Systems Neuroscience Commons^™

Towards Identifying Fear And Safety Network States Across Sex, Rhonda Kolaric

Dissertations, Theses, and Capstone Projects

Post-traumatic stress disorder (PTSD) is a trauma- and stressor-related disorder with a lifetime prevalence of 5-6% in men, and 10-12% in women (National Center for PTSD). Generalized anxiety disorder (GAD) is a highly prevalent anxiety- and depression-related psychiatric disorder with a lifetime prevalence of 1-2% in men, and 3-4% in women (National Institutes of Health). Both of these disorders disproportionately affect women. A hallmark feature of both disorders is the maladaptive generalization of fear, in which defensive responses extend beyond the original traumatic or threatening stimulus to neutral or unrelated cues. This overgeneralization can become debilitating, disrupting cognitive, emotional, and …

How To Search For The Engram: Optogenetics And Network Dynamics, Claudia Garcia Jou

Dissertations, Theses, and Capstone Projects

Memories are thought to be encoded by ensembles of neurons called "engram cells", because their artificial activation with optogenetics leads to the behavioral expression of a memory. However, the physiological mechanisms that mediate this process remain unknown. In this thesis, I investigate how optogenetic stimulation of memory-tagged cells changes neuronal firing, spatial coding, and the geometry of neural manifolds. I used an active place avoidance task and a foraging task to label engram cells in the dorsal hippocampus with Channelrhodopsin2 (ChR2). I then recorded the hippocampal activity response to optogenetic stimulation in mice under anesthesia, head-fixed, or freely moving. I …

Design And Advancement Of Analytical Frameworks For In Vivo Single-Photon Calcium Imaging To Characterize Temporal- And Treatment-Dependent Neural Adaptations To Opioid Exposure And Withdrawal In The Medial Prefrontal Cortex, Alexia R. Alsum Dr.

Theses and Dissertations--Pharmacy

Despite the availability of several approved medications for opioid use disorder (OUD), it remains a significant public health concern characterized by persistent neurobiological adaptations that drive relapse and impede successful recovery. The medial prefrontal cortex (mPFC), a region critical for executive control and decision-making, undergoes pronounced functional changes during chronic opioid exposure and withdrawal, yet the cellular mechanisms underlying these adaptations remain poorly understood. This dissertation aims to investigate longitudinal alterations in mPFC neural activity across opioid exposure and withdrawal using in vivo single-photon calcium imaging and newly developed computational frameworks.

Following standard preprocessing to extract and normalize calcium traces, …

The Science Of Sound: Studying The Cognitive, Emotional, And Physiological Effects Of Frequency, Genre, And Music, Jett Yarborough

Senior Honors Theses

Music influences emotion, physiology, and cognition, yet little is known about how the frequency it is tuned to affects these influences. Prior research has shown that music tuned to 432 Hz can reduce stress, lower blood pressure, and improve sleep. My colleagues and I conducted two studies to investigate this. Our research found that music tuned to 432 Hz promotes a significant increase in memory retention and induces a state of focus and relaxation. These results suggest that shifting from the standard tuning frequency of 440 Hz to 432 Hz could have a profoundly positive impact on our daily lives. …

Computational Approaches For Diagnosing Neurological Impairments And Restoring Functional Movement, Serhii Bahdasariants

Graduate Theses, Dissertations, and Problem Reports (ETD)

Movement is the primary means by which the nervous system converts intention into interaction with the environment. Voluntary limb motion enables standing, walking, reaching, and grasping—actions that underpin self‑care, communication, and economic participation. When diseases or injuries disrupt the pathways that couple neural commands to muscle forces—whether through cortical stroke, spinal cord injury, or peripheral nerve damage—mechanical outcomes such as weakness, loss of coordination, and ultimately reduced mobility emerge. These impairments cascade into secondary complications, increased dependence on caregivers, and diminished quality of life. Quantifying how the lesion alters the mechanics of movement is therefore essential for designing targeted interventions …

Neuroendocrine Regulation Of The Luteinizing Hormone Surge And Puberty Onset In Sheep, Max J. Griesgraber

Graduate Theses, Dissertations, and Problem Reports (ETD)

Gonadotropin-releasing hormone (GnRH), luteinizing hormone (LH), and follicle stimulating hormone (FSH) are essential for the reproduction of all mammalian species, including both sheep and humans. GnRH is secreted by hypothalamic neurons into the hypophyseal portal vasculature in a pulsatile manner, which then acts within the anterior pituitary to elicit the release of LH and FSH into wider systemic circulation. In females LH and FSH act on the ovaries to promote estradiol (E2) production, follicular development, and under certain conditions in regard to LH, ovulation. Furthermore, while E2 inhibits GnRH and subsequent LH secretion under most conditions, at high concentrations E2 …

Dissecting The Tissue-Specific Contributions To Seizures, Cardiorespiratory Dysfunction, And Sudden Death In The Kv1.1 Mouse Model Of Epilepsy Using Conditional Knockout Approaches, Kelsey Paulhus

Biological Sciences Theses and Dissertations

Sudden unexpected death in epilepsy (SUDEP), the primary cause of mortality in epilepsy, remains poorly understood. Studies suggest seizures may trigger dangerous signals affecting the heart and lungs leading to collapse and death. The Kv1.1 deficiency mouse model mirrors clinical SUDEP cases, showing spontaneous seizures, cardiorespiratory issues, and premature death. However, this model lacks regional specificity in Kv1.1 deletion, hindering insights into SUDEP’s mechanisms and anatomical substrates.

This dissertation employs three distinct conditional knockout (cKO) techniques to investigate the individual roles for the forebrain, brainstem, and heart in SUDEP related phenotypes. The findings reveal that the forebrain alone can trigger …

Evaluating The Potential Of Using Eeg To Monitor Cognitive Workload In Simulated Suborbital Flight, Erik Seedhouse

Journal of Aviation/Aerospace Education & Research

Mental workload can be assessed using electrophysiological measures of brain activity, such as electroencephalography (EEG). EEG signals reveal cortical electrical activity. This cortical activity was recorded using specialized headsets. The focus of this research was to study cognitive performance (CP) in four pilots during simulated suborbital flights under nominal day and night profiles and under contingency day and night profiles. A 14-channel EMOTIV EEG headset measured the participants' brain activity while they flew simulated flights in a Suborbital Spaceflight Simulator (SSFS). Several sessions of EEG data were recorded from each subject, and feature extraction was applied. Data revealed that real-time …

Linking Spinal Cord Circuits With Upper Limb Sensorimotor Control In Adults With Cerebral Palsy, Saihari Dukkipati

Theses & Dissertations

Cerebral palsy (CP) is the most common neurological disorder originating in childhood, but most of the people living with CP are currently adults. While people with CP continue to get older, the amount of research focused on adults has been rather limited. The early childhood insults leading to CP are thought to originate in the brain, but the effects on the entire neuromuscular system across the lifespan have only recently started to be explored. Of note, recent neuroimaging evidence suggests that the cervical spinal cord structure is atypical in adults with CP. However, it is largely unclear how the neurophysiological …

The Neurological Asymmetry Of Self-Face Recognition, Aleksandra Janowska, Brianna Balugas, Matthew Pardillo, Victoria Mistretta, Katherine Chavarria, Janet Brenya, Taylor Shelansky, Vanessa Martinez, Kitty Pagano, Nathira Ahmad, Samantha Zorns, Abigail Straus, Sarah Sierra, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

While the desire to uncover the neural correlates of consciousness has taken numerous directions, self-face recognition has been a constant in attempts to isolate aspects of self-awareness. The neuroimaging revolution of the 1990s brought about systematic attempts to isolate the underlying neural basis of self-face recognition. These studies, including some of the first fMRI (functional magnetic resonance imaging) examinations, revealed a right-hemisphere bias for self-face recognition in a diverse set of regions including the insula, the dorsal frontal lobe, the temporal parietal junction, and the medial temporal cortex. In this systematic review, we provide confirmation of these data (which are …

Open Neuroscience Initiative, Austin Lim

College of Science and Health Full Text Publications

The Open Neuroscience Initiative is a free-to-use textbook

This project began as a means to overcoming the financial burden that face undergraduate neuroscience students when buying textbooks. By compiling and writing a completely free-to-access textbook that covers the foundations of a typical college introduction to neuroscience course, students would have one less obstacle to overcome in their educational career, allowing them to focus their valuable time and attention on learning rather than finances. To make this project a reality, I began with a humble tweet in May 2019 that managed to gain a tiny bit of traction among the neuroscience …

Spinal Motor Neuron Excitability And Balance Control Changes Following Downslope Walking, Nikki Aitcheson-Huehn

Theses and Dissertations (Comprehensive)

Downslope walking (DSW) has been proposed as a rehabilitation tool for people with Multiple Sclerosis (PwMS) although there are mixed findings in young adults (YA) regarding the balance control changes, despite both populations experiencing depressed spinal motor neuron (MN) pool excitability. Our aim was to determine whether YAs could demonstrate improved balance control in conjunction with SOL H reflex depression (estimate of spinal MN excitability) following DSW. We also aimed to determine whether reciprocal inhibition was a potential mechanism for H reflex depression via conditioned SOL H reflexes. Thirty young adults (23±1.4y, 6 males) were assigned to 30-minutes of DSW …

Can A Comprehensive Transition Plan To Barefoot Running Be The Solution To The Injury Epidemic In American Endurance Runners?, Michael A. Scarlett

CMC Senior Theses

Fossils belonging to the genus Homo, dating as far back as two million years ago, exhibit uniquely efficient features suggesting that early humans had evolved to become exceptional endurance runners. Although they did not have the cushion or stability-control features provided in our modern day running shoes, our early human ancestors experienced far less of the running-related injuries we experience today. The injury rate has been estimated as high as 90% annually for Americans training for a marathon and as high as 79% annually for all American endurance runners. There is an injury epidemic in conventionally shod populations that …

Co-Modulation Masking Release Begins In The Auditory Periphery, Kareem R. Hussein, Agudemu Borjigan, Mark Sayles

The Summer Undergraduate Research Fellowship (SURF) Symposium

Understanding speech in noisy environments can be difficult, especially for people with hearing loss. The background noise can cover up the sounds of interest. Normally, the auditory system works to alleviate this problem by tagging and then cancelling the noise. Our experiments are aimed at understanding the mechanism of this noise cancellation process. We hypothesize that non-linear signal processing in the mammalian cochlea (the most peripheral part of the auditory system) is the basis of noise cancellation. To test this hypothesis, we measured the responses of auditory-nerve fibers (ANFs) to sounds embedded in background noise with different statistical properties. ANFs …

Pathological Effects Of Repeated Concussive Tbi In Mouse Models: Periventricular Damage And Ventriculomegaly, Richard H. Wolferz Jr.

Honors Scholar Theses

Repeated concussive traumatic brain injury (rcTBI) is the most prominent form of head injury affecting the brain, with an estimated 1.7 million Americans affected each year (Kuhn 2012). Neurologists have been concerned about the danger of repeated head impacts since the 1920’s, but researchers have only begun to understand the long-term effects of rcTBI (McKee 2009). Although symptoms can be as mild as dizziness, current research suggests that multiple concussions can lead to a progressive degenerative brain disease known as chronic traumatic encephalopathy (CTE) (Luo 2008, McKee 2009, Kane 2013). Research on the brain is just beginning to scratch the …

Clique Topology Reveals Intrinsic Geometric Structure In Neural Correlations, Chad Giusti, Eva Pastalkova, Carina Curto, Vladimir Itskov

Department of Mathematics: Faculty Publications

Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonlinear monotone transformations. These features can be used to detect both random and geometric structure, and depend only on the relative ordering of matrix entries. We then analyzed the activity of pyramidal neurons in rat hippocampus, recorded while the animal was exploring a 2D environment, and confirmed that our method is able to detect geometric organization using …

Map Kinases Couple Hindbrain-Derived Catecholamine Signals To Hypothalamic Adrenocortical Control Mechanisms During Glycemia-Related Challenges, Arshad Khan, Kimberly Kaminski, Graciela Sanchez-Watts, Todd Ponzio, J. Kuzmiski, Jaideep Bains, Alan Watts

Selected Works Temporary Series

No abstract provided.

Map Kinases Couple Hindbrain-Derived Catecholamine Signals To Hypothalamic Adrenocortical Control Mechanisms During Glycemia-Related Challenges, Khan, Kimberly Kaminski, Graciela Sanchez-Watts, Todd Ponzio, J. Kuzmiski, Jaideep Bains, Alan Watts

Departmental Papers (Biology)

No abstract provided.

A Role For The Forebrain In Mediating Time-Of-Day Differences In Glucocorticoid Counterregulatory Responses To Hypoglycemia In Rats, Lori Gorton, Arshad Khan, Maryann Bohland, Graciela Sanchez-Watts, Casey Donovan, Alan Watts

Selected Works Temporary Series

No abstract provided.

A Role For The Forebrain In Mediating Time-Of-Day Differences In Glucocorticoid Counterregulatory Responses To Hypoglycemia In Rats, Gorton, Arshad Khan, Maryann Bohland, Graciela Sanchez-Watts, Casey Donovan, Alan Watts

Departmental Papers (Biology)

No abstract provided.

Catecholaminergic Control Of Mitogen-Activated Protein Kinase Signaling In Paraventricular Neuroendocrine Neurons In Vivo And In Vitro: A Proposed Role During Glycemic Challenges, Arshad Khan, Todd Ponzio, Graciela Sanchez-Watts, B. Stanley, Glenn Hatton, Alan Watts

Selected Works Temporary Series

No abstract provided.

Catecholaminergic Control Of Mitogen-Activated Protein Kinase Signaling In Paraventricular Neuroendocrine Neurons In Vivo And In Vitro: A Proposed Role During Glycemic Challenges, Khan, Todd Ponzio, Graciela Sanchez-Watts, B. Stanley, Glenn Hatton, Alan Watts

Departmental Papers (Biology)

No abstract provided.

Activation In Neural Networks Controlling Ingestive Behaviors: What Does It Mean, And How Do We Map And Measure It?, Alan Watts, Arshad Khan, Graciela Sanchez-Watts, Dawna Salter, Christina Neuner

Selected Works Temporary Series

No abstract provided.

Activation In Neural Networks Controlling Ingestive Behaviors: What Does It Mean, And How Do We Map And Measure It?, Watts, Arshad Khan, Graciela Sanchez-Watts, Dawna Salter, Christina Neuner

Departmental Papers (Biology)

No abstract provided.

Lateral Hypothalamic Signaling Mechanisms Underlying Feeding Stimulation: Differential Contributions Of Src Family Tyrosine Kinases To Feeding Triggered Either By Nmda Injection Or By Food Deprivation, Arshad Khan, Herman Cheung, Elizabeth Gillard, Jennifer Palarca, Derek Welsbie, James Gurd, B. Stanley

Selected Works Temporary Series

No abstract provided.

Lateral Hypothalamic Signaling Mechanisms Underlying Feeding Stimulation: Differential Contributions Of Src Family Tyrosine Kinases To Feeding Triggered Either By Nmda Injection Or By Food Deprivation, Khan, Herman Cheung, Elizabeth Gillard, Jennifer Palarca, Derek Welsbie, James Gurd, B. Stanley

Departmental Papers (Biology)

No abstract provided.

Intravenous 2-Deoxy-D-Glucose Injection Rapidly Elevates Levels Of The Phosphorylated Forms Of P44/42 Mitogen-Activated Protein Kinases (Extracellularly Regulated Kinases 1/2) In Rat Hypothalamic Parvicellular Paraventricular Neurons, Arshad Khan, Alan Watts

Selected Works Temporary Series

No abstract provided.

Intravenous 2-Deoxy-D-Glucose Injection Rapidly Elevates Levels Of The Phosphorylated Forms Of P44/42 Mitogen-Activated Protein Kinases (Extracellularly Regulated Kinases 1/2) In Rat Hypothalamic Parvicellular Paraventricular Neurons, Khan, Alan Watts

Departmental Papers (Biology)

No abstract provided.

Lateral Hypothalamic Nmda Receptor Subunits Nr2a And/Or Nr2b Mediate Eating: Immunochemical/Behavioral Evidence, Arshad Khan, Margarita Curras, Jennifer Dao, Faizi Jamal, Rishi Goel, Elizabeth Gillard, Stefany Wolfsohn, B. Stanley

Selected Works Temporary Series

No abstract provided.

Lateral Hypothalamic Nmda Receptor Subunits Nr2a And/Or Nr2b Mediate Eating: Immunochemical/Behavioral Evidence, Khan, Margarita Curras, Jennifer Dao, Faizi Jamal, Rishi Goel, Elizabeth Gillard, Stefany Wolfsohn, B. Stanley

Departmental Papers (Biology)

No abstract provided.