods, the retrosplenial cortex spontaneously reinstates patterns of activity specifically related to the locations of spatial landmarks; (3) The secondary motor cortex, in contrast, reinstates a conjunction of spatial and non-spatial information, in the forms of recent trajectories undertaken in an environment and the locations of visuo-tactile landmarks, respectively. Together, these results elaborate a spatial code that is heavily redundant and dispersed, with a link to mnemonic processing — a neural correlate of parallel and distributed engrams.

Analysis of bovine movement and behavior is crucial in detecting their motor disorders and maintaining their welfare. Quantitative gait analysis methods have been designed to facilitate this task, but the on-site subjective assessment of the gait pattern remains prominent and depends on human expertise. Gait pattern could be assessed in feedlot cattle using AI as a substitute for the absence of human diagnosis, but creating an AI diagnosis procedure requires substantial behavioral information for training the AI tool. One solution for obtaining behavioral information is to use AI-assisted tools for diagnosis based on recordings of cattle movement. In this study, we created a three-dimensional digital representation of walking cattle to generate the required information and compare its applicability to that of the actual gait patterns. We used video recordings of cattle walking and trotting, and then used them as reference to create three-dimensional pose representations. Then, we introduced variations to these representations by altering specific aspects of the original walking cow model and its environment. We then tested the combined representations against the real data to see if they can prove useful in training a deep neural network for detecting gait pattern and features. This method can compensate for the scarcity of behavioral data, provide information to create mathematical representations of specific behaviors and be used for the development of smart-phone-based diagnosis systems.

This thesis investigates the stability of points on the motor cortex of the mouse produced using optogenetic stimulation. Mice were implanted with fiber optic probes in four areas of the motor cortex and one in a non-motor area for control. They received stimulation of various frequency and duration as they engaged in six different voluntary and automatic behaviour. Control stimulation was also administered via a separate optic probe located on the side of the apparatus. The general findings are that the outcome of the stimulation depends on the ongoing behaviour of the mouse at the time of stimulation. Thus, stimulation effects are unstable, and behaviour is a contributing factor.

This thesis investigates the stability of points on the motor cortex of the mouse produced using optogenetic stimulation. Mice were implanted with fiber optic probes in four areas of the motor cortex and one in a non-motor area for control. They received stimulation of various frequency and duration as they engaged in six different voluntary and automatic behaviour. Control stimulation was also administered via a separate optic probe located on the side of the apparatus. The general findings are that the outcome of the stimulation depends on the ongoing behaviour of the mouse at the time of stimulation. Thus, stimulation effects are unstable, and behaviour is a contributing factor.

From the waking hours into the depths of sleep, the hippocampus and the neocortex engage in an enigmatic dialogue on that which occurs, that which had occurred and that which could occur eventually. Together, this information weaves the memories of our past and the knowledge of our world. Yet, if one attempts to eavesdrop on this conversation, they would be perplexed to discover that the details that would give rise to such sophisticated structures could mostly be diluted into the mapping of space. What invisible bonds may tie space and memory in the brain, this present thesis offers no answers for. What it does offer, instead, are more enigmas to be fancied over and more confusions to be resolved: (1) The neural representation of space is found across multiple regions of the dorsal cortex and necessitates an intact hippocampus to form; (2) During offline periods, the retrosplenial cortex spontaneously reinstates patterns of activity specifically related to the locations of spatial landmarks; (3) The secondary motor cortex, in contrast, reinstates a conjunction of spatial and non-spatial information, in the forms of recent trajectories undertaken in an environment and the locations of visuo-tactile landmarks, respectively. Together, these results elaborate a spatial code that is heavily redundant and dispersed, with a link to mnemonic processing — a neural correlate of parallel and distributed engrams.

From the waking hours into the depths of sleep, the hippocampus and the neocortex engage in an enigmatic dialogue on that which occurs, that which had occurred and that which could occur eventually. Together, this information weaves the memories of our past and the knowledge of our world. Yet, if one attempts to eavesdrop on this conversation, they would be perplexed to discover that the details that would give rise to such sophisticated structures could mostly be diluted into the mapping of space. What invisible bonds may tie space and memory in the brain, this present thesis offers no answers for. What it does offer, instead, are more enigmas to be fancied over and more confusions to be resolved: (1) The neural representation of space is found across multiple regions of the dorsal cortex and necessitates an intact hippocampus to form; (2) During offline periods, the retrosplenial cortex spontaneously reinstates patterns of activity specifically related to the locations of spatial landmarks; (3) The secondary motor cortex, in contrast, reinstates a conjunction of spatial and non-spatial information, in the forms of recent trajectories undertaken in an environment and the locations of visuo-tactile landmarks, respectively. Together, these results elaborate a spatial code that is heavily redundant and dispersed, with a link to mnemonic processing — a neural correlate of parallel and distributed engrams.

There are two theories of how the neocortex processes sound. The feature detection theory posits that cortical neurons process sound to extract its features, whereas, in the decoding theory, cortical neurons are viewed as the decoders of “sound objects”: specific spectrotemporal patterns. In this thesis, I assess both theories in a set of longitudinal experiments with simple and complex sounds presented to awake and isoflurane-anesthetized mice. For the feature detection theory, the auditory cortex (AC) maps of tone frequency and frequency modulation (FM) rate are updated. In these maps, new areas and topographic gradients are discovered. The maps are stable across a recording period and reproducible between brain states. Moreover, a region in the primary AC encodes for the FM direction, crucial in the perception of complex sounds. Finally, fast FM rate topographic areas are the most involved in processing MVocs. For the prediction theory, both AC and the dorsal neocortex (DC) were considered. First, network analysis revealed that AC and DC work together to process sounds, with the interaction level determined by acoustic complexity and brain state. Second, a classification analysis showed that both cortices are informative of the stimuli, with AC twice as informative as DC. Isoflurane-anesthesia maintains the informative power of AC but vanishes the power of DC, except for simple sounds. Lastly, a regression analysis between sounds and behavior (predictors) and the cortical activity (response) was performed to assess the power of stimuli to explain the cortical activity. The sound stimuli could explain AC and DC activity up to 68% and 32%, respectively. The higher explanation power of sound is observed for more complex sounds in the awake state. To conclude, despite the simplicity of the feature detection theory, the detection theory provides a superior understanding of the neocortical functions in auditory processing.

There are two theories of how the neocortex processes sound. The feature detection theory posits that cortical neurons process sound to extract its features, whereas, in the decoding theory, cortical neurons are viewed as the decoders of “sound objects”: specific spectrotemporal patterns. In this thesis, I assess both theories in a set of longitudinal experiments with simple and complex sounds presented to awake and isoflurane-anesthetized mice. For the feature detection theory, the auditory cortex (AC) maps of tone frequency and frequency modulation (FM) rate are updated. In these maps, new areas and topographic gradients are discovered. The maps are stable across a recording period and reproducible between brain states. Moreover, a region in the primary AC encodes for the FM direction, crucial in the perception of complex sounds. Finally, fast FM rate topographic areas are the most involved in processing MVocs. For the prediction theory, both AC and the dorsal neocortex (DC) were considered. First, network analysis revealed that AC and DC work together to process sounds, with the interaction level determined by acoustic complexity and brain state. Second, a classification analysis showed that both cortices are informative of the stimuli, with AC twice as informative as DC. Isoflurane-anesthesia maintains the informative power of AC but vanishes the power of DC, except for simple sounds. Lastly, a regression analysis between sounds and behavior (predictors) and the cortical activity (response) was performed to assess the power of stimuli to explain the cortical activity. The sound stimuli could explain AC and DC activity up to 68% and 32%, respectively. The higher explanation power of sound is observed for more complex sounds in the awake state. To conclude, despite the simplicity of the feature detection theory, the detection theory provides a superior understanding of the neocortical functions in auditory processing.

This thesis investigates the stability of points on the motor cortex of the mouse produced using optogenetic stimulation. Mice were implanted with fiber optic probes in four areas of the motor cortex and one in a non-motor area for control. They received stimulation of various frequency and duration as they engaged in six different voluntary and automatic behaviour. Control stimulation was also administered via a separate optic probe located on the side of the apparatus. The general findings are that the outcome of the stimulation depends on the ongoing behaviour of the mouse at the time of stimulation. Thus, stimulation effects are unstable, and behaviour is a contributing factor.

From the waking hours into the depths of sleep, the hippocampus and the neocortex engage in an enigmatic dialogue on that which occurs, that which had occurred and that which could occur eventually. Together, this information weaves the memories of our past and the knowledge of our world. Yet, if one attempts to eavesdrop on this conversation, they would be perplexed to discover that the details that would give rise to such sophisticated structures could mostly be diluted into the mapping of space. What invisible bonds may tie space and memory in the brain, this present thesis offers no answers for. What it does offer, instead, are more enigmas to be fancied over and more confusions to be resolved: (1) The neural representation of space is found across multiple regions of the dorsal cortex and necessitates an intact hippocampus to form; (2) During offline periods, the retrosplenial cortex spontaneously reinstates patterns of activity specifically related to the locations of spatial landmarks; (3) The secondary motor cortex, in contrast, reinstates a conjunction of spatial and non-spatial information, in the forms of recent trajectories undertaken in an environment and the locations of visuo-tactile landmarks, respectively. Together, these results elaborate a spatial code that is heavily redundant and dispersed, with a link to mnemonic processing — a neural correlate of parallel and distributed engrams.

Traditionally, behavioural research of Alzheimer disease animal models involved specialized experiments that require dedicated apparatus and presence of experimenter. However, experiment apparatus and the interaction between animals and experimenters can influence the behaviours of the animals, and result in difficulty in reproducibility. One recent innovation is to study behaviours of Alzheimer disease mouse model in their homecages. This thesis presents an experiment using automated homecages to observe the homecage behaviours of 5xFAD mouse models over 26 weeks. By measuring daily activity level, circadian rhythm and excursion behaviours, the experiment successfully produces measurements consistent with prior knowledge and provides some further insight in the behaviours of the mouse model. This thesis validates the approach using homecage behaviours as a paradigm for AD animal research.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

Coordinated activity in the hippocampal-neocortical network around hippocampal sharp-wave ripples (SWRs) plays an instrumental role in memory processing in the brain. SWRs occur in both sleep and awake states, though under two significantly different behavioural and chemical circumstances. Previous studies have reported different patterns of peri-SWR neocortical modulations between these states; however, their findings have been limited to one or a few discrete regions of the neocortex. To extend previous findings, we conducted wide-field optical imaging of the mouse neocortical voltage and glutamate activity combined with hippocampal electrophysiological recording. We found topographically- and temporally-organized patterns of neocortical glutamate and voltage activity around sleep and awake SWRs, though with pronounced differences. These findings highlight the state-dependency of the hippocampal-neocortical network’s computations and possibly functions. Moreover, they provide a spatiotemporal map of the neocortex around SWRs that could guide future studies on the role of hippocampal-neocortical interactions in memory consolidation.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

This thesis examines the effects of chronic noise stress on neocortical and hippocampal-amygdala networks and their behavioural correlates. Psychological symptoms of stress, including anxiety and depression, are thought to be caused by alterations in functional connectivity within the brain. A functional pathway has been established between the basolateral amygdala, which mediates emotional responses to stressors, the ventral hippocampus which provides context to emotional memories and experiences, and medial prefrontal cortex, which alters attention and perception of stressors. This network is adaptive in the presence of an acute stressor, allowing an organism to optimally prepare and deal with the source of stress, but may become dysfunctional when exposed to chronic stress. The hypotheses that chronic noise stress correlates to neocortical hyperconnectivity and decreased synchrony between the amygdala and hippocampus, correlates to altered behaviour, and correlates to altered brain morphology were tested in head-fixed mice using optical imaging and behavioural recordings.

In classic measures of fear induced freezing behavior, animals stop all movement except breathing. Many large-scale recording techniques in modern neuroscience such as wide-field and two-photon fluorescent imaging require animals be in a head-fixed preparation. Here we demonstrate that it is possible to measure freezing behavior in head-fixed mice based on video measurements of motion, the pupillary response, and electromyography of neck muscles. Animals were either conditioned to form an association between a tone (conditioned stimulus; CS) and a footshock (unconditioned stimulus; US) or were presented both tones and footshocks explicitly unpaired. Animals who were conditioned to form an association showed less movement, and a stronger pupil response when presented with the CS. We outline key considerations which are likely important in establishing a strong fear response in a head-fixed preparation.

Alzheimer’s Disease (AD) is a one of the largest health crises in the world. Noise stress is identified as one of the risk factors for AD development. A series of research demonstrates the adverse of effects of both pre- and post-natal auditory/noise stress on the brain development in adult offspring and adults APPNL-G-F mice, a mouse model of AD. There are limited but expensive pharmaceutical interventions to treat AD and most of the treatment options are not for cure or prevention, but to slow down the progression of the disease. The aim of this thesis was to examine the effect of tactile stimulation (TS) on AD-like symptoms and pathology. The results from this study suggest that TS improves the AD-like symptoms of cognition, motor, and anxiety-like behaviours, and that these improvements are associated with reduced AD pathology in APP mice.

Alzheimer’s Disease (AD) is a one of the largest health crises in the world. Noise stress is identified as one of the risk factors for AD development. A series of research demonstrates the adverse of effects of both pre- and post-natal auditory/noise stress on the brain development in adult offspring and adults APPNL-G-F mice, a mouse model of AD. There are limited but expensive pharmaceutical interventions to treat AD and most of the treatment options are not for cure or prevention, but to slow down the progression of the disease. The aim of this thesis was to examine the effect of tactile stimulation (TS) on AD-like symptoms and pathology. The results from this study suggest that TS improves the AD-like symptoms of cognition, motor, and anxiety-like behaviours, and that these improvements are associated with reduced AD pathology in APP mice.

Alzheimer’s Disease (AD) is a one of the largest health crises in the world. Noise stress is identified as one of the risk factors for AD development. A series of research demonstrates the adverse of effects of both pre- and post-natal auditory/noise stress on the brain development in adult offspring and adults APPNL-G-F mice, a mouse model of AD. There are limited but expensive pharmaceutical interventions to treat AD and most of the treatment options are not for cure or prevention, but to slow down the progression of the disease. The aim of this thesis was to examine the effect of tactile stimulation (TS) on AD-like symptoms and pathology. The results from this study suggest that TS improves the AD-like symptoms of cognition, motor, and anxiety-like behaviours, and that these improvements are associated with reduced AD pathology in APP mice.