Biology subjects

Johnson, G. W.

Publications and source records attributed to Johnson, G. W..

14 recordsLinked to original sources

bioRxiv2025

Generalized brain-state modeling with KenazLBM

The large-scale functional state of a human brain remains difficult to characterize, much less predict. Regardless, techniques have been engineered to electrically neuromodulate the brain to treat a subset of neurologic and psychiatric disorders with moderate efficacy. Accurate characterization of a brains instantaneous functional state has stymied the development of more effective neuromodulation paradigms. Advanced computational methods are required to address this gap and enable large-scale neuroscience. Here we define the concept of generalized brain-state modeling across humans as Large Brain-State Modeling (LBM) and present KenazLBM as the worlds first example. KenazLBM can instantaneously characterize the functional state of a persons brain with raw iEEG data, and predict future brain-states. KenazLBM was trained on over 17.9 billion unique multichannel tokens from people undergoing intracranial electroencephalography (iEEG) recordings, and has learned to interrelate brain-states between people into a common interpretable topology. Most importantly, the model generalizes to unseen subject data with significant recording channel heterogeneity from the training set. We offer KenazLBM as a first generalized brain-state model to serve as a new paradigm of basic neuroscience inquiry and potential translation into neuromodulation therapeutics.

neuroscience↗

bioRxiv2024

Collapse of Interictal Suppressive Networks Permits Seizure Spread

How do networks in the brain limit seizure activity? In the Interictal Suppression Hypothesis (ISH), we recently postulated that high inward connectivity to seizure onset zones (SOZs) from non-involved zones (NIZs) is a sign of broader network suppression at rest. If broad networks appear to be responsible for interictal SOZ suppression, what changes during seizure initiation, spread, and termination? For patients with drug resistant epilepsy, intracranial monitoring offers a view into the electrographic networks which organize around and in response to the SOZ. In this manuscript, we investigate network dynamics in the peri-ictal periods to assess possible mechanisms of seizure suppression and the consequences of this suppression being overwhelmed. Peri-ictal network dynamics were derived from stereo electroencephalography (SEEG) recordings from 75 patients with drug-resistant epilepsy undergoing pre-surgical evaluation at Vanderbilt University Medical Center. We computed directed connectivity from 5-second windows in the periods between, immediately before, during, and after seizures. After aligning all network connectivity matrices between seizures and patients, we calculated net connectivity changes from the SOZ, propagative zone (PZ), and NIZ. Across all seizure types, we observed two distinct phases as seizures initiated and evolved: a large rapid increase in directed communication towards the SOZ from NIZ followed by a collapse in network connectivity. During this first phase, SOZs could be distinguished from all other regions (One-Way ANOVA, p=8.32x10-19 - 2.22x10-7, lower range to upper range of p-values). In the second phase and post-ictal period, SOZ inward connectivity decreased yet remained distinct (One-Way ANOVA, p= 2.58x10-10-1.66x10-2). Furthermore, NIZs appeared to drive the increase in inward SOZ connectivity while global connectivity between NIZs concordantly decreased. Stratifying by seizure subtype, we found that consciousness-impairing seizures show loss of inward connectivity from the NIZ earlier than conscious sparing seizures (one-way ANOVA, p<0.01 after false discovery correction). Tracking network reorganization against a surrogate for seizure involvement highlighted a possible antagonism between seizure propagation to the NIZ and the NIZs ability to maintain high connectivity to the SOZ. Finally, we found that inclusion of peri-ictal connectivity improved SOZ classification accuracy from previous models to a combined area under the curve of 93%. Overall, NIZs appear to actively respond to seizure onset and increase inhibitory signaling towards the SOZ, possibly in an attempt to thwart seizure activity. This inhibition appears to be insufficient to prevent seizure onset, and furthermore, loss of normal communication in the rest of the brain between NIZs may contribute to loss of consciousness during larger seizures. Dynamic connectivity patterns uncovered in this work may: i) allow more accurate delineation of surgical targets in focal epilepsy, ii) reveal why inward suppression of SOZs interictally may nonetheless be insufficient to prevent all seizures, and iii) provide insight into mechanisms of loss of consciousness during certain seizures.

neuroscience↗

bioRxiv2024

Mesolimbic local field potentials are modulated by motor control

Background and ObjectivesWhile historically cortico-basal ganglia-thalamocortical loops were believed to process limbic and sensorimotor data in parallel, there is now evidence to suggest that the two information streams can be processed in a single open loop. However, the limbic-motor interface remains insufficiently characterized. We sought to further investigate how extrastriatal regions may regulate motor output by examining electrophysiological activity in these areas during a response inhibition paradigm. MethodsWe recorded local field potentials (LFPs) from epilepsy patients implanted with intracranial depth electrodes for seizure localization purposes. Participants performed the stop-signal task, during which they made speeded choice reactions to "go" stimuli and occasionally inhibited their reactions in the incident of a "stop" signal. To compare power during movement and the absence of movement, we applied a Wilcoxon signed-rank test. Additionally, we performed a linear mixed-effects model to relate power in limbic regions to power in the motor cortex. Finally, we implemented exploratory analyses to identify power differences for correct go versus correct stop trials and for correct stop versus incorrect stop trials using cluster-based permutation testing. Results14 patients participated. A comparison between movement and baseline fixation revealed that motor response is associated with reduced beta (15-35 Hz) power in the amygdala, hippocampus, and motor cortex and reduced gamma (35-100 Hz) power in the amygdala and hippocampus. Moreover, average beta and gamma power in the amygdala and hippocampus during motor execution were positively associated with average beta and gamma power in the motor cortex. Additionally, we identified significant differences between correct go and stop trials in delta (1-4 Hz) power for all three regions and in theta (4-8 Hz) power for the amygdala and motor cortex. Likewise, we identified significant differences between correct and incorrect stop trials in delta power for the hippocampus and motor cortex, in theta power for the motor cortex, in alpha (8-15 Hz) and beta power for the amygdala and motor cortex, and in gamma power for all three areas. DiscussionThese correlations between neural oscillations in the hippocampus and amygdala and movement strengthen the notion of mesolimbic modulation of motor activity.

neuroscience↗

bioRxiv2024

Brain-state modeling using electroencephalography: Application to adaptive closed-loop neuromodulation for epilepsy

The progress of developing an effective closed-loop neuromodulation system for many neurological pathologies is hindered by the difficulties in accurately capturing a useful representation of a brains instantaneous functional state. Existing approaches rely on expert labeling of electroencephalography data to develop biomarkers of neurophysiological pathology. These techniques do not capture the highly complex functional states of the brain that are presumed to exist between labeled states or allow for the likely possibility of variation among identically labeled states. Thus, we propose BrainState, a self-supervised technique to model an arbitrarily complex instantaneous functional state of a brain using neural multivariate timeseries data. Application of BrainState to intracranial electroencephalography data from patients with epilepsy was able to capture diverse pre-seizure states and quantify nuanced effects of neuromodulation. We anticipate that BrainState will enable the development of sophisticated closed-loop neuromodulation systems for a diverse array of neurological pathologies.

neuroscience↗

bioRxiv2024

Reward Circuit Local Field Potential Modulations Precede Risk Taking

Risk taking behavior is a symptom of multiple neuropsychiatric disorders and often lacks effective treatments. Reward circuitry regions including the amygdala, orbitofrontal cortex, insula, and anterior cingulate have been implicated in risk-taking by neuroimaging studies. Electrophysiological activity associated with risk taking in these regions is not well understood in humans. Further characterizing the neural signalling that underlies risk-taking may provide therapeutic insight into disorders associated with risk-taking. Eleven patients with pharmacoresistant epilepsy who underwent stereotactic electroencephalography with electrodes in the amygdala, orbitofrontal cortex, insula, and/or anterior cingulate participated. Patients participated in a gambling task where they wagered on a visible playing card being higher than a hidden card, betting $5 or $20 on this outcome, while local field potentials were recorded from implanted electrodes. We used cluster-based permutation testing to identify reward prediction error signals by comparing oscillatory power following unexpected and expected rewards. We also used cluster-based permutation testing to compare power preceding high and low bets in high-risk (<50% chance of winning) trials and two-way ANOVA with bet and risk level to identify signals associated with risky, risk averse, and optimized decisions. We used linear mixed effects models to evaluate the relationship between reward prediction error and risky decision signals across trials, and a linear regression model for associations between risky decision signal power and Barratt Impulsiveness Scale scores for each patient. Reward prediction error signals were identified in the amygdala (p=0.0066), anterior cingulate (p=0.0092), and orbitofrontal cortex (p=6.0E-4, p=4.0E-4). Risky decisions were predicted by increased oscillatory power in high-gamma frequency range during card presentation in the orbitofrontal cortex (p=0.0022), and by increased power following bet cue presentation across the theta-to-beta range in the orbitofrontal cortex (p=0.0022), high-gamma in the anterior cingulate (p=0.0004), and high-gamma in the insula (p=0.0014). Risk averse decisions were predicted by decreased orbitofrontal cortex gamma power (p=2.0E-4). Optimized decisions that maximized earnings were preceded by decreases within the theta to beta range in orbitofrontal cortex (p=2.0E-4), broad frequencies in amygdala (p=2.0E-4), and theta to low-gamma in insula (p=4.0E-4). Insula risky decision power was associated with orbitofrontal cortex high-gamma reward prediction error signal (p=0.0048) and with patient impulsivity (p=0.00478). Our findings identify and help characterize reward circuitry activity predictive of risk-taking in humans. These findings may serve as potential biomarkers to inform the development of novel treatment strategies such as closed loop neuromodulation for disorders of risk taking.

neuroscience↗

bioRxiv2024

Depression Attenuates Caudate and Dorsolateral Prefrontal Cortex Alpha and Beta Power Response to Reward

Depression is a prevalent psychiatric condition and a common comorbidity across neurological disorders. Common symptoms include anhedonia, negative emotional biases, and cognitive dysfunction. Beta (15-30 Hz) neural oscillations have been shown to increase during reward-based learning within fronto-striatal reward networks. Corticostriatal beta oscillations have also been implicated in cognitive functions including working memory. However, the relationship between beta oscillations and depression remains unknown. Using intracranial recordings, we aimed to investigate how depression modulates the spectral power of neural oscillations in corticostriatal structures during reward feedback in a working memory task. Thirty movement disorder patients undergoing awake deep brain stimulation surgery with electrode trajectories traversing the caudate or dorsolateral prefrontal cortex (DLPFC) participated in this study. We recorded local field potential data intraoperatively as subjects completed a 2-back verbal working memory task where they identified whether a word matched the word presented two trials prior. Subjects received reward in the form of visual feedback for correct answers. Word stimuli had either a positive, negative, or neutral emotional valence. Subjects completed the Beck Depression Inventory-II preoperatively, and we used a cut-off score of 14 to identify patients with depression. We found that caudate and DLPFC power increased in the alpha (8-15 Hz) and beta range during reward feedback and that this increase was significantly greater for subjects without depression compared to depressed subjects. In non-depressed patients, positive feedback stimuli evoked significantly higher beta power in the caudate during reward compared to neutral and negative stimuli. In depressed patients, emotional valence did not affect reward-related caudate spectral power, while DLPFC alpha power was significantly higher following positive emotional stimuli in comparison to neutral but not negative stimuli. We additionally found that anti-depressant medications (ADMs) generally blunted alpha and beta reward signaling processes in the DLPFC. This blunting effect on reward-related alpha power in the DLPFC, however, was reversed in depressed patients, indicating that the effects of ADMs on reward signaling processes may depend on whether a patient is exhibiting depression symptoms. Our findings suggest that depression suppresses the alpha and beta power response to both reward and emotional stimuli during working memory, indicating power attenuation in these frequency bands may contribute to emotional and cognitive depression symptoms.

neuroscience↗

bioRxiv2023

Brain-wide human oscillatory LFP activity during visual working memory

Oscillatory activity is thought to be a marker of cognitive processes, although its role and distribution across the brain during working memory has been a matter of debate. To understand how oscillatory activity differentiates tasks and brain areas in humans, we recorded local field potentials (LFPs) in 12 adults as they performed visual-spatial and shape-matching memory tasks. Tasks were designed to engage working memory processes at a range of delay intervals between stimulus delivery and response initiation. LFPs were recorded using intracranial depth electrodes implanted to localize seizures for management of intractable epilepsy. Task-related LFP power analyses revealed an extensive network of cortical regions that were activated during the presentation of visual stimuli and during their maintenance in working memory, including occipital, parietal, temporal, insular, and prefrontal cortical areas, and subcortical structures including the amygdala and hippocampus. Across most brain areas, the appearance of a stimulus produced broadband power increase, while gamma power was evident during the delay interval of the working memory task. Notable differences between areas included that occipital cortex was characterized by elevated power in the high gamma (100-150 Hz) range during the 500 ms of visual stimulus presentation, which was less pronounced or absent in other areas. A decrease in power centered in beta frequency (16-40 Hz) was also observed after the stimulus presentation, whose magnitude differed across areas. These results reveal the interplay of oscillatory activity across a broad network, and region-specific signatures of oscillatory processes associated with visual working memory.

neuroscience↗

bioRxiv2023

Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context

Diffusion MRI (dMRI) streamline tractography is the gold-standard for in vivo estimation of white matter (WM) pathways in the brain. However, the high angular resolution dMRI acquisitions capable of fitting the microstructural models needed for tractography are often time-consuming and not routinely collected clinically, restricting the scope of tractography analyses. To address this limitation, we build on recent advances in deep learning which have demonstrated that streamline propagation can be learned from dMRI directly without traditional model fitting. Specifically, we propose learning the streamline propagator from T1w MRI to facilitate arbitrary tractography analyses when dMRI is unavailable. To do so, we present a novel convolutional-recurrent neural network (CoRNN) trained in a teacher-student framework that leverages T1w MRI, associated anatomical context, and streamline memory from data acquired for the Human Connectome Project. We characterize our approach under two common tractography paradigms, WM bundle analysis and structural connectomics, and find approximately a 5-15% difference between measures computed from streamlines generated with our approach and those generated using traditional dMRI tractography. When placed in the literature, these results suggest that the accuracy of WM measures computed from T1w MRI with our method is on the level of scan-rescan dMRI variability and raise an important question: is tractography truly a microstructural phenomenon, or has dMRI merely facilitated its discovery and implementation?

bioengineering↗

bioRxiv2022

Corticostriatal Beta Power Changes Associated with Cognitive Function in Parkinsons Disease

Cognitive impairment (CI) is the most frequent nonmotor symptom in Parkinsons Disease (PD) and is associated with deficits in executive functions such as working memory. Previous studies have demonstrated that caudate beta power is involved in learning and working memory. Decreased dopamine in motor cortico-striato-thalamo-cortical (CSTC) circuits results in increased beta power and PD motor symptoms. Analogous changes in cognitive CSTC circuits, including the caudate and dorsolateral prefrontal cortex (DLPFC), may contribute to PD CI. The objective of our study is to evaluate whether beta power changes in caudate and DLPFC contribute to cognitive impairment in PD patients. To investigate this, we used local field potential (LFP) recordings during deep brain stimulation surgery in 15 PD patients. LFP signals from DLPFC and caudate were performed at rest and during a verbal working memory task. We examined beta power changes during the working memory task and relationship of beta power to pre-operative neuropsychological testing results. Beta power decreased in both DLPFC and caudate during encoding of correct trials, whereas beta power increased in DLPFC and caudate during feedback for correct responses. Subjects with cognitive impairment showed smaller decreases in caudate and DLPFC beta power during encoding, greater increases in beta power during feedback, and lower average resting-state beta power. Additionally, reduced caudate beta power during encoding correlated with better memory scores on pre-operative neuropsychological testing, while greater DLPFC beta power during feedback correlated with worse scores in the attention domain. Our findings suggest that similar to the relationship between beta power in motor CSTC circuits and PD motor symptoms, beta power changes in parallel cognitive CSTC circuits may be correlated with cognitive symptoms in PD patients.

neuroscience↗

bioRxiv2022

Deep learning segmentation of the nucleus basalis of Meynert on 3T MRI

The nucleus basalis of Meynert (NBM) is a key subcortical structure that is important in arousal, cognition, brain network modulation, and has been explored as a deep brain stimulation target. It has also been implicated in several disease states, including Alzheimers disease, Parkinsons disease, and temporal lobe epilepsy (TLE). Given the small size of NBM and variability between patients, NBM is difficult to study; thus, accurate, patient-specific segmentation is needed. We investigated whether a deep learning network could produce accurate, patient-specific segmentations of NBM on commonly utilized 3T MRI. It is difficult to accurately segment NBM on 3T MRI, with 7T being preferred. Paired 3T and 7T MRI datasets of 21 healthy subjects were obtained, with 6 completely withheld for testing. NBM was expertly segmented on 7T MRI, providing accurate labels for the paired 3T MRI. An external dataset of 14 patients with TLE was used to test the model on brains with neurological disorders. A 3D-Unet convolutional neural network was constructed, and a 5-fold cross-validation was performed. The model was evaluated on healthy subjects using the held-out test dataset and the external dataset of TLE patients. The model demonstrated significantly improved dice coefficient over the standard probabilistic atlas for both healthy subjects (0.68MEAN{+/-}0.08SD vs. 0.47{+/-}0.06, p=0.0089, t-test) and TLE patients (0.63{+/-}0.08 vs. 0.38{+/-}0.19, p=0.0001). Additionally, the centroid distance was significantly decreased when using the model in patients with TLE (1.22{+/-}0.33mm, 3.25{+/-}2.57mm, p=0.0110). We developed the first model, to our knowledge, for automatic and accurate patient-specific segmentation of the NBM.

neuroscience↗

bioRxiv2022

The Interictal Suppression Hypothesis in Focal Epilepsy: Electrographic and Structural Evaluation

Why are people with focal epilepsy not constantly seizing? Previous molecular work has implicated gamma-aminobutyric acid balance as integral to seizure generation and termination, but is the high-level distributed brain network involved in suppressing seizures? Recent intracranial electrographic evidence has suggested that seizure onset zones have an increased inward connectivity. Accordingly, we hypothesize that seizure onset zones are actively suppressed by the rest of the brain network during interictal states. We tested this hypothesis on 81 subjects with drug resistant focal epilepsy undergoing presurgical evaluation. We utilized intracranial electrographic resting-state and neurostimulation recordings to evaluate the network connectivity of seizure onset, propagative, and non-involved regions. We then utilized diffusion imaging to acquire estimates of white matter connectivity to evaluate structure-function coupling effects on connectivity findings. Finally, using our observations, we generated a resting-state classification model to assist clinicians in detecting seizure onset and propagative zones without the need for multiple ictal recordings. Our findings indicate that seizure onset and propagative zones demonstrate markedly increased inward connectivity and decreased outward connectivity on both resting-state and neurostimulation analyses. When controlling for distance between regions, the difference between inward vs. outward connectivity remained stable up to 80 mm between brain connections. Structure-function coupling analyses revealed that seizure onset zones exhibit abnormally enhanced coupling (hypercoupling) of surrounding regions compared to presumably healthy tissue. Using these observations, our classification models achieved a maximum held-out testing set accuracy of 92.0{+/-}2.2%. These results indicate that seizure onset zones are actively segregated and suppressed by a widespread brain network. Furthermore, this electrographically observed functional suppression is disproportionate to any observed structural connectivity alterations of the seizure onset zones. These findings have implications for the identification of seizure onset zones using only brief resting-sate recordings to reduce patient morbidity and augment the presurgical evaluation of drug resistant epilepsy. Furthermore, testing of the interictal suppression hypothesis can provide insight into potential new resective, ablative, and neuromodulation approaches to improve surgical success rates in those suffering from drug resistant focal epilepsy.

neuroscience↗

bioRxiv2022

Localizing temporal lobe seizure onset zones using deep learning on SEEG cortico-cortical evoked potentials

In drug resistant temporal lobe epilepsy, automated tools for seizure onset zone (SOZ) localization using brief interictal recordings would supplement presurgical evaluations and improve care. Thus, we sought to localize SOZs by training a multi-channel convolutional neural network on stereo-EEG (SEEG) cortico-cortical evoked potentials. We performed single pulse electrical stimulation with 10 drug resistant temporal lobe epilepsy patients implanted with SEEG. Using the 500,000 unique post-stimulation SEEG epochs, we trained a multi-channel one-dimensional convolutional neural network to determine whether an SOZ was stimulated. SOZs were classified with a mean leave-one-patient-out testing sensitivity of 78.1% and specificity of 74.6%. To achieve maximum accuracy, the model requires a 0-350 ms post stimulation time period. Post-hoc analysis revealed that the model accurately classified unilateral vs bilateral mesial temporal lobe seizure onset, and neocortical SOZs. This is the first demonstration, to our knowledge, that a deep learning framework can be used to accurately classify SOZs using cortico-cortical evoked potentials. Our findings suggest accurate classification of SOZs relies on a complex temporal evolution of evoked potentials within 350 ms of stimulation. Validation in a larger dataset could provide a practical clinical tool for the presurgical evaluation of drug resistant epilepsy.

neuroscience↗

bioRxiv2020

PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images

PurposeDiffusion weighted MRI imaging (DWI) is often subject to low signal-to-noise ratios (SNRs) and artifacts. Recent work has produced software tools that can correct individual problems, but these tools have not been combined with each other and with quality assurance (QA). A single integrated pipeline is proposed to perform DWI preprocessing with a spectrum of tools and produce an intuitive QA document. MethodsThe proposed pipeline, built around the FSL, MRTrix3, and ANTs software packages, performs DWI denoising; inter-scan intensity normalization; susceptibility-, eddy current-, and motion-induced artifact correction; and slice-wise signal drop-out imputation. To perform QA on the raw and preprocessed data and each preprocessing operation, the pipeline documents qualitative visualizations, quantitative plots, gradient verifications, and tensor goodness-of-fit and fractional anisotropy analyses. ResultsRaw DWI data were preprocessed and quality checked with the proposed pipeline and demonstrated improved SNRs; physiologic intensity ratios; corrected susceptibility-, eddy current-, and motion-induced artifacts; imputed signal-lost slices; and improved tensor fits. The pipeline identified incorrect gradient configurations and file-type conversion errors and was shown to be effective on externally available datasets. ConclusionThe proposed pipeline is a single integrated pipeline that combines established diffusion preprocessing tools from major MRI-focused software packages with intuitive QA.

bioengineering↗

bioRxiv2017

Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases

Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207-222 nm) efficiently kills bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently kills airborne aerosolized viruses, a very low dose of 2 mJ/cm2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.

bioengineering↗