Systems Neuroscience Commons^™

Mapping And Modeling Threat-Evoked Brain States After Early Life Adversity, Taylor W. Uselman

Biomedical Sciences ETDs

Early life adversity (ELA) increases lifelong neuropsychiatric vulnerability. Yet how ELA reorganizes brain-wide activity and circuit coordination across later experience remains unclear. This dissertation tests the hypothesis that ELA alters adult brain-wide activity and responses to threat through disrupted coordination among neural systems that regulate emotional experience, including prefrontal-limbic and monoaminergic systems. Longitudinal manganese-enhanced MRI of adult mice exposed to standard or fragmented early care, combined with computational processing and statistical modeling, quantified brain states before, during, and long after innate predator threat. These studies established that acute threat evokes large-scale, distributed brain activity that evolves over time. ELA potentiates …

Transcranial Ac Modulation Of Cerebellar Nuclear Activity In Awake Animals, Nuran Kavakli

Dissertations

Entrainment of cerebellar nuclear (CN) cells via cerebellar transcranial alternating current stimulation (ctACS) has been reported in animals under ketamine/xylazine anesthesia. Our main objective was to demonstrate modulation of CN activity in unanesthetized, freely moving animals using ctACS. Multi-channel carbon-fiber electrodes were implanted into the interpositus nucleus for recording multi-unit (MU) activity, and thin-film electrodes were implanted subcutaneously over the posterior cerebellum for stimulation. A frequency-domain-based metric was developed to quantify modulation from MU signals. The results demonstrated modulation in a wide range of frequencies (4 Hz-300 Hz) as in anesthetized animals. In contrast, the amplitude of the peak in …

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 …

Modeling Synaptic Dysfunction As Neural Contagion: A Graph-Based Sedr Framework For Simulating Signal Spread, Michelle Marfo, Dr. Padmanabhan Seshaiyer, Alonso Ogueda-Oliva

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Influence Of Task On The Geometry Of A Perceptual Space, Jonathan D. Victor, Mary M. Conte

MODVIS Workshop

Perceptual spaces are representations of a sensory or cognitive domain in which the domain’s elements correspond to points, and distances between these points are perceptual differences. Proximity relationships within a perceptual space can support a variety of functions, including discrimination, grouping, learning, and generalization. These diverse functions may use the features of the domain in different ways, resulting in task-dependent influences on the geometry of the space.

To identify and characterize these influences, we focused on a domain of visual textures. These textures varied across many dimensions, including mean luminance and low- and high-order spatial correlations, which formed the axes …

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 …

Robust And Generalizable Representations In The Hippocampus, Hung-Tu Chen

Dartmouth College Ph.D Dissertations

An intelligent system must balance generalizing across similar experiences with maintaining the distinctiveness of each experience. This thesis explores how the hippocampus manages this balance through its neural representations to support adaptive behavior. In Chapter 1, I provide an overview of key hippocampal phenomena that contribute to this process, including remapping, splitter signal, and replay. In Chapter 2, I challenge the concept of random remapping by showing that it is possible to predict, better than chance, how a given experience will be encoded in the hippocampus across different subjects. This suggests that encoding of related experiences, which was previously thought …

Local Geometry Of Elementary Visual Computations, Peter Neri

MODVIS Workshop

Visual operators (e.g. edge detectors) are classically modelled using small circuits involving canonical computations, such as template-matching and gain control. Circuit models explain many aspects of the empirical descriptors that are used to characterize local visual operators, from sensitivity to classification images. Notwithstanding their utility, these models fail to provide a unified framework encompassing the variety of effects observed experimentally, such as the impact of contrast, SNR, and attention on the above descriptors. My goal is to start with a simple, plausible geometrical representation of the perceptual operation carried out by the observer, and to show that this representation is …

Characterization Of Perceptual Spaces From Triadic Similarity Judgments, Jonathan Victor

MODVIS Workshop

Perceptual spaces are mental workspaces that organize a sensory or cognitive domain into a format that supports functions such as comparison, grouping, learning, and generalization. Determining the geometry of a perceptual space – i.e., the properties of the perceptual distances within the space -- is thus crucial not only to understand these intermediate levels of processing at an algorithmic level, but also as a starting point for comparison with neural measures of similarity. While perceptual spaces are often taken to be Euclidean or nearly so (the classic example is trichromatic color space), this assumption, when tested, is often violated. Moreover, …

Mapping The Neural Circuits That Underlie Metabolic Vs. Emotional Regulation Of Food-Seeking Behavior, Xu Zhang

Dissertations and Theses (Open Access)

Flexibly adjusting food-seeking behaviors based on metabolic needs and environmental threats is crucial for animal survival. In humans, maladaptive food-seeking behaviors that contravene energy homeostasis, which is often driven by food-associated cues with hedonic reward values, lead to obesity and eating disorders. However, the neural mechanisms underlying the modulation of cued food-seeking behaviors by distinct metabolic and threat states remain elusive. Using an approach-food vs. avoid-predator threat conflict test in rats, we identified a subpopulation of neurons in the anterior portion of the paraventricular thalamic nucleus (aPVT) which express corticotrophin-releasing factor (CRF) and are preferentially recruited to respond to food …

Biophysical Model Of Retraction Motor Neurons And Their Modification By Operant Conditioning, Maria Rasheed

Dissertations and Theses (Open Access)

Operant conditioning (OC) is a form of associative learning in which an animal modifies its behavior based on the consequences that follow that behavior. Despite its ubiquity, the underlying mechanisms of OC are poorly understood. Insights into the mechanisms of OC can be obtained by studying Aplysia feeding behavior as it can be modified by OC. This behavior is mediated by a central pattern generator (CPG) network in the buccal ganglia that contains a relatively small number of neurons. This CPG generates rhythmic motor patterns (BMPs) that move food into the gut by closing a tongue-like structure (i.e., radula) during …

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

Cortical Representation Of Learning Social Interactions In Freely Moving Non-Human Primates, Melissa Franch

Dissertations and Theses (Open Access)

The motivation and capacity to be social is necessary for human survival. Successful learning of complex, prosocial behavior stems from the ability to perceive and respond to visual cues, such as the body language and facial expressions, from others in our environment. This dependence on visual information to guide social interaction is especially true for humans and non-human primates. Although recent studies in primate neurophysiology discovered neurons that can encode socially relevant variables, like reward and social actions, the underlying neural mechanisms of learning advanced social concepts, such as cooperation, are not well understood. Further, previous work has identified …

Gap Junctions And Synchronization Clusters In The Thalamic Reticular Nuclei, Anca R. Radulescu, Michael Anderson

Biology and Medicine Through Mathematics Conference

No abstract provided.

Task-Driven Influences On Fixational Eye Movements, Jonathan Victor, Yen-Chu Lin, Michele Rucci

MODVIS Workshop

There is now compelling evidence that the spatiotemporal remapping carried out by fixational eye movements (FEMs) is an essential step in visual processing. Moreover, the overall Brownian-like statistics of FEMs are calibrated to map fine spatial detail into the temporal frequency range to which retinal circuitry is tuned. Here, we tested the hypothesis that the detailed spatial characteristics of FEMs can be adjusted to task demands via cognitive influences that operate even in the absence of a visual stimulus. We examined FEMs in a task that required subjects (N=6) to report which of two letters was displayed. Trials were blocked; …

Active Encoding Of Space Through Time, Michele Rucci, Jonathan D. Victor

MODVIS Workshop

No abstract provided.

The Genomics Of Autism-Related Genes Il1rapl1 And Il1rapl2: Insights Into Their Cortical Distribution, Cell-Type Specificity, And Developmental Trajectories, Jacob Weaver

MUSC Theses and Dissertations

Neuropsychiatric disorders have a significant impact on modern society. These disorders affect a large percentage of the population: schizophrenia has a world-wide prevalence of 1% and autism spectrum disorders (ASD) affects 1 in 59 school-aged children in the US. There is substantial evidence that most neuropsychiatric disorders have a genetic component. Thus, with the advent of high throughput sequencing much effort has gone into identifying genetic variants associated with these disorders. The emerging picture from these studies is a complex one where hundreds of genes with small effects interact with a varied landscape of common variants to result in disease. …

Spatial Processing Of Conspecific Signals In Weakly Electric Fish: From Sensory Image To Neural Population Coding, Oak Everette Milam

Graduate Theses, Dissertations, and Problem Reports (ETD)

In this dissertation, I examine how an animal’s nervous system encodes spatially realistic conspecific signals in their environment and how the encoding mechanisms support behavioral sensitivity. I begin by modeling changes in the electrosensory signals exchanged by weakly electric fish in a social context. During this behavior, I estimate how the spatial structure of conspecific stimuli influences sensory responses at the electroreceptive periphery. I then quantify how space is represented in the hindbrain, specifically in the primary sensory area called the electrosensory lateral line lobe. I show that behavioral sensitivity is influenced by the heterogeneous properties of the pyramidal cell …

Characterization Of Local And Global Statistics In Three Kinds Of Medical Images, And An Example Of Their Role In A Clinical Judgment, Jonathan Victor, Amanda Simon, Craig K. Abbey

MODVIS Workshop

No abstract provided.

A Two-Layer Model Explains Higher-Order Feature Selectivity Of V2 Neurons, Timothy D. Oleskiw, Justin D. Lieber, J. Anthony Movshon, Eero P. Simoncelli

MODVIS Workshop

Neurons in cortical area V2 respond selectively to higher-order visual features, such as the quasi-periodic structure of natural texture. However, a functional account of how V2 neurons build selectivity for complex natural image features from their inputs – V1 neurons locally tuned for orientation and spatial frequency – remains elusive.

We made single-unit recordings in area V2 in two fixating rhesus macaques. We presented stimuli composed of multiple superimposed grating patches that localize contrast energy in space, orientation, and scale. V2 activity is modeled via a two-layer linear-nonlinear network, optimized to use a sparse combination of V1-like outputs to account …

Impact Of Brain State On Visual And Prefrontal Population Coding In Behaving Animals, Russell Milton

Dissertations and Theses (Open Access)

Patterns of neural activity in the brain constantly shift between different processing states. Earlier studies have established that the ongoing, spontaneous activity has major repercussions regarding how the brain processes incoming sensory stimuli. However, the interaction between behavioral activity and brain states throughout the cortical hierarchy of primates has not been understood. In particular, technical considerations have greatly limited the range of physical activities in which primate neuronal activity can be recorded. We have implemented two separate strategies to overcome these limitations. First, we have advanced wireless electrophysiological methodologies that enable recording high-yield neuronal data from animals as they freely …

Energy As A Limiting Factor In Neuronal Seizure Control: A Mathematical Model, Sophia E. Epstein

CMC Senior Theses

The majority of seizures are self-limiting. Within a few minutes, the observed neuronal synchrony and deviant dynamics of a tonic-clonic or generalized seizure often terminate. However, a small epilesia partialis continua can occur for years. The mechanisms that regulate subcortical activity of neuronal firing and seizure control are poorly understood. Published studies, however, through PET scans, ketogenic treatments, and in vivo mouse experiments, observe hypermetabolism followed by metabolic suppression. These observations indicate that energy can play a key role in mediating seizure dynamics. In this research, I seek to explore this hypothesis and propose a mathematical framework to model how …

The Classification Of Basket Neural Cells In The Mammalian Neocortex, Sreya Pudi

Senior Theses

Basket neuronal cells of the mammalian neocortex have been classically categorized into two or more groups. Originally, it was thought that the large and small types are the naturally occurring groups that emerge from reasons that relate to neurobiological function and anatomical position. Later, a study based on anatomical and physiological features of these neurons introduced a third type, the net basket cell which is intermediate in size as compared to the large and small types. In this study, multivariate analysis was used to test the hypothesis that the large and small types are morphologically distinct groups. The results of …

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 …

Cortical Dynamics Of Language, Kiefer Forseth

Dissertations and Theses (Open Access)

The human capability for fluent speech profoundly directs inter-personal communication and, by extension, self-expression. Language is lost in millions of people each year due to trauma, stroke, neurodegeneration, and neoplasms with devastating impact to social interaction and quality of life. The following investigations were designed to elucidate the neurobiological foundation of speech production, building towards a universal cognitive model of language in the brain. Understanding the dynamical mechanisms supporting cortical network behavior will significantly advance the understanding of how both focal and disconnection injuries yield neurological deficits, informing the development of therapeutic approaches.

Nonlinear Control Of Biological Dynamical Systems, Megan J. Morrison

Biology and Medicine Through Mathematics Conference

No abstract provided.

Mechanisms Of Value-Biased Prioritization In Fast Sensorimotor Decision Making, Kivilcim Afacan-Seref

Dissertations and Theses

In dynamic environments, split-second sensorimotor decisions must be prioritized according to potential payoffs to maximize overall rewards. The impact of relative value on deliberative perceptual judgments has been examined extensively, but relatively little is known about value-biasing mechanisms in the common situation where physical evidence is strong but the time to act is severely limited. This research examines the behavioral and electrophysiological indices of how value biases split-second perceptual decisions and the possible mechanisms underlying the process. In prominent decision models, a noisy but statistically stationary representation of sensory evidence is integrated over time to an action-triggering bound, and value-biases …

Neuromechanical Tuning For Arm Motor Control, Russell Lee Hardesty Jr

Graduate Theses, Dissertations, and Problem Reports (ETD)

Movement is a fundamental behavior that allows us to interact with the external world. Its importance to human health is most evident when it becomes impaired due to disease or injury. Physical and occupational rehabilitation remains the most common treatment for these types of disorders. Although therapeutic interventions may improve motor function, residual deficits are common for many pathologies, such as stroke. The development of novel therapeutics is dependent upon a better understanding of the underlying mechanisms that govern movement. Movement of the human body adheres to the principles of classic Newtonian mechanics. However, due to the inherent complexity of …

Understanding Object Motion Encoding In The Mammalian Retina., Victor Julian Depiero

Electronic Theses and Dissertations

Phototransduction, transmission of visual information down the optic nerve incurs delays on the order of 50 – 100ms. This implies that the neuronal representation of a moving object should lag behind the object’s actual position. However, studies have demonstrated that the visual system compensates for neuronal delays using a predictive mechanism called phase advancing, which shifts the population response toward the leading edge of a moving object’s retinal image. To understand how this compensation is achieved in the retina, I investigated cellular and synaptic mechanisms that drive phase advancing. I used three approaches, each testing phase advancing at a …

Functional Organization Of Cortical Maps For Ocular Dominance And Light-Dark Polarity In Primary Visual Cortex, Sohrab Najafian, Jian Zhong Jin, Jose-Manuel Alonso

MODVIS Workshop

No abstract provided.