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Alignment of brain embeddings and artificial contextual embeddings in natural language points to common geometric patterns

Goldstein, Ariel; Grinstein-Dabush, Avigail; Schain, Mariano; Wang, Haocheng; Hong, Zhuoqiao; Aubrey, Bobbi; Schain, Mariano; Nastase, Samuel A; Zada, Zaid; Ham, Eric; Feder, Amir; Gazula, Harshvardhan; Buchnik, Eliav; Doyle, Werner; Devore, Sasha; Dugan, Patricia; Reichart, Roi; Friedman, Daniel; Brenner, Michael; Hassidim, Avinatan; Devinsky, Orrin; Flinker, Adeen; Hasson, Uri
Contextual embeddings, derived from deep language models (DLMs), provide a continuous vectorial representation of language. This embedding space differs fundamentally from the symbolic representations posited by traditional psycholinguistics. We hypothesize that language areas in the human brain, similar to DLMs, rely on a continuous embedding space to represent language. To test this hypothesis, we densely record the neural activity patterns in the inferior frontal gyrus (IFG) of three participants using dense intracranial arrays while they listened to a 30-minute podcast. From these fine-grained spatiotemporal neural recordings, we derive a continuous vectorial representation for each word (i.e., a brain embedding) in each patient. Using stringent zero-shot mapping we demonstrate that brain embeddings in the IFG and the DLM contextual embedding space have common geometric patterns. The common geometric patterns allow us to predict the brain embedding in IFG of a given left-out word based solely on its geometrical relationship to other non-overlapping words in the podcast. Furthermore, we show that contextual embeddings capture the geometry of IFG embeddings better than static word embeddings. The continuous brain embedding space exposes a vector-based neural code for natural language processing in the human brain.
PMID: 38553456
ISSN: 2041-1723
CID: 5645352

Clinical outcomes among initial survivors of cryptogenic new-onset refractory status epilepsy (NORSE)

Costello, Daniel J; Matthews, Elizabeth; Aurangzeb, Sidra; Doran, Elisabeth; Stack, Jessica; Wesselingh, Robb; Dugan, Patricia; Choi, Hyunmi; Depondt, Chantal; Devinsky, Orrin; Doherty, Colin; Kwan, Patrick; Monif, Mastura; O'Brien, Terence J; Sen, Arjune; Gaspard, Nicolas
OBJECTIVE:New-onset refractory status epilepticus (NORSE) is a rare but severe clinical syndrome. Despite rigorous evaluation, the underlying cause is unknown in 30%-50% of patients and treatment strategies are largely empirical. The aim of this study was to describe clinical outcomes in a cohort of well-phenotyped, thoroughly investigated patients who survived the initial phase of cryptogenic NORSE managed in specialist centers. METHODS:Well-characterized cases of cryptogenic NORSE were identified through the EPIGEN and Critical Care EEG Monitoring Research Consortia (CCEMRC) during the period 2005-2019. Treating epileptologists reported on post-NORSE survival rates and sequelae in patients after discharge from hospital. Among survivors >6 months post-discharge, we report the rates and severity of active epilepsy, global disability, vocational, and global cognitive and mental health outcomes. We attempt to identify determinants of outcome. RESULTS:Among 48 patients who survived the acute phase of NORSE to the point of discharge from hospital, 9 had died at last follow-up, of whom 7 died within 6 months of discharge from the tertiary care center. The remaining 39 patients had high rates of active epilepsy as well as vocational, cognitive, and psychiatric comorbidities. The epilepsy was usually multifocal and typically drug resistant. Only a minority of patients had a good functional outcome. Therapeutic interventions were heterogenous during the acute phase of the illness. There was no clear relationship between the nature of treatment and clinical outcomes. SIGNIFICANCE/CONCLUSIONS:Among survivors of cryptogenic NORSE, longer-term outcomes in most patients were life altering and often catastrophic. Treatment remains empirical and variable. There is a pressing need to understand the etiology of cryptogenic NORSE and to develop tailored treatment strategies.
PMID: 38498313
ISSN: 1528-1167
CID: 5640142

Prediction tools and risk stratification in epilepsy surgery

Hadady, Levente; Sperling, Michael R; Alcala-Zermeno, Juan Luis; French, Jacqueline A; Dugan, Patricia; Jehi, Lara; Fabó, Dániel; Klivényi, Péter; Rubboli, Guido; Beniczky, Sándor
OBJECTIVE:This study was undertaken to conduct external validation of previously published epilepsy surgery prediction tools using a large independent multicenter dataset and to assess whether these tools can stratify patients for being operated on and for becoming free of disabling seizures (International League Against Epilepsy stage 1 and 2). METHODS:We analyzed a dataset of 1562 patients, not used for tool development. We applied two scales: Epilepsy Surgery Grading Scale (ESGS) and Seizure Freedom Score (SFS); and two versions of Epilepsy Surgery Nomogram (ESN): the original version and the modified version, which included electroencephalographic data. For the ESNs, we used calibration curves and concordance indexes. We stratified the patients into three tiers for assessing the chances of attaining freedom from disabling seizures after surgery: high (ESGS = 1, SFS = 3-4, ESNs > 70%), moderate (ESGS = 2, SFS = 2, ESNs = 40%-70%), and low (ESGS = 2, SFS = 0-1, ESNs < 40%). We compared the three tiers as stratified by these tools, concerning the proportion of patients who were operated on, and for the proportion of patients who became free of disabling seizures. RESULTS:The concordance indexes for the various versions of the nomograms were between .56 and .69. Both scales (ESGS, SFS) and nomograms accurately stratified the patients for becoming free of disabling seizures, with significant differences among the three tiers (p < .05). In addition, ESGS and the modified ESN accurately stratified the patients for having been offered surgery, with significant difference among the three tiers (p < .05). SIGNIFICANCE/CONCLUSIONS:ESGS and the modified ESN (at thresholds of 40% and 70%) stratify patients undergoing presurgical evaluation into three tiers, with high, moderate, and low chance for favorable outcome, with significant differences between the groups concerning having surgery and becoming free of disabling seizures. Stratifying patients for epilepsy surgery has the potential to help select the optimal candidates in underprivileged areas and better allocate resources in developed countries.
PMID: 38060351
ISSN: 1528-1167
CID: 5591352

Timing and location of speech errors induced by direct cortical stimulation

Kabakoff, Heather; Yu, Leyao; Friedman, Daniel; Dugan, Patricia; Doyle, Werner K; Devinsky, Orrin; Flinker, Adeen
Cortical regions supporting speech production are commonly established using neuroimaging techniques in both research and clinical settings. However, for neurosurgical purposes, structural function is routinely mapped peri-operatively using direct electrocortical stimulation. While this method is the gold standard for identification of eloquent cortical regions to preserve in neurosurgical patients, there is lack of specificity of the actual underlying cognitive processes being interrupted. To address this, we propose mapping the temporal dynamics of speech arrest across peri-sylvian cortices by quantifying the latency between stimulation and speech deficits. In doing so, we are able to substantiate hypotheses about distinct region-specific functional roles (e.g. planning versus motor execution). In this retrospective observational study, we analysed 20 patients (12 female; age range 14-43) with refractory epilepsy who underwent continuous extra-operative intracranial EEG monitoring of an automatic speech task during clinical bedside language mapping. Latency to speech arrest was calculated as time from stimulation onset to speech arrest onset, controlling for individual speech rate. Most instances of motor-based arrest (87.5% of 96 instances) were in sensorimotor cortex with mid-range latencies to speech arrest with a distributional peak at 0.47 s. Speech arrest occurred in numerous regions, with relatively short latencies in supramarginal gyrus (0.46 s), superior temporal gyrus (0.51 s) and middle temporal gyrus (0.54 s), followed by relatively long latencies in sensorimotor cortex (0.72 s) and especially long latencies in inferior frontal gyrus (0.95 s). Non-parametric testing for speech arrest revealed that region predicted latency; latencies in supramarginal gyrus and in superior temporal gyrus were shorter than in sensorimotor cortex and in inferior frontal gyrus. Sensorimotor cortex is primarily responsible for motor-based arrest. Latencies to speech arrest in supramarginal gyrus and superior temporal gyrus (and to a lesser extent middle temporal gyrus) align with latencies to motor-based arrest in sensorimotor cortex. This pattern of relatively quick cessation of speech suggests that stimulating these regions interferes with the outgoing motor execution. In contrast, the latencies to speech arrest in inferior frontal gyrus and in ventral regions of sensorimotor cortex were significantly longer than those in temporoparietal regions. Longer latencies in the more frontal areas (including inferior frontal gyrus and ventral areas of precentral gyrus and postcentral gyrus) suggest that stimulating these areas interrupts a higher-level speech production process involved in planning. These results implicate the ventral specialization of sensorimotor cortex (including both precentral and postcentral gyri) for speech planning above and beyond motor execution.
PMID: 38505231
ISSN: 2632-1297
CID: 5640502

Machine Learning to Classify Relative Seizure Frequency From Chronic Electrocorticography

Sun, Yueqiu; Friedman, Daniel; Dugan, Patricia; Holmes, Manisha; Wu, Xiaojing; Liu, Anli
PURPOSE/OBJECTIVE:Brain responsive neurostimulation (NeuroPace) treats patients with refractory focal epilepsy and provides chronic electrocorticography (ECoG). We explored how machine learning algorithms applied to interictal ECoG could assess clinical response to changes in neurostimulation parameters. METHODS:We identified five responsive neurostimulation patients each with ≥200 continuous days of stable medication and detection settings (median, 358 days per patient). For each patient, interictal ECoG segments for each month were labeled as "high" or "low" to represent relatively high or low long-episode (i.e., seizure) count compared with the median monthly long-episode count. Power from six conventional frequency bands from four responsive neurostimulation channels were extracted as features. For each patient, five machine learning algorithms were trained on 80% of ECoG, then tested on the remaining 20%. Classifiers were scored by the area-under-the-receiver-operating-characteristic curve. We explored how individual circadian cycles of seizure activity could inform classifier building. RESULTS:Support vector machine or gradient boosting models achieved the best performance, ranging from 0.705 (fair) to 0.892 (excellent) across patients. High gamma power was the most important feature, tending to decrease during low-seizure-frequency epochs. For two subjects, training on ECoG recorded during the circadian ictal peak resulted in comparable model performance, despite less data used. CONCLUSIONS:Machine learning analysis on retrospective background ECoG can classify relative seizure frequency for an individual patient. High gamma power was the most informative, whereas individual circadian patterns of seizure activity can guide model building. Machine learning classifiers built on interictal ECoG may guide stimulation programming.
PMID: 34049367
ISSN: 1537-1603
CID: 5418582

Rare Genetic Variation and Outcome of Surgery for Mesial Temporal Lobe Epilepsy

Perucca, Piero; Stanley, Kate; Harris, Natasha; McIntosh, Anne M; Asadi-Pooya, Ali A; Mikati, Mohamad A; Andrade, Danielle M; Dugan, Patricia; Depondt, Chantal; Choi, Hyunmi; Heinzen, Erin L; Cavalleri, Gianpiero L; Buono, Russell J; Devinsky, Orrin; Sperling, Michael R; Berkovic, Samuel F; Delanty, Norman; Goldstein, David B; O'Brien, Terence J
OBJECTIVE:Genetic factors have long been debated as a cause of failure of surgery for mesial temporal lobe epilepsy (MTLE). We investigated whether rare genetic variation influences seizure outcomes of MTLE surgery. METHODS:We performed an international, multicenter, whole exome sequencing study of patients who underwent surgery for drug-resistant, unilateral MTLE with normal magnetic resonance imaging (MRI) or MRI evidence of hippocampal sclerosis and ≥2-year postsurgical follow-up. Patients with either sustained seizure freedom (favorable outcome) or ongoing uncontrolled seizures since surgery (unfavorable outcome) were included. Exomes of controls without epilepsy were also included. Gene set burden analyses were carried out to identify genes with significant enrichment of rare deleterious variants in patients compared to controls. RESULTS:Nine centers from 3 continents contributed 206 patients operated for drug-resistant unilateral MTLE, of whom 196 (149 with favorable outcome and 47 with unfavorable outcome) were included after stringent quality control. Compared to 8,718 controls, MTLE cases carried a higher burden of ultrarare missense variants in constrained genes that are intolerant to loss-of-function (LoF) variants (odds ratio [OR] = 2.6, 95% confidence interval [CI] = 1.9-3.5, p = 1.3E-09) and in genes encoding voltage-gated cation channels (OR = 2.4, 95% CI = 1.4-3.8, p = 2.7E-04). Proportions of subjects with such variants were comparable between patients with favorable outcome and those with unfavorable outcome, with no significant between-group differences. INTERPRETATION/CONCLUSIONS:Rare variation contributes to the genetic architecture of MTLE, but does not appear to have a major role in failure of MTLE surgery. These findings can be incorporated into presurgical decision-making and counseling. ANN NEUROL 2022.
PMID: 36534060
ISSN: 1531-8249
CID: 5409262

Temporal dynamics of neural responses in human visual cortex

Groen, Iris I A; Piantoni, Giovanni; Montenegro, Stephanie; Flinker, Adeen; Devore, Sasha; Devinsky, Orrin; Doyle, Werner; Dugan, Patricia; Friedman, Daniel; Ramsey, Nick; Petridou, Natalia; Winawer, Jonathan
Neural responses to visual stimuli exhibit complex temporal dynamics, including sub-additive temporal summation, response reduction with repeated or sustained stimuli (adaptation), and slower dynamics at low contrast. These phenomena are often studied independently. Here, we demonstrate these phenomena within the same experiment and model the underlying neural computations with a single computational model. We extracted time-varying responses from electrocorticographic (ECoG) recordings from patients presented with stimuli that varied in contrast, duration, and inter-stimulus interval (ISI). Aggregating data across patients from both sexes yielded 98 electrodes with robust visual responses, covering both earlier (V1-V3) and higher-order (V3a/b, LO, TO, IPS) retinotopic maps. In all regions, the temporal dynamics of neural responses exhibit several non-linear features: peak response amplitude saturates with high contrast and longer stimulus durations; the response to a second stimulus is suppressed for short ISIs and recovers for longer ISIs; response latency decreases with increasing contrast. These features are accurately captured by a computational model comprised of a small set of canonical neuronal operations: linear filtering, rectification, exponentiation, and a delayed divisive normalization. We find that an increased normalization term captures both contrast- and adaptation-related response reductions, suggesting potentially shared underlying mechanisms. We additionally demonstrate both changes and invariance in temporal response dynamics between earlier and higher-order visual areas. Together, our results reveal the presence of a wide range of temporal and contrast-dependent neuronal dynamics in the human visual cortex, and demonstrate that a simple model captures these dynamics at millisecond resolution.SIGNIFICANCE STATEMENTSensory inputs and neural responses change continuously over time. It is especially challenging to understand a system that has both dynamic inputs and outputs. Here we use a computational modeling approach that specifies computations to convert a time-varying input stimulus to a neural response time course, and use this to predict neural activity measured in the human visual cortex. We show that this computational model predicts a wide variety of complex neural response shapes that we induced experimentally by manipulating the duration, repetition and contrast of visual stimuli. By comparing data and model predictions, we uncover systematic properties of temporal dynamics of neural signals, allowing us to better understand how the brain processes dynamic sensory information.
PMID: 35999054
ISSN: 1529-2401
CID: 5338232

Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states

Alasfour, Abdulwahab; Gabriel, Paolo; Jiang, Xi; Shamie, Isaac; Melloni, Lucia; Thesen, Thomas; Dugan, Patricia; Friedman, Daniel; Doyle, Werner; Devinsky, Orin; Gonda, David; Sattar, Shifteh; Wang, Sonya; Halgren, Eric; Gilja, Vikash
In analyzing the neural correlates of naturalistic and unstructured behaviors, features of neural activity that are ignored in a trial-based experimental paradigm can be more fully studied and investigated. Here, we analyze neural activity from two patients using electrocorticography (ECoG) and stereo-electroencephalography (sEEG) recordings, and reveal that multiple neural signal characteristics exist that discriminate between unstructured and naturalistic behavioral states such as "engaging in dialogue" and "using electronics". Using the high gamma amplitude as an estimate of neuronal firing rate, we demonstrate that behavioral states in a naturalistic setting are discriminable based on long-term mean shifts, variance shifts, and differences in the specific neural activity's covariance structure. Both the rapid and slow changes in high gamma band activity separate unstructured behavioral states. We also use Gaussian process factor analysis (GPFA) to show the existence of salient spatiotemporal features with variable smoothness in time. Further, we demonstrate that both temporally smooth and stochastic spatiotemporal activity can be used to differentiate unstructured behavioral states. This is the first attempt to elucidate how different neural signal features contain information about behavioral states collected outside the conventional experimental paradigm.
PMID: 35939509
ISSN: 1553-7358
CID: 5286572

Impact of the COVID-19 pandemic on people with epilepsy: findings from the US arm of the COV-E study

Dugan, Patricia; Carroll, Elizabeth; Thorpe, Jennifer; Jette, Nathalie; Agarwal, Parul; Ashby, Samantha; Hanna, Jane; French, Jacqueline; Devinsky, Orrin; Sen, Arjune
OBJECTIVES/OBJECTIVE:As part of the COVID-19 and Epilepsy (COV-E) global study, we aimed to understand the impact of COVID-19 on the medical care and well-being of people with epilepsy (PWE) in the United States, based on their perspectives and those of their caregivers. METHODS:Separate surveys designed for PWE and their caregivers were circulated from April 2020 to July 2021; modifications in March 2021 included a question about COVID-19 vaccination status. RESULTS:We received 788 responses, 71% from PWE (n = 559) and 29% (n=229) from caregivers of persons with epilepsy. A third (n = 308) of respondents reported a change in their health or in the health of the person they care for. Twenty-seven percent (n = 210) reported issues related to worsening mental health. Of respondents taking ASMs (n = 769), 10% (n= 78) reported difficulty taking medications on time, mostly due to stress causing forgetfulness. Less than half of respondents received counseling on mental health and stress. Less than half of the PWE reported having discussions with their healthcare providers about sleep, ASMs and potential side effects, while a larger proportion of caregivers (81%) reported having had discussions with their healthcare providers on the same topics. More PWE and caregivers reported that COVID-19 related measures caused adverse impact on their health in the post-vaccine period than during the pre-vaccine period, citing mental health issues as the primary reason. SIGNIFICANCE/CONCLUSIONS:Our findings indicate that the impact of the COVID-19 pandemic in the US on PWE is multifaceted. Apart from the increased risk of poor COVID-19 outcomes, the pandemic has also had negative effects on mental health and self-management. Healthcare providers must be vigilant for increased emotional distress in PWE during the pandemic and consider the importance of effective counseling to diminish risks related to exacerbated treatment gaps.
PMID: 35929180
ISSN: 2470-9239
CID: 5288312

Genomics in the presurgical epilepsy evaluation

Moloney, Patrick B; Dugan, Patricia; Widdess-Walsh, Peter; Devinsky, Orrin; Delanty, Norman
Epilepsy surgery should be considered in all patients with drug-resistant focal epilepsy. The diagnostic presurgical evaluation aims to delineate the epileptogenic zone and its relationship to eloquent brain regions. Genetic testing is not yet routine in presurgical evaluations, despite many monogenic causes of severe epilepsies, including some focal epilepsies. This review highlights genomic data that may inform decisions regarding epilepsy surgery candidacy and strategy. Focal epilepsies due to pathogenic variants in mechanistic target of rapamycin pathway genes are amenable to surgery if clinical, electroencephalography and imaging data are concordant. Epilepsy surgery outcomes are less favourable in patients with pathogenic variants in ion channel genes such as SCN1A. However, genomic data should not be used in isolation to contraindicate epilepsy surgery and should be considered alongside other diagnostic modalities. The additional role of somatic mosaicism in the pathogenesis of focal epilepsies may have implications for surgical planning and prognostication. Here, we advocate for including genomic data in the presurgical evaluation and multidisciplinary discussion for many epilepsy surgery candidates. We encourage neurologists to perform genetic testing in patients with focal non-lesional epilepsy, epilepsy in the setting of intellectual disability and epilepsy due to specific malformations of cortical development. The integration of genomics into the presurgical evaluation assists selection of patients for resective surgery and fosters a personalised medicine approach, where precision or targeted therapies are considered alongside surgical procedures.
PMID: 35691218
ISSN: 1872-6844
CID: 5279562