Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data.

Widefield calcium imaging enables recording of large-scale neural activity across the mouse dorsal cortex. In order to examine the relationship of these neural signals to the resulting behavior, it is critical to demix the recordings into meaningful spatial and temporal components that can be mapped onto well-defined brain regions. However, no current tools satisfactorily extract the activity of the different brain regions in individual mice in a data-driven manner, while taking into account mouse-specific and preparation-specific differences. Here, we introduce Localized semi-Nonnegative Matrix Factorization (LocaNMF), a method that efficiently decomposes widefield video data and allows us to directly compare activity across multiple mice by outputting mouse-specific localized functional regions that are significantly more interpretable than more traditional decomposition techniques. Moreover, it provides a natural subspace to directly compare correlation maps and neural dynamics across different behaviors, mice, and experimental conditions, and enables identification of task- and movement-related brain regions.

Performance Limitations in Sensorimotor Control: Trade-Offs Between Neural Computation and Accuracy in Tracking Fast Movements.

The ability to move fast and accurately track moving objects is fundamentally constrained by the biophysics of neurons and dynamics of the muscles involved. Yet the corresponding trade-offs between these factors and tracking motor commands have not been rigorously quantified. We use feedback control principles to quantify performance limitations of the sensorimotor control system (SCS) to track fast periodic movements. We show that (1) linear models of the SCS fail to predict known undesirable phenomena, including skipped cycles, overshoot and undershoot, produced when tracking signals in the "fast regime," while nonlinear pulsatile control models can predict such undesirable phenomena, and (2) tools from nonlinear control theory allow us to characterize fundamental limitations in this fast regime. Using a validated and tractable nonlinear model of the SCS, we derive an analytical upper bound on frequencies that the SCS model can reliably track before producing such undesirable phenomena as a function of the neurons' biophysical constraints and muscle dynamics. The performance limitations derived here have important implications in sensorimotor control. For example, if the primary motor cortex is compromised due to disease or damage, the theory suggests ways to manipulate muscle dynamics by adding the necessary compensatory forces using an assistive neuroprosthetic device to restore motor performance and, more important, fast and agile movements. Just how one should compensate can be informed by our SCS model and the theory developed here.

µSim: A goal-driven framework for elucidating the neural control of movement through musculoskeletal modeling.

How does the motor cortex (MC) produce purposeful and generalizable movements from the complex musculoskeletal system in a dynamic environment? To elucidate the underlying neural dynamics, we use a goal-driven approach to model MC by considering its goal as a controller driving the musculoskeletal system through desired states to achieve movement. Specifically, we formulate the MC as a recurrent neural network (RNN) controller producing muscle commands while receiving sensory feedback from biologically accurate musculoskeletal models. Given this real-time simulated feedback implemented in advanced physics simulation engines, we use deep reinforcement learning to train the RNN to achieve desired movements under specified neural and musculoskeletal constraints. Activity of the trained model can accurately decode experimentally recorded neural population dynamics and single-unit MC activity, while generalizing well to testing conditions significantly different from training. Simultaneous goal- and data- driven modeling in which we use the recorded neural activity as observed states of the MC further enhances direct and generalizable single-unit decoding. Finally, we show that this framework elucidates computational principles of how neural dynamics enable flexible control of movement and make this framework easy-to-use for future experiments.

Artificial neural network-based rapid predictor of biological nerve fiber activation for DBS applications.

Objective.Computational models are powerful tools that can enable the optimization of deep brain stimulation (DBS). To enhance the clinical practicality of these models, their computational expense and required technical expertise must be minimized. An important aspect of DBS models is the prediction of neural activation in response to electrical stimulation. Existing rapid predictors of activation simplify implementation and reduce prediction runtime, but at the expense of accuracy. We sought to address this issue by leveraging the speed and generalization abilities of artificial neural networks (ANNs) to create a novel predictor of neural fiber activation in response to DBS.Approach.We developed six variations of an ANN-based predictor to predict the response of individual, myelinated axons to extracellular electrical stimulation. ANNs were trained using datasets generated from a finite-element model of an implanted DBS system together with multi-compartment cable models of axons. We evaluated the ANN-based predictors using three white matter pathways derived from group-averaged connectome data within a patient-specific tissue conductivity field, comparing both predicted stimulus activation thresholds and pathway recruitment across a clinically relevant range of stimulus amplitudes and pulse widths.Main results.The top-performing ANN could predict the thresholds of axons with a mean absolute error (MAE) of 0.037 V, and pathway recruitment with an MAE of 0.079%, across all parameters. The ANNs reduced the time required to predict the thresholds of 288 axons by four to five orders of magnitude when compared to multi-compartment cable models.Significance.We demonstrated that ANNs can be fast, accurate, and robust predictors of neural activation in response to DBS.

Behavioral Classification of Sequential Neural Activity Using Time Varying Recurrent Neural Networks.

Shifts in data distribution across time can strongly affect early classification of time-series data. When decoding behavior from neural activity, early detection of behavior may help in devising corrective neural stimulation before the onset of behavior. Recurrent Neural Networks (RNNs) are common models for sequence data. However, standard RNNs are not able to handle data with temporal distributional shifts to guarantee robust classification across time. To enable the network to utilize all temporal features of the neural input data, and to enhance the memory of an RNN, we propose a novel approach: RNNs with time-varying weights, here termed Time-Varying RNNs (TV-RNNs). These models are able to not only predict the class of the time-sequence correctly but also lead to accurate classification earlier in the sequence than standard RNNs. In this work, we focus on early sequential classification of brain-wide neural activity across time using TV-RNNs applied to a variety of neural data from mice and humans, as subjects perform motor tasks. Finally, we explore the contribution of different brain regions on behavior classification using SHapley Additive exPlanation (SHAP) value, and find that the somatosensory and premotor regions play a large role in behavioral classification.

Motor deficit and lack of overt dystonia in Dlx conditional Dyt1 knockout mice.

DYT1 or DYT-TOR1A dystonia is early-onset generalized dystonia caused by a trinucleotide deletion of GAG in the TOR1A or DYT1 gene leads to the loss of a glutamic acid residue in the resulting torsinA protein. A mouse model with overt dystonia is of unique importance to better understand the DYT1 pathophysiology and evaluate preclinical drug efficacy. DYT1 dystonia is likely a network disorder involving multiple brain regions, particularly the basal ganglia. Tor1a conditional knockout in the striatum or cerebral cortex leads to motor deficits, suggesting the importance of corticostriatal connection in the pathogenesis of dystonia. Indeed, corticostriatal long-term depression impairment has been demonstrated in multiple targeted DYT1 mouse models. Pappas and colleagues developed a conditional knockout line (Dlx-CKO) that inactivated Tor1a in the forebrain and surprisingly displayed overt dystonia. We set out to validate whether conditional knockout affecting both cortex and striatum would lead to overt dystonia and whether machine learning-based video behavioral analysis could be used to facilitate high throughput preclinical drug screening. We generated Dlx-CKO mice and found no overt dystonia or motor deficits at 4 months. At 8 months, retesting revealed motor deficits in rotarod, beam walking, grip strength, and hyperactivity in the open field; however, no overt dystonia was visually discernible or through the machine learning-based video analysis. Consistent with other targeted DYT1 mouse models, we observed age-dependent deficits in the beam walking test, which is likely a better motor behavioral test for preclinical drug testing but more labor-intensive when overt dystonia is absent.

First- versus Third-Generation EGFR Tyrosine Kinase Inhibitors in EGFR-Mutated Non-Small Cell Lung Cancer Patients with Brain Metastases.

Introduction: Up to 50% of non-small cell lung cancer (NSCLC) harbor EGFR alterations, the most common etiology behind brain metastases (BMs). First-generation EGFR-directed tyrosine kinase inhibitors (EGFR-TKI) are limited by blood-brain barrier penetration and T790M tumor mutations, wherein third-generation EGFR-TKIs, like Osimertinib, have shown greater activity. However, their efficacy has not been well-studied in later therapy lines in NSCLC patients with BMs (NSCLC-BM). We sought to compare outcomes of NSCLC-BM treated with either first- or third-generation EGFR-TKIs in first-line and 2nd-to-5th-line settings. Methods: A retrospective review of NSCLC-BM patients diagnosed during 2010-2019 at Cleveland Clinic, Ohio, US, a quaternary-care center, was performed and reported following 'strengthening the reporting of observational studies in epidemiology' (STROBE) guidelines. Data regarding socio-demographic, histopathological, molecular characteristics, and clinical outcomes were collected. Primary outcomes were median overall survival (mOS) and progression-free survival (mPFS). Multivariable Cox proportional hazards modeling and propensity score matching were utilized to adjust for confounders. Results: 239 NSCLC-BM patients with EGFR alterations were identified, of which 107 received EGFR-TKIs after diagnosis of BMs. 77.6% (83/107) received it as first-line treatment, and 30.8% (33/107) received it in later (2nd-5th) lines of therapy, with nine patients receiving it in both settings. 64 of 107 patients received first-generation (erlotinib/gefitinib) TKIs, with 53 receiving them in the first line setting and 13 receiving it in the 2nd-5th lines of therapy. 50 patients received Osimertinib as third-generation EGFR-TKI, 30 in first-line, and 20 in the 2nd-5th lines of therapy. Univariable analysis in first-line therapy demonstrated mOS of first- and third-generation EGFR-TKIs as 18.2 and 19.4 months, respectively (p = 0.57), while unadjusted mPFS of first- and third-generation EGFR-TKIs was 9.3 and 13.8 months, respectively (p = 0.14). In 2nd-5th line therapy, for first- and third-generation EGFR-TKIs, mOS was 17.3 and 11.9 months, (p = 0.19), while mPFS was 10.4 and 6.08 months, respectively (p = 0.41). After adjusting for age, performance status, presence of extracranial metastases, whole-brain radiotherapy, and presence of leptomeningeal metastases, hazard ratio (HR) for OS was 1.25 (95% CI 0.63-2.49, p = 0.52) for first-line therapy. Adjusted HR for mOS in 2nd-to-5th line therapy was 1.60 (95% CI 0.55-4.69, p = 0.39). Conclusions: No difference in survival was detected between first- and third-generation EGFR-TKIs in either first or 2nd-to-5th lines of therapy. Larger prospective studies are warranted reporting intracranial lesion size, EGFR alteration and expression levels in primary tumor and brain metastases, and response rates.

Combination of EGFR-Directed Tyrosine Kinase Inhibitors (EGFR-TKI) with Radiotherapy in Brain Metastases from Non-Small Cell Lung Cancer: A 2010-2019 Retrospective Cohort Study.

INTRODUCTION: Traditionally, brain metastases have been treated with stereotactic radiosurgery (SRS), whole-brain radiation (WBRT), and/or surgical resection. Non-small cell lung cancers (NSCLC), over half of which carry EGFR mutations, are the leading cause of brain metastases. EGFR-directed tyrosine kinase inhibitors (TKI) have shown promise in NSCLC; but their utility in NSCLC brain metastases (NSCLCBM) remains unclear. This work sought to investigate whether combining EGFR-TKI with WBRT and/or SRS improves overall survival (OS) in NSCLCBM. METHODS: A retrospective review of NSCLCBM patients diagnosed during 2010-2019 at a tertiary-care US center was performed and reported following the 'strengthening the reporting of observational studies in epidemiology' (STROBE) guidelines. Data regarding socio-demographic and histopathological characteristics, molecular attributes, treatment strategies, and clinical outcomes were collected. Concurrent therapy was defined as the combination of EGFR-TKI and radiotherapy given within 28 days of each other. RESULTS: A total of 239 patients with EGFR mutations were included. Of these, 32 patients had been treated with WBRT only, 51 patients received SRS only, 36 patients received SRS and WBRT only, 18 were given EGFR-TKI and SRS, and 29 were given EGFR-TKI and WBRT. Median OS for the WBRT-only group was 3.23 months, for SRS + WBRT it was 3.17 months, for EGFR-TKI + WBRT 15.50 months, for SRS only 21.73 months, and for EGFR-TKI + SRS 23.63 months. Multivariable analysis demonstrated significantly higher OS in the SRS-only group (HR = 0.38, 95% CI 0.17-0.84, p = 0.017) compared to the WBRT reference group. There were no significant differences in overall survival for the SRS + WBRT combination cohort (HR = 1.30, 95% CI = 0.60, 2.82, p = 0.50), EGFR-TKIs and WBRT combination cohort (HR = 0.93, 95% CI = 0.41, 2.08, p = 0.85), or the EGFR-TKI + SRS cohort (HR = 0.46, 95% CI = 0.20, 1.09, p = 0.07). CONCLUSIONS: NSCLCBM patients treated with SRS had a significantly higher OS compared to patients treated with WBRT-only. While sample-size limitations and investigator-associated selection bias may limit the generalizability of these results, phase II/III clinicals trials are warranted to investigate synergistic efficacy of EGFR-TKI and SRS.

Extrapulmonary tuberculosis presentation in the form of a chest wall abscess with no pulmonary involvement in the UK: a case report.

The presentation of an extrapulmonary manifestation of tuberculous (TB) infection to a tertiary care facility in the UK is a rare event given its low prevalence. This case report focuses on an atypical presentation of an extrapulmonary tuberculosis (EPTB) infection in the form of a chest wall abscess. This was recognized and managed appropriately. This case however elucidates vital learning as migration from around the globe would contribute to an increasing number of TB/EPTB infections. The wide array and indolent nature of their presentation creates diagnostic and treatment challenges. Appreciation for the epidemiology, risk factors, effective and prompt treatment with follow up protocols would help develop pathways for better care. Within the UK, despite it being a low-risk country for TB, there is need for increased awareness, education with established management pathways and governance for TB and EPTB infections.

Modeling the behavior of multiple subjects using a Cauchy-Schwarz regularized Partitioned Subspace Variational AutoEncoder (CS-PS-VAE).

Effectively modeling and quantifying behavior is essential for our understanding of the brain. Modeling behavior across different subjects in a unified manner remains a significant challenge in the field of behavioral quantification, which necessitates partitioning the behavioral data into features that are common across subjects, and others that are distinct to each subject. We build on a semi-supervised approach to partition the subspace adequately known as a Partitioned Subspace Variational AutoEncoder (PS-VAE), and propose a novel regularization based on the Cauchy-Schwarz divergence to model the distinct features across subjects. Our model, called the Cauchy-Schwarz regularized Partitioned Subspace Variational AutoEncoder (CS-PS-VAE), successfully models continuously varying differences in behavior, and models distinct features of the behavioral videos across subjects in an unsupervised manner. This method is also successful at uncovering the relationships between recorded neural data and the ensuing behavior.

Recurrent neural networks controlling musculoskeletal models predict motor cortex activity during novel limb movements.

Goal-driven networks trained to perform a task analogous to that performed by biological neural populations are being increasingly utilized as insightful computational models of motor control. The resulting dynamics of the trained networks are then analyzed to uncover the neural strategies employed by the motor cortex to produce movements. However, these networks do not take into account the role of sensory feedback in producing movement, nor do they consider the complex biophysical underpinnings of the underlying musculoskeletal system. Moreover, these models can not be used in context of predictive neuromechanical simulations for hypothesis generation and prediction of neural strategies during novel movements. In this research, we adapt state-of-the-art deep reinforcement learning (DRL) algorithms to train a controller to drive a developed anatomically accurate monkey arm model to track experimentally recorded kinematics. We validate that the trained controller mimics biologically observed neural strategies to produce movement. The trained controller generalizes well to unobserved conditions as well as to perturbation analyses. The recorded firing rates of motor cortex neurons can be predicted from the controller activity with high accuracy even on unseen conditions. Finally, we validate that the trained controller outperforms existing goal-driven and representational models of motor cortex in single neuron decoding accuracy, thus showing the utility of the complex underpinnings of anatomically accurate models in shaping motor cortex neural activity during limb movements. The learned controller can be used for hypothesis generation and prediction of neural strategies during novel movements and unobserved conditions.

Motor cortex activity across movement speeds is predicted by network-level strategies for generating muscle activity.

Learned movements can be skillfully performed at different paces. What neural strategies produce this flexibility? Can they be predicted and understood by network modeling? We trained monkeys to perform a cycling task at different speeds, and trained artificial recurrent networks to generate the empirical muscle-activity patterns. Network solutions reflected the principle that smooth well-behaved dynamics require low trajectory tangling. Network solutions had a consistent form, which yielded quantitative and qualitative predictions. To evaluate predictions, we analyzed motor cortex activity recorded during the same task. Responses supported the hypothesis that the dominant neural signals reflect not muscle activity, but network-level strategies for generating muscle activity. Single-neuron responses were better accounted for by network activity than by muscle activity. Similarly, neural population trajectories shared their organization not with muscle trajectories, but with network solutions. Thus, cortical activity could be understood based on the need to generate muscle activity via dynamics that allow smooth, robust control over movement speed.

Update on the Management of Brain Metastasis.

Brain metastases occur in almost one-third of adult patients with solid tumor malignancies and lead to considerable patient morbidity and mortality. The rising incidence of brain metastases has been ascribed to the development of better imaging and screening techniques and the formulation of better systemic therapies. Until recently, the multimodal management of brain metastases focused primarily on the utilization of neurosurgical techniques, with varying combinations of whole-brain radiation therapy and stereotactic radio-surgical procedures. Over the past 2 decades, in particular, the increment in knowledge pertaining to molecular genetics and the pathogenesis of brain metastases has led to significant developments in targeted therapies and immunotherapies. This review article highlights the recent updates in the management of brain metastases with an emphasis on novel systemic therapies.

Motor cortical influence relies on task-specific activity covariation.

During limb movement, spinal circuits facilitate the alternating activation of antagonistic flexor and extensor muscles. Yet antagonist cocontraction is often required to stabilize joints, like when loads are handled. Previous results suggest that these different muscle activation patterns are mediated by separate flexion- and extension-related motor cortical output populations, while others suggest recruitment of task-specific populations. To distinguish between hypotheses, we developed a paradigm in which mice toggle between forelimb tasks requiring antagonist alternation or cocontraction and measured activity in motor cortical layer 5b. Our results conform to neither hypothesis: consistent flexion- and extension-related activity is not observed across tasks, and no task-specific populations are observed. Instead, activity covariation among motor cortical neurons dramatically changes between tasks, thereby altering the relation between neural and muscle activity. This is also observed specifically for corticospinal neurons. Collectively, our findings indicate that motor cortex drives different muscle activation patterns via task-specific activity covariation.

Novel Therapeutic Approaches in Neoplastic Meningitis.

Central nervous system (CNS) metastasis from systemic cancers can involve the brain parenchyma, leptomeninges, or the dura. Neoplastic meningitis (NM), also known by different terms, including leptomeningeal carcinomatosis and carcinomatous meningitis, occurs due to solid tumors and hematologic malignancies and is associated with a poor prognosis. The current management paradigm entails a multimodal approach focused on palliation with surgery, radiation, and chemotherapy, which may be administered systemically or directly into the cerebrospinal fluid (CSF). This review focuses on novel therapeutic approaches, including targeted and immunotherapeutic agents under investigation, that have shown promise in NM arising from solid tumors.

Mesoscale cortex-wide neural dynamics predict self-initiated actions in mice several seconds prior to movement.

Volition - the sense of control or agency over one's voluntary actions - is widely recognized as the basis of both human subjective experience and natural behavior in nonhuman animals. Several human studies have found peaks in neural activity preceding voluntary actions, for example the readiness potential (RP), and some have shown upcoming actions could be decoded even before awareness. Others propose that random processes underlie and explain pre-movement neural activity. Here, we seek to address these issues by evaluating whether pre-movement neural activity in mice contains structure beyond that present in random neural activity. Implementing a self-initiated water-rewarded lever-pull paradigm in mice while recording widefield [Ca++] neural activity we find that cortical activity changes in variance seconds prior to movement and that upcoming lever pulls could be predicted between 3 and 5 s (or more in some cases) prior to movement. We found inhibition of motor cortex starting at approximately 5 s prior to lever pulls and activation of motor cortex starting at approximately 2 s prior to a random unrewarded left limb movement. We show that mice, like humans, are biased toward commencing self-initiated actions during specific phases of neural activity but that the pre-movement neural code changes over time in some mice and is widely distributed as behavior prediction improved when using all vs. single cortical areas. These findings support the presence of structured multi-second neural dynamics preceding self-initiated action beyond that expected from random processes. Our results also suggest that neural mechanisms underlying self-initiated action could be preserved between mice and humans.

Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis.

A key aspect of neuroscience research is the development of powerful, general-purpose data analyses that process large datasets. Unfortunately, modern data analyses have a hidden dependence upon complex computing infrastructure (e.g., software and hardware), which acts as an unaddressed deterrent to analysis users. Although existing analyses are increasingly shared as open-source software, the infrastructure and knowledge needed to deploy these analyses efficiently still pose significant barriers to use. In this work, we develop Neuroscience Cloud Analysis As a Service (NeuroCAAS): a fully automated open-source analysis platform offering automatic infrastructure reproducibility for any data analysis. We show how NeuroCAAS supports the design of simpler, more powerful data analyses and that many popular data analysis tools offered through NeuroCAAS outperform counterparts on typical infrastructure. Pairing rigorous infrastructure management with cloud resources, NeuroCAAS dramatically accelerates the dissemination and use of new data analyses for neuroscientific discovery.

Next-generation brain observatories.

We propose centralized brain observatories for large-scale recordings of neural activity in mice and non-human primates coupled with cloud-based data analysis and sharing. Such observatories will advance reproducible systems neuroscience and democratize access to the most advanced tools and data.

Uncovering the effect of different brain regions on behavioral classification using recurrent neural networks.

As our ability to record neural activity from a larger number of brain areas increases, we need to develop tools to understand how this activity is related to ongoing behavior. Recurrent neural networks (RNNs) have been shown to perform successful classification for sequence data. However, they are black box models: once trained, it is difficult to uncover the mechanisms that they are using to classify. In this study, we analyze the effect of RNNs on classifying behavior using a simulated dataset and a widefield neural activity dataset as mice perform a self-initiated behavior. We show that RNNs are comparable to, or outperform, traditional classification methods such as Support Vector Machine (SVM), and can also lead to accurate prediction of behavior. Using dimensionality reduction, we visualize the activity of the RNNs to better understand the classification mechanisms of the RNNs. Finally, we are able to accurately pinpoint the effect of different regions on behavioral classification. This study highlights the utility and interpretability of RNNs while classifying behavior using neural activity from different regions.

Chronic, cortex-wide imaging of specific cell populations during behavior.

Measurements of neuronal activity across brain areas are important for understanding the neural correlates of cognitive and motor processes such as attention, decision-making and action selection. However, techniques that allow cellular resolution measurements are expensive and require a high degree of technical expertise, which limits their broad use. Wide-field imaging of genetically encoded indicators is a high-throughput, cost-effective and flexible approach to measure activity of specific cell populations with high temporal resolution and a cortex-wide field of view. Here we outline our protocol for assembling a wide-field macroscope setup, performing surgery to prepare the intact skull and imaging neural activity chronically in behaving, transgenic mice. Further, we highlight a processing pipeline that leverages novel, cloud-based methods to analyze large-scale imaging datasets. The protocol targets laboratories that are seeking to build macroscopes, optimize surgical procedures for long-term chronic imaging and/or analyze cortex-wide neuronal recordings. The entire protocol, including steps for assembly and calibration of the macroscope, surgical preparation, imaging and data analysis, requires a total of 8 h. It is designed to be accessible to laboratories with limited expertise in imaging methods or interest in high-throughput imaging during behavior.