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Mujica-Parodi, L. R.

Publications and source records attributed to Mujica-Parodi, L. R..

18 recordsLinked to original sources

Mechanistic simulation identifies predictive dose-dependent biomarkers of propofol anesthesia

Understanding how receptor-level pharmacological modulation reorganizes large-scale brain circuits remains a central challenge in neuropharmacology. We introduce a multiscale mechanistic model with explicit core-matrix thalamocortical architecture, driven solely by GABA-A modulation without parameter fitting to any anesthesia data, to examine how propofol reorganizes brainwide activity from individual receptors to systems-level circuits. The model exhibits anesthetic effects spanning individual synaptic conductances to widespread changes in spiking, field potentials, and coherence. Without training on any task-specific data, our simulation of sensory processing in a standard auditory oddball paradigm matches independent macaque datasets. The same simulation, unmodified, also reproduces changes to functional connectivity in anesthetized humans, exhibiting selective attenuation of matrix thalamocortical loops relative to core loops. Most importantly, the simulation identified a dose-dependent biomarker of propofol concentration -- elevated residual inter-stimulus cortical activity -- that was subsequently confirmed in empirical macaque data where it had previously gone unnoticed. This simulation-first discovery, arising from mechanistic circuit dynamics rather than statistical comparison of clinical populations, illustrates a generative framework for translating receptor-level modulation into circuit-scale biomarkers with potential applications across predictive neuropharmacology.

neuroscience↗

A biophysical corticostriatal model predicts learning-dependent 7T fMRI dynamics and individual reward bias in humans

Circuit-level computational models can do more than explain existing data; they can generate novel hypotheses and capture individual differences in human populations. We demonstrate this using a biophysical corticostriatal model, transforming simulated neuronal activity from local field potential (LFP) into functional magnetic resonance imaging (fMRI) signals via the balloon model, and finally generating behavioral outcomes. We then validate the results against those obtained from human subjects. The model generates a counterintuitive yet testable prediction. Although prefrontal-striatal coherence demonstrates an increase at the neural LFP scale during learning, the same circuit-- passed through the hemodynamic transform---predicts a decrease in prefrontal-striatal BOLD correlation, driven by category-selective representations that emerge in cortex but not striatum. This prediction is confirmed in fMRI data optimized for single-subject-level detection sensitivity. The model further enables single-subject fitting of a behavioral outcome, classifying individuals into those differentially responding to positive versus negative reward bias. Established biomarkers, including activation measured by the amplitude of low-frequency fluctuations and dopaminergic effects on hemodynamic latency, are also conserved across LFP and fMRI scales. These findings reposition circuit models as generative tools for human neuroscience, capable of producing mechanistically grounded hypotheses and parsing individual variation in ways inaccessible to data-driven approaches alone.

neuroscience↗

Computational modeling of neurotransmitter cycling predicts human brain glutamate and GABA dynamics in response to administration of exogenous ketones

Administration of ketones is used as a therapeutic option in multiple conditions, including epilepsy, mental health disorders, and brain aging. A proposed mechanism of action involves the modulation of glutamate and GABA, the brains primary excitatory and inhibitory neurotransmitters, which jointly regulate the excitatory-inhibitory balance. However, the precise mechanism by which ketones influence these neurotransmitters remains unclear. In this study, we hypothesize that ketones modulate glutamate and GABA through the pseudomalate-spartate shuttle (PMAS). To test this, we developed a computational model of neurotransmitter cycling centered on the PMAS, simulating the temporal dynamics and steady-state concentrations of glutamate and GABA as functions of ketone metabolism. We then compared the model outputs with MRS data from ketone administration experiments and found agreement with the model predictions, providing quantitative support for the model. Building on this agreement, we performed metabolic control analysis, which identified partial displacement of glucose metabolism through the PMAS as the dominant mechanism underlying the observed reductions in glutamate and GABA and revealed key enzymes that selectively modulate each neurotransmitter. Overall, the model provides researchers and clinicians with a framework for hypothesis testing and treatment optimization, while also serving as a foundation for future model expansions.

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Fast voxel and structural MRI realignment to mitigate inter-acquisition motion for spectroscopy

Magnetic resonance spectroscopy (MRS) non-invasively measures the biochemical composition within a predefined brain region, enabling quantification of neurochemicals with biological and clinical relevance, such as N-acetylaspartate, creatine, choline, glutamate, and gamma-aminobutyric acid. However, accurate MRS quantification is compromised by subject motion displacing the prescribed location, a common problem during long scans or with motion-prone populations such as children and patients. Furthermore, displacement into bone tissue contaminates MRS data with noisy artifacts, often rendering them unusable. While promising solutions exist to address motion-related issues, many rely on specialized infrastructure and expertise available only at a limited number of research centers. We propose a fast and straightforward method that acquires a head scout (18 s) MRI sequence following potential motion, automatically repositions the prescribed voxel with the scanners built-in AutoAlign function, and realigns the T1-weighted image to the updated position for anatomical segmentation. Using voxels prescribed in the prefrontal cortex, thalamus, and left superior temporal gyrus, we demonstrated that this realignment method successfully restored displaced voxels to their intended locations, eliminating bone contamination while improving voxel targeting through greater overlap with intended regions and more consistent voxel placement across subjects. This solution offers a quick and practical way for correcting subject motion between scans by combining available tools that are readily accessible even to new users, while more sophisticated motion correction technologies continue to develop towards broader adoption.

neuroscience↗

Spatially convergent fMRI signatures of diabetes and male sex identify genetic vulnerabilities to accelerated brain aging

Age-related cognitive decline results from complex interactions between neuroendocrine and neurometabolic processes that undergo lifelong degredation, yet the mechanisms underlying these interactions remain poorly understood. This study examined the effects of diabetes and sex on functional brain networks across aging through analysis of two large cohorts (N=1,621 total) using both 3T and 7T functional MRI, complemented by spatial transcriptomic data from over 14,000 genes from six post-mortem brains. Four networks-- cingulo-opercular, default mode, salience, and lateral somatomotor--exhibited significant functional decline in both individuals with diabetes and independently in males. Gene expression analysis of vulnerable networks revealed significant overexpression of insulin-dependent glucose transporters, dopaminergic and GABAergic synaptic genes, and VEGFA-VEGFR2 pathway components. These findings suggest functionally-specific circuit vulnerability to metabolic and hormonal dysregulation, potentially offering targets for early intervention before irreversible neurodegeneration occurs.

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Ketosis Elevates Antioxidants and Enhances Neural Function Through Improved Bioenergetics: A 1H MR Spectroscopy Study

Ketosis is known to alter the balance of neuroactive amino acids and enhance neural function when compared to a glycolytic condition. However, its influence on other metabolites, such as antioxidants and neural energy markers, and the mechanisms by which ketosis improves neural function remain unclear. Here, we measure the neurochemical effects of acute ketosis on the human brain using ultra-high-field 1H MR Spectroscopy (MRS) and investigate the subsequent impact on neural function through resting-state functional magnetic resonance imaging (rsfMRI). In a within-subjects design, N = 63 healthy adults from across the lifespan underwent 1H MRS and rsfMRI scans before and after consuming individually weight-dosed and calorically-matched ketone monoester or glucose drinks. Ketone monoester administration, but not glucose, significantly elevated cerebral antioxidants and energy markers while decreasing GABA, glutamate, and glutamine levels in the posterior cingulate cortex (PCC). Notably, increased bioenergetics, specifically an increase in total creatine, correlated with greater improvements in neural function as measured using rsfMRI. Our results integrate metabolic and functional neuroimaging findings, offering a comprehensive understanding of ketosis-induced changes in brain chemistry and functional network dynamics, yielding valuable insights into potential mechanisms by which ketosis imparts its neural benefits.

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Brain signaling becomes less integrated and more segregated with age

The integration-segregation framework is a popular first step to understand brain dynamics because it simplifies brain dynamics into two states based on global vs. local signaling patterns. However, there is no consensus for how to best define what the two states look like. Here, we map integration and segregation to order and disorder states from the Ising model in physics to calculate state probabilities, Pint and Pseg, from functional MRI data. We find that integration/segregation decreases/increases with age across three databases, and changes are consistent with weakened connection strength among regions rather than topological connectivity based on structural and diffusion MRI data. AUTHOR SUMMARYThe integration-segregation framework succinctly captures the tradeoff brains face between seamless function (more integration) in light of energetic constrains (more segregation). Despite its ubiquitous use in the field, there is no consensus on its definition with various graph theoretical properties being proposed. Here, we define the two states based on the underlying mechanism of neuronal coupling strength to provide a physical foundation for the framework. We find that younger adults brains are close to perfectly balancing between integration and segregation, while older adults brains veer off towards random signaling.

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New learning principles emerge from biomimetic computational primitives

Although computational models have deepened our understanding of neuroscience, it is still highly challenging to link actual low-level physiological activity (spiking, field potentials) and biochemistry (transmitters and receptors) with high-level cognitive abilities (decision-making, working memory) nor with corresponding disorders. We introduce an anatomically-organized multi-scale model directly generating simulated physiology from which extended neural and cognitive phenomena emerge. The model produces spiking, fields, phase synchronies, and synaptic change, directly generating working memory, decisions, and categorization, all of which were then validated on extensive experimental macaque data from which the model received zero prior training of any kind. Moreover, the simulation uncovered a previously unknown neural code specifically predicting upcoming erroneous ("incongruous") behaviors, also subsequently confirmed in empirical data. The biomimetic model thus directly and predictively links novel decision and reinforcement signals, of computational interest, with novel spiking and field codes, of potential behavioral and clinical relevance.

neuroscience↗

Leveraging Julia's automated differentiation and symbolic computation to increase spectral DCM flexibility and speed

Using neuroimaging and electrophysiological data to infer neural parameter estimations from theoretical circuits requires solving the inverse problem. Here, we provide a new Julia language package designed to i) compose complex dynamical models in a simple and modular way with ModelingToolkit.jl, ii) implement parameter fitting based on spectral dynamic causal modeling (sDCM) using the Laplace approximation, analogous to MATLAB implementation in SPM12, and iii) leverage Julias unique strengths to increase accuracy and speed by employing Automatic Differentiation during the fitting procedure. To illustrate the utility of our flexible modular approach, we provide a method to improve correction for fMRI scanner field strengths (1.5T, 3T, 7T) when fitting models to real data.

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D--hydroxybutyrate stabilizes the hippocampal CA3-CA1 circuit during acute insulin resistance.

1.The brain primarily relies on glycolysis for mitochondrial respiration but switches to alternative fuels such as ketone bodies (KBs) when less glucose is available. Neuronal KB uptake, which does not rely on glucose transporter 4 (GLUT4) or insulin, has shown promising clinical applicability in alleviating the neurological and cognitive effects of disorders with hypometabolic components. However, the specific mechanisms by which such interventions affect neuronal functions are poorly understood. In this study, we pharmacologically blocked GLUT4 to investigate the effects of exogenous KB D--hydroxybutyrate (D-Hb) on mouse brain metabolism during acute insulin resistance (AIR). We found that both AIR and D-Hb had distinct impacts across neuronal compartments: AIR decreased synaptic activity and long-term potentiation (LTP) and impaired axonal conduction, synchronization, and action potential (AP) properties, while D-Hb rescued neuronal functions associated with axonal conduction, synchronization, and LTP. 2. Significance statementThis study investigates the impact of acute insulin resistance on the functionality of the hippocampal circuit and the potential protective effects of ketone body supplementation. By inhibiting GLUT4 receptors to induce acute insulin resistance, we reveal several detrimental changes caused by impaired neuronal glucose uptake. These changes include impairments in synaptic activity, axonal conduction, and neuronal firing properties. The study further examines the distinctive effects of acute insulin resistance and the rescue agent D-{beta}Hb on synaptic activity, long-term potentiation, axonal conduction, synchronization, and neuronal firing. By shedding light on neuronal responses during insulin resistance, this investigation advances our understanding of neurological disorders associated with hypometabolism and highlights the potential therapeutic value of D-{beta}Hb.

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Ketosis regulates K+ ion channels, strengthening brain-wide signaling disrupted by age.

Aging is associated with impaired signaling between brain regions when measured using resting-state fMRI. This age-related destabilization and desynchronization of brain networks reverses itself when the brain switches from metabolizing glucose to ketones. Here, we probe the mechanistic basis for these effects. First, we established their neuronal basis using two datasets acquired from resting-state EEG (Lifespan: standard diet, 20-80 years, N = 201; Metabolic: individually weight-dosed and calorically-matched glucose and ketone ester challenge, age = 26.9 {+/-} 11.2 years, N = 36). Then, using the multi-scale Larter-Breakspear neural mass model, we identified the unique set of mechanistic parameters consistent with our clinical data. Together, our results implicate potassium (K+) gradient dysregulation as a mechanism for age-related neural desynchronization and its reversal with ketosis, the latter finding of which is consistent with direct measurement of ion channels.

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Ion Gradient-driven Bifurcations of a Multi-Scale Neuronal Model

Metabolic limitations within the brain frequently arise in the context of aging and disease. As the largest consumers of energy within the brain, ion pumps that maintain the neuronal membrane potential are the most affected when energy supply becomes limited. To characterize the effects of such limitations, we analyze the ion gradients present in the Larter-Breakspear neural mass model. We show the existence and locations of Neimark-Sacker and period-doubling bifurcations in the sodium, calcium, and potassium reversal potentials, and demonstrate that these bifurcations form physiologically relevant bounds of ion gradient variability. Within these bounds, we show how depolarization of the gradients will cause decreased neural activity. We also show that the depolarization of ion gradients decreases inter-regional coherence, causing a shift in the critical point at which the coupling occurs and thereby inducing loss of synchrony between regions. In this way, we show that the Larter-Breakspear model captures ion gradient variability present at the microscale level and propagates these changes to the macroscale effects congruent with those observed in human neuroimaging studies.

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Percolation Theory Identifies Critical Constraints on White Matter Tract Development

We perform targeted attack, a systematic computational unlinking of the network, to analyze its effects on global communication across the network through its giant cluster. Across diffusion magnetic resonance images from individuals in the UK Biobank, Adolescent Brain Cognitive Development Study and Developing Human Connectome Project, we find that targeted attack procedures on increasing white matter tract lengths and densities are remarkably invariant to aging and disease. Time-reversing the attack computation suggests a mechanism for how brains develop, for which we derive an analytical equation using percolation theory. Based on a close match between theory and experiment, our results demonstrate that tracts are limited to emanate from regions already in the giant cluster and tracts that appear earliest in neurodevelopment are those that become the longest and densest. SignificanceAs brains develop through neural growth and specialization, what mechanism ensures that new neurons are integrated into a fully connected brain, avoiding "bridges to nowhere"? Here, we study brain structure development from the perspective of percolation, a global measure of communication. Analyzing over 35,000 diffusion MRI scans on human individuals, from newborns to adults, we identify the following rules of brain neurogenesis through percolation theory: earlier tracts become longer and denser while maintaining a giant cluster. This signature, invariant to age or mental health, suggests a fundamental condition for the brain to function as an emergent whole.

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Quantifying control circuit regulation in the human brain.

As a field, control systems engineering has developed quantitative methods to characterize the regulation of systems or processes, whose functioning is ubiquitous within synthetic systems. In this context, a control circuit is objectively "well regulated" when discrepancy between desired and achieved output trajectories is minimized, and "robust" to the degree that it is able to regulate well in response to a wide range of stimuli. Most psychiatric disorders are assumed to reflect dysregulation of brain circuits. Yet, probing circuit regulation requires fundamentally different analytic strategies than the correlations relied upon for analyses of connectivity and their resultant networks. Here, we demonstrate how well-established methods for system identification in control systems engineering may be applied to functional magnetic resonance imaging (fMRI) data to extract generative computational models of human brain circuits. These provide two quantitative measures of direct relevance for psychiatric disorders: a circuits sensitivity to external perturbation and its dysregulation.

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Parameter estimation for correlated Ornstein-Uhlenbeck time-series

In this article, we develop a Maximum likelihood (ML) approach to estimate parameters from correlated time traces that originate from coupled Ornstein-Uhlenbeck processes. The most common technique to characterize the correlation between time-series is to calculate the Pearson correlation coefficient. Here we show that for time series with memory (or a characteristic relaxation time), our method gives more reliable results, but also results in coupling coefficients and their uncertainties given the data. We investigate how these uncertainties depend on the number of samples, the relaxation times and sampling time. To validate our analytic results, we performed simulations over a wide range of correlation coefficients both using our maximum likelihood solutions and Markov-Chain Monte-Carlo (MCMC) simulations. We found that both ML and MCMC result in the same parameter estimations. We also found that when analyzing the same data, the ML and MCMC uncertainties are strongly correlated, while ML underestimates the uncertainties by a factor of 1.5 to 3 over a large range of parameters. For large datasets, we can therfore use the less computationally expensive maximum likelihood method to run over the whole dataset, and then we can use MCMC on a few samples to determine the factor by which the ML method underestimates the uncertainties. To illustrate the application of our method, we apply it to time series of brain activation using fMRI measurements of the human default mode network. We show that our method significantly improves the interpretation of multi-subject measurements of correlations between brain regions by providing parameter confidence intervals for individual measurements, which allows for distinguishing between the variance from differences between subjects from variance due to measurement error.

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A data-driven predictome for cognitive, psychiatric, medical, and lifestyle factors on the brain

Most neuroimaging studies individually provide evidence on a narrow aspect of the human brain function, on distinct data sets that often suffer from small sample sizes. More generally, the high technical and cost demands of neuroimaging studies (combined with the statistical unreliability of neuroimaging pilot studies) may lead to observational bias, discouraging discovery of less obvious associations that nonetheless have important neurological implications. To address these problems, we built a machine-learning based classification framework, NeuroPredictome, optimized for the reliability and robustness of its associations. NeuroPredictome is grounded in a large-scale dataset, UK-Biobank (N=19,831), which includes resting and task functional MRI as well as structural T1-weighted and diffusion tensor imaging. Participants were assessed with respect to a comprehensive set of 5,034 phenotypes, including the physical and lifestyle factors most relevant to general medicine. Results generated by data-driven classifiers were then cross-validated, using deep-learning textual analyses, against 14,371 peer-reviewed research articles, providing an unbiased hypothesis-generator of linkages between diverse phenotypes and the brain. Our results show that neuroimaging reveals as many neurological links to physical and lifestyle factors as to cognitive factors, supporting a more integrative approach to medicine that considers disease interactions between multiple organs and systems.

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Development of an MRI Compatible Nasal Drug Delivery Method: Probing Nicotine Addiction Dynamics

BackgroundSubstance abuse is a fundamentally dynamic disease, characterized by repeated oscillation between craving, drug self-administration, reward, and satiety. To model nicotine addiction as a control system, an MR-compatible nicotine delivery system is needed to elicit cyclical cravings. MethodUsing a concentric nebulizer, inserted into one nostril, we delivered each dose--each equivalent to a single cigarette puff--using a syringe pump by nebulizing the nicotine solution using pressurized medical air. A control mechanism permits dual modes: one delivers puffs on a fixed interval programmed by researchers; with the other, subjects press a button to self-administer each nicotine dose. Subjects were therefore able to intuitively "smoke" the equivalent of a cigarette, one "puff" at a time. We dosed each "puff" such that one cigarette would be equal, in nicotine content, to 10 puffs. ResultsWe tested the viability of this delivery method for studying the brains response to nicotine addiction in three steps. First, we established the pharmacokinetics of nicotine delivery, using a dosing scheme designed to gradually achieve saturation, as with a cigarette. Second, we lengthened the time between micro-doses to elicit craving cycles, using both fixed-interval and subject-driven behavior. Finally, we confirmed that the fixed-interval protocol reliably activates brain circuits linked to addiction. ConclusionOur MR-compatible nasal delivery method enables the measurement of neural circuit responses to drug doses on a single-subject level, allowing the development of data-driven predictive models to quantify individual dysregulations of the reward control circuit causing addiction.

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Younger, but not older, brains are poised at a critical point of functional activity

Brain aging is associated with hypometabolism and associated global changes in functional connectivity. Using fMRI, we show that network synchrony, a collective property of brain activity, decreases with age. Applying quantitative methods from statistical physics, we provide a generative (Ising) model for these changes as a function of the average communication strength between brain regions. In particular, we find healthy brains to be poised at a critical point of this communication strength, enabling a balance between segregated (to functional domains) and integrated (between domains) patterns of synchrony. However, one characteristic of criticality is a high sensitivity to small changes. Thus, minute weakening of pairwise communication between regions, as seen in the aging brain, gives rise to qualitatively abrupt changes in synchrony. Finally, by experimentally modulating metabolic activity in younger adults, we show how metabolism alone-independent of other changes associated with aging-can provide a mechanism for global changes in synchrony.

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