Matthew T. Harrison’s research while affiliated with Brown University and other places

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Publications (58)


MINDFUL score correlates with performance over time
a Illustration of how the MINDFUL metric is calculated. Each dot symbolizes neural features at a given time bin in any given session, colored by whether the time bin is included for estimating the reference distribution (yellow), or for comparison (blue), or neither (gray). The difference in distributions is quantified by Kullback–Leibler divergence (KLD) between the reference distribution, p0 and the comparison distribution, pi. b Binned samples of neural features were grouped according to decoder performance in terms of angle error (AE), including data from all sessions. A total of 45 different distributions were generated, with AE increasing in 4° intervals from 0° to 180°. Bins with low AE (<4°) were chosen as the reference distribution, and compared against the other 44 for T11 (left panel) and T5 (right panel). The dotted line which represents the best linear regression fit, along with the Pearson correlation coefficients, r, is shown. c The reference distribution was estimated from neural features (NF) time bins where AE < 4°, limited to day 0 where the decoder was first deployed for T11, and day 0 and 5 for T5. For subsequent sessions, neural distributions for comparison were constructed using an overlapping sliding window of 60 s at 1 s intervals. The KLD (right y-axis) is overlaid onto median AE calculated from the same sliding window (left y-axis in blue) across all recorded sessions for T11 (left panel) and T5 (right panel). Gray lines indicate the beginning of the sessions. Pearson and Spearman rank correlation, r and ρ, respectively, quantify the relationship between the KLD and median AE. Insets present examples of cursor control of the task in the first and last session. For T11, cursor trajectories for all trials during a 5-min block are shown. Each color represents a peripheral target in a center-out-and-back task. For T5, cursor trajectories of the first 20 trials of a block are shown, along with the corresponding target presented at a random location on the screen in each trial.
Incorporating decoder outputs in the MINDFUL score maintains a high correlation with performance
a The KLD (right y-axis) between distributions of decoded directional vectors, X̂\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{X}$$\end{document}, with respect to the sub-selected time bins from the first session(s) overlaid onto median AE (left y-axis in blue) across all recorded sessions for T11 (left panel) and T5 (right panel). Subsequent neural distributions and median AE were updated every 1 s over a 60-s sliding window. Pearson r, and Spearman rank correlation coefficients ρ, between KLD and median AE are shown. b The KLD between distributions of X̂\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{X}$$\end{document} and X̂lag\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\hat{X}}_{{lag}}$$\end{document} overlaid onto median AE. c The KLD between distributions of the combination of derived neural features (as shown in Fig. 1c), decoded directional vectors, X̂\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{X}$$\end{document}, and X̂lag\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\hat{X}}_{{lag}}$$\end{document}, overlaid onto median AE.
Changes in feature tunings across sessions correlate with KLD
a Changes in preferred directions (PD) and b modulation depth (MD) of significantly tuned features used in the decoder (relative to the tuning of the first day for which the feature was significantly tuned) for T11. Features were ordered by hierarchical clustering to visualize groups of features with similar tuning changes behavior (see “Methods”). Gray color indicates features that were not significantly tuned in that session. c Fitted cosine tuning curves for sample units across days for T11 illustrating changes in MD and channel dropout, respectively (color curves); Triangle markers denote PDs for sessions with significant tuning. d Changes in cosine tuning PD and e MD for significantly tuned features used in the decoder for T5. f Fitted cosine tuning curves for sample units across days of T5 illustrating changes in MD and PD, respectively. g T11 Tuning similarity across days represented by interpolated Pearson correlations between pairs of tuning maps (see “Methods”). h T5 tuning similarity across session days. i T11 mean KLD of neural distributions between sessions negatively correlates with the tuning similarity (Pearson r = −0.812, p < 10⁻³⁰ , see “Methods”). Each dot corresponds to a pair of sessions with the color indicating the number of days apart. j T5 mean KLD of neural distributions between days negatively correlates with the tuning similarity (Pearson r = −0.776, p < 10⁻⁴ ).
Instability reflected in neural latent space
a Projection of neural features of subsequent sessions onto the top two task-dependent PCs latent space of neural features on decoder day 0 using dPCA. Fine lines are trial trajectories and bold lines are trial averages per goal directions. Different colors correspond to the goal direction. b Projection of neural features for T5. For comparison simplicity, the random-target task was visualized and colored by discretizing the goal directions of each trial into eight even movement directions as in a center-out-and-back task.
Sub-selecting instances of low AE for reference and using longer window length improve correlation between MINDFUL and AE
a Spearman correlation coefficients of KLD of NF, X̂\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{X}$$\end{document}, and X̂lag\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\hat{X}}_{lag}$$\end{document}, to AE when sub-selecting time bins with different quantiles of AE as the reference. Each quantile approximately contains an even number of observations. b Spearman correlation coefficients of KLD to AE when using different window lengths to estimate target distributions.

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Measuring instability in chronic human intracortical neural recordings towards stable, long-term brain-computer interfaces
  • Article
  • Full-text available

October 2024

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24 Reads

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4 Citations

Communications Biology

Tsam Kiu Pun

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Mona Khoshnevis

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Tommy Hosman

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[...]

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Intracortical brain-computer interfaces (iBCIs) enable people with tetraplegia to gain intuitive cursor control from movement intentions. To translate to practical use, iBCIs should provide reliable performance for extended periods of time. However, performance begins to degrade as the relationship between kinematic intention and recorded neural activity shifts compared to when the decoder was initially trained. In addition to developing decoders to better handle long-term instability, identifying when to recalibrate will also optimize performance. We propose a method, “MINDFUL”, to measure instabilities in neural data for useful long-term iBCI, without needing labels of user intentions. Longitudinal data were analyzed from two BrainGate2 participants with tetraplegia as they used fixed decoders to control a computer cursor spanning 142 days and 28 days, respectively. We demonstrate a measure of instability that correlates with changes in closed-loop cursor performance solely based on the recorded neural activity (Pearson r = 0.93 and 0.72, respectively). This result suggests a strategy to infer online iBCI performance from neural data alone and to determine when recalibration should take place for practical long-term use.

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Measuring instability in chronic human intracortical neural recordings towards stable, long-term brain-computer interfaces

March 2024

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12 Reads

Intracortical brain-computer interfaces (iBCIs) enable people with tetraplegia to gain intuitive cursor control from movement intentions. To translate to practical use, iBCIs should provide reliable performance for extended periods of time. However, performance begins to degrade as the relationship between kinematic intention and recorded neural activity shifts compared to when the decoder was initially trained. In addition to developing decoders to better handle long-term instability, identifying when to recalibrate will also optimize performance. We propose a method to measure instability in neural data without needing to label user intentions. Longitudinal data were analyzed from two BrainGate2 participants with tetraplegia as they used fixed decoders to control a computer cursor spanning 142 days and 28 days, respectively. We demonstrate a measure of instability that correlates with changes in closed-loop cursor performance solely based on the recorded neural activity (Pearson r = 0.93 and 0.72, respectively). This result suggests a strategy to infer online iBCI performance from neural data alone and to determine when recalibration should take place for practical long-term use.


Prefrontal network engagement by deep brain stimulation in limbic hubs

January 2024

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105 Reads

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2 Citations

Prefrontal circuits in the human brain play an important role in cognitive and affective processing. Neuromodulation therapies delivered to certain key hubs within these circuits are being used with increasing frequency to treat a host of neuropsychiatric disorders. However, the detailed neurophysiological effects of stimulation to these hubs are largely unknown. Here, we performed intracranial recordings across prefrontal networks while delivering electrical stimulation to two well-established white matter hubs involved in cognitive regulation and depression: the subcallosal cingulate (SCC) and ventral capsule/ventral striatum (VC/VS). We demonstrate a shared frontotemporal circuit consisting of the ventromedial prefrontal cortex, amygdala, and lateral orbitofrontal cortex where gamma oscillations are differentially modulated by stimulation target. Additionally, we found participant-specific responses to stimulation in the dorsal anterior cingulate cortex and demonstrate the capacity for further tuning of neural activity using current-steered stimulation. Our findings indicate a potential neurophysiological mechanism for the dissociable therapeutic effects seen across the SCC and VC/VS targets for psychiatric neuromodulation and our results lay the groundwork for personalized, network-guided neurostimulation therapy.




Periodic Artifact Removal With Applications to Deep Brain Stimulation

September 2022

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86 Reads

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4 Citations

IEEE transactions on neural systems and rehabilitation engineering: a publication of the IEEE Engineering in Medicine and Biology Society

Deep brain stimulation (DBS) therapies have shown clinical success in the treatment of a number of neurological illnesses, including obsessive-compulsive disorder, epilepsy, and Parkinson’s disease. An emerging strategy for increasing the efficacy of DBS therapies is to develop closed-loop, adaptive DBS systems that can sense biomarkers associated with particular symptoms and in response, adjust DBS parameters in real-time. The development of such systems requires extensive analysis of the underlying neural signals while DBS is on, so that candidate biomarkers can be identified and the effects of varying the DBS parameters can be better understood. However, DBS creates high amplitude, high frequency stimulation artifacts that prevent the underlying neural signals and thus the biological mechanisms underlying DBS from being analyzed. Additionally, DBS devices often require low sampling rates, which alias the artifact frequency, and rely on wireless data transmission methods that can create signal recordings with missing data of unknown length. Thus, traditional artifact removal methods cannot be applied to this setting. We present a novel periodic artifact removal algorithm for DBS applications that can accurately remove stimulation artifacts in the presence of missing data and in some cases where the stimulation frequency exceeds the Nyquist frequency. The numerical examples suggest that, if implemented on dedicated hardware, this algorithm has the potential to be used in embedded closed-loop DBS therapies to remove DBS stimulation artifacts and hence, to aid in the discovery of candidate biomarkers in real-time. Code for our proposed algorithm is publicly available on Github.


Frontotemporal network engagement by human intracranial stimulation in limbic hubs

September 2022

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120 Reads

Background Prefrontal circuits in the human brain play an important role in cognitive and affective processing. Neuromodulation therapies delivered to certain key hubs within these circuits are being used with increasing frequency to treat a host of neuropsychiatric disorders. However, the detailed neurophysiological effects of stimulation to these hubs are largely unknown. Methods Here, we performed intracranial recordings across prefrontal networks while delivering electrical stimulation to two well-established white matter hubs involved in cognitive regulation and depression: the subcallosal cingulate (SCC) and ventral capsule/ventral striatum (VC/VS). Results We demonstrate a shared frontotemporal circuit consisting of the ventromedial PFC, amygdala, and lateral orbitofrontal cortex where gamma oscillations are differentially modulated by stimulation target. Additionally, we found subject-specific responses to stimulation in the dorsal anterior cingulate cortex and demonstrate the capacity for further tuning of neural activity using current-steered stimulation. Conclusions Our findings indicate a potential neurophysiological mechanism for the dissociable therapeutic effects seen across the SCC and VC/VS DBS targets for psychiatric neuromodulation and our results lay the groundwork for personalized, network-guided neurostimulation therapy.


FIGURE 2 | Illustration of packet loss correction and PELP. (A) The relative timing of the samples contained in received packets can be uncertain. Adjusting timing solely with PacketGenTime leads to many inaccurate overlaps, systemTicks will accumulate error over long recordings, the approach from Sellers et al. (2021) ensures consistency within runs but offsets at losses, while PELP can ensure exact reconstruction. (B) PELP begins by grouping contiguous packets (blue, first row) into continuous runs (blue, second row) where each run is separated from adjacent runs by losses (dashed-red). Loss sizes are estimated but uncertain. The stimulation period is analytically determined using all the data. For each pair of subsequent runs, the root mean squared error (RMSE) between a stimulation model and the samples in the two runs is computed for a range of loss sizes centered around the estimate (indicated by E = for each size). A new stimulation model is fit for each loss estimate. The loss size that minimizes the RMSE is selected as the true loss size.
FIGURE 3 | Illustration of simulation components. (A) The root mean squared amplitude (A o ) of the stimulation model is set relative to that of the neural signal of interest (A) according to a target ratio R. (B) The amplitude of each stimulation pulse is varied on a cycle-wise basis where the amplitude of each pulse is sampled from a normal distribution with mean A o and standard deviation V. (C) Inaccuracies in period estimation, drifting sampling rate, and frequency variability are modeled by adding a drift factor d to the stimulation period in the model.
FIGURE 4 | Features of simulation. (A) Stimulation model fit to EEG data. Raw data are shown in gray and the model is shown in blue. (B) Histogram of missing data gap lengths for all experiments. (C) Histogram of continuous run lengths for all experiments. (D) Histogram of longest continuous runs in each experiment.
FIGURE 5 | Accuracy of loss estimation as a function of amplitude ratio, amplitude variability, and uncertainty. The accuracy of loss estimation was computed for 100 simulated trials with 20% of the packets removed. More accurate parameter combinations are indicated by darker values in the colormap. Amplitude ratios (A) ranged from 0 to 4, amplitude variability (B) ranged from 0% to 10%, and uncertainty ranged from 0 to 50 samples.
PELP: Accounting for Missing Data in Neural Time Series by Periodic Estimation of Lost Packets

July 2022

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66 Reads

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3 Citations

Recent advances in wireless data transmission technology have the potential to revolutionize clinical neuroscience. Today sensing-capable electrical stimulators, known as "bidirectional devices", are used to acquire chronic brain activity from humans in natural environments. However, with wireless transmission come potential failures in data transmission, and not all available devices correctly account for missing data or provide precise timing for when data losses occur. Our inability to precisely reconstruct time-domain neural signals makes it difficult to apply subsequent neural signal processing techniques and analyses. Here, our goal was to accurately reconstruct time-domain neural signals impacted by data loss during wireless transmission. Towards this end, we developed a method termed Periodic Estimation of Lost Packets (PELP). PELP leverages the highly periodic nature of stimulation artifacts to precisely determine when data losses occur. Using simulated stimulation waveforms added to human EEG data, we show that PELP is robust to a range of stimulation waveforms and noise characteristics. Then, we applied PELP to local field potential (LFP) recordings collected using an implantable, bidirectional DBS platform operating at various telemetry bandwidths. By effectively accounting for the timing of missing data, PELP enables the analysis of neural time series data collected via wireless transmission-a prerequisite for better understanding the brain-behavior relationships underlying neurological and psychiatric disorders.



Estimation of Periodic Signals with Applications to Deep Brain Stimulation

May 2022

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26 Reads

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1 Citation

Deep brain stimulation (DBS) therapies have shown clinical success in the treatment of a number of neurological illnesses, including obsessive-compulsive disorder, depression, and Parkinson's disease. An emerging strategy for increasing the efficacy of DBS therapies is to develop closed-loop, adaptive DBS systems that can sense biomarkers associated with particular symptoms and in response, adjust DBS parameters in real-time. The development of such systems requires extensive analysis of the underlying neural signals while DBS is on, so that candidate biomarkers can be identified and the effects of varying the DBS parameters can be better understood. However, DBS creates high amplitude, high frequency stimulation artifacts that prevent the underlying neural signals and thus the biological mechanisms underlying DBS from being analyzed. Additionally, DBS devices often require low sampling rates, which alias the artifact frequency, and rely on wireless data transmission methods that can create signal recordings with missing data of unknown length. Thus, traditional artifact removal methods cannot be applied to this setting. We present a novel periodic artifact removal algorithm for DBS applications that can accurately remove stimulation artifacts in the presence of missing data and in some cases where the stimulation frequency exceeds the Nyquist frequency. The numerical examples suggest that, if implemented on dedicated hardware, this algorithm has the potential to be used in embedded closed-loop DBS therapies to remove DBS stimulation artifacts and hence, to aid in the discovery of candidate biomarkers in real-time. Code for our proposed algorithm is publicly available on Github.


Citations (44)


... Aside from plausible mechanisms of BCI learning, another notable observation in both BCI and non-BCI studies is the occurrence of representational driftdefined as a consistent shift in the representation of task variables despite that the associated behavioral and environmental conditions remain unchanged [32][33][34][35][36][37][38] . In BCI settings, this adversely affects performance and learning progress and necessitates frequent decoder calibration and possible corrective approaches to misclassified/missing data 9,[39][40][41] . Together, these observations and the lack of understanding of their underlying causes during continued BCI use have been a major impediment to BCI large scale translation with full autonomy 42 43 . ...

Reference:

Meta plasticity and Continual Learning: Mechanisms sub serving Brain Computer Interface Proficiency
Measuring instability in chronic human intracortical neural recordings towards stable, long-term brain-computer interfaces

Communications Biology

... Future work may focus on inter-hemispheric PFC interactions across the corpus callosum to elucidate even further. Given that the PFC receives input from several limbic regions (Allawala et al., 2023), the PFC activity observed here was very likely influenced by the amygdala, hippocampus, basal ganglia, and thalamic nuclei as well (Mayberg et al., 1999;Zheng et al., 2018). Future research could employ similar techniques to explore larger scale networks and determine how limbic structures provide information to PFC subregions. ...

Prefrontal network engagement by deep brain stimulation in limbic hubs

... To avoid ringing artefacts caused by the large spike that occurs between the direct and residual artefact [18] ERNA Signal decomposition Template extraction and EEMD [24] Evoked RESPONSE Curve fitting [25] Evoked response Curve fitting in divided segments [26] Evoked response Overlaying and averaging [27] LFP (beta) Template subtraction Moving average template [16,28] Evoked response, LFP (gamma) Period-based reconstruction [29] LFP Unsupervised dictionary learning [30] Evoked response Periodic fitting with optimisation [31] LFP Visual selection and interpolation [32] Evoked response ERNA: evoked resonant neural activity. LFP: local field potential. ...

Periodic Artifact Removal With Applications to Deep Brain Stimulation

IEEE transactions on neural systems and rehabilitation engineering: a publication of the IEEE Engineering in Medicine and Biology Society

... Evaluating and successfully mitigating all sources of artifact in neural data sensed from chronically implanted leads is a challenging task. This work builds upon our previous work on the removal of high amplitude stimulation artifacts from neural data collected onboard sensing-capable DBS devices Chen et al., 2022). In this study, our goal was to better understand the impact of high amplitude, high frequency stimulation on VC/VS recordings collected from bidirectional DBS platforms. ...

Estimation of Periodic Signals with Applications to Deep Brain Stimulation

... In DBS applications, the artifact removal problem is further complicated by the following: (1) while the stimulation frequency can be set by the DBS device, the device setting provides an estimate of the stimulation frequency that is not accurate enough for successful artifact removal; (2) power constraints of DBS devices often require low sampling rates (e.g., 200-250 Hz), which in turn alias the stimulation frequency near the frequencies of underlying signals of interest; and (3) DBS recordings are often broken into many time segments with unknown phases, e.g., due to modulation of device settings or missing data of unknown length, the latter of which is a common limitation of the wireless data transmission methods used by some DBS devices [4]. While many methods for removing DBS stimulation artifacts exist (see, for instance, [5]- [9]), no single method, to the authors' knowledge, addresses all of the aforementioned complications, which are often found in real data. ...

PELP: accounting for missing data in neural time series by Periodic Estimation of Lost Packets
  • Citing Preprint
  • February 2022

... With the Summit RC+S alone, there are several published studies where PELP could be useful for post hoc data cleaning O'Day et al., 2020;Petrucci et al., 2020;Gilron et al., 2021;Gregg et al., 2021;Johnson et al., 2021;Provenza et al., 2021). PELP improves over existing solutions (Sellers et al., 2021) for analyses requiring highly accurate timing for small loss sizes, thereby reducing timing offsets, delocalization, and attenuation (Dastin-van Rijn et al., 2021b). In these circumstances, PELP enables near perfect timing and could enable biomarker exploration and task-locked analyses for these studies. ...

How do packet losses affect measures of averaged neural signalsƒ
  • Citing Conference Paper
  • November 2021

... However, most studies lasted between 1 and 7 days (N = 17), followed by studies that lasted between 100 and 150 days (N = 8), studies that lasted longer than 150 days (N = 5), and studies that lasted between 50 and 100 days (N = 2), one study lasted 10 days. Lastly, in one study (Provenza et al., 2021), we could not define the duration of the EMA data collection. ...

Long-term ecological assessment of intracranial electrophysiology synchronized to behavioral markers in obsessive-compulsive disorder

Nature Medicine

... The most widely reported biomarker for PD is the power of beta band (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30) oscillations in the basal ganglia, which increase prominently in the pathological state (9,10), and there is a correlation between the reduction in beta power in the STN and the improvement in bradykinesia with treatment (8,9,11). We observed a correlation between bradykinesia and STN beta power at different amplitudes of 125 Hz DT DBS (8). ...

Uncovering biomarkers during therapeutic neuromodulation with PARRM: Period-based Artifact Reconstruction and Removal Method

Cell Reports Methods

... In the ON STN-DBS recordings, DBS artefacts were removed from the ECoG and STN-LFP data using the period-based artefact reconstruction and removal method 113 . To ensure comparability of information content between OFF therapy and ON STN-DBS conditions, the data of STN-LFP contacts designated as stimulation contacts in the ON STN-DBS recording were also excluded from the corresponding OFF therapy recording. ...

Uncovering Biomarkers During Therapeutic Neuromodulation with PARRM: Period-Based Artifact Reconstruction and Removal Method
  • Citing Article
  • January 2020

SSRN Electronic Journal

... That is, the assumptions of disease modeling often inadequately address how disease burden manifests in unequal societies . There are, however, examples of studies that have used mathematical modeling to examine phenomena where inequalities manifest, such as the spread of HIV and HCV in persons who inject drugs [19][20][21] or with regards to infectious spread in prisons [22]. More recently, scholars have offered syntheses that have remarked on the need to color mathematical modeling with social forces [23][24][25][26], or commented on how targeting poor populations can lead to better outcomes in tuberculosis [27]. ...

Network structure and rapid HIV transmission among people who inject drugs: A simulation-based analysis

Epidemics