Jonathan E. Rubin
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View article: How cortico-basal ganglia-thalamic subnetworks can shift decision policies to increase reward rate
How cortico-basal ganglia-thalamic subnetworks can shift decision policies to increase reward rate Open
All mammals exhibit flexible decision policies that depend, at least in part, on the cortico-basal ganglia-thalamic (CBGT) pathways. Yet understanding how the complex connectivity, dynamics, and plasticity of CBGT circuits translate into e…
View article: Rhythm generation, robustness, and control in stick insect locomotion: modeling and analysis
Rhythm generation, robustness, and control in stick insect locomotion: modeling and analysis Open
Stick insect stepping patterns have been studied for insights about locomotor rhythm generation and control, because the underlying neural system is relatively accessible experimentally and produces a variety of rhythmic outputs. Harnessin…
View article: Distinct dopaminergic spike-timing-dependent plasticity rules are suited to different functional roles
Distinct dopaminergic spike-timing-dependent plasticity rules are suited to different functional roles Open
Various mathematical models have been formulated to describe the changes in synaptic strengths resulting from spike-timing-dependent plasticity (STDP). A subset of these models include a third factor, dopamine, which interacts with spike t…
View article: Reduced TRPC3 conductance underlies altered SNr activity under dopamine depletion: predictions from data-driven network models
Reduced TRPC3 conductance underlies altered SNr activity under dopamine depletion: predictions from data-driven network models Open
Sufficient loss of dopamine within the basal ganglia (BG) leads to neuronal activity changes, including altered firing rates and firing patterns, thought to underlie parkinsonian motor symptoms. Yet, within BG neuronal populations, baselin…
View article: On the role of L-type Ca<sup>2+</sup> and BK channels in a biophysical model of cartwheel interneurons
On the role of L-type Ca<sup>2+</sup> and BK channels in a biophysical model of cartwheel interneurons Open
Cartwheel interneurons (CWCs) in the auditory system exhibit a range of activity patterns relevant to auditory function and pathologies. Although experiments have shown how these patterns can vary across individual neurons and can change u…
View article: Cardiogenic and chronobiological mechanisms in seizure-induced sinus arrhythmias
Cardiogenic and chronobiological mechanisms in seizure-induced sinus arrhythmias Open
Seizure-induced cardiac arrhythmias, such as ictal (during seizure) or postictal (post-seizure) sinus arrhythmias, are potential triggers for sudden unexpected death in epilepsy. Traditionally, these arrhythmias have been attributed to cha…
View article: State modulation in spatial networks with three interneuron subtypes
State modulation in spatial networks with three interneuron subtypes Open
Several inhibitory interneuron subtypes have been identified as critical in regulating sensory responses. However, the specific contribution of each interneuron subtype remains uncertain. In this work, we explore the contributions of cell …
View article: Rhythm Generation, Robustness, and Control in Stick Insect Locomotion: Modeling and Analysis
Rhythm Generation, Robustness, and Control in Stick Insect Locomotion: Modeling and Analysis Open
Stick insect stepping patterns have been studied for insights about locomotor rhythm generation and control, because the underlying neural system is relatively accessible experimentally and produces a variety of rhythmic outputs. Harnessin…
View article: Rhythm Generation, Robustness, and Control in Stick Insect Locomotion: Modeling and Analysis
Rhythm Generation, Robustness, and Control in Stick Insect Locomotion: Modeling and Analysis Open
Stick insect stepping patterns have been studied for insights about locomotor rhythm generation and control, because the underlying neural system is relatively accessible experimentally and produces a variety of rhythmic outputs. Harnessin…
View article: How the dynamic interplay of cortico-basal ganglia-thalamic pathways shapes the time course of deliberation and commitment
How the dynamic interplay of cortico-basal ganglia-thalamic pathways shapes the time course of deliberation and commitment Open
Although the cortico-basal ganglia-thalamic (CBGT) network is identified as a central circuit for decision-making, the dynamic interplay of multiple control pathways within this network in shaping decision trajectories remains poorly under…
View article: CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making
CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making Open
Here we introduce CBGTPy, a virtual environment for designing and testing goal-directed agents with internal dynamics that are modeled on the cortico-basal-ganglia-thalamic (CBGT) pathways in the mammalian brain. CBGTPy enables researchers…
View article: Energy of Functional Brain States Correlates With Cognition in Adolescent‐Onset Schizophrenia and Healthy Persons
Energy of Functional Brain States Correlates With Cognition in Adolescent‐Onset Schizophrenia and Healthy Persons Open
Adolescent‐onset schizophrenia (AOS) is relatively rare, under‐studied, and associated with more severe cognitive impairments and poorer outcomes than adult‐onset schizophrenia. Neuroimaging has shown altered regional activations (first‐or…
View article: An accessible approach to density estimation neural networks with data preprocessing
An accessible approach to density estimation neural networks with data preprocessing Open
Density estimation neural networks (DENNs) represent a form of artificial neural network designed to provide an efficient approach to the Bayesian estimation of a probability density on a model parameter space, conditioned on an empirical …
View article: Arkypallidal neurons in the external globus pallidus can mediate inhibitory control by altering competition in the striatum
Arkypallidal neurons in the external globus pallidus can mediate inhibitory control by altering competition in the striatum Open
Reactive inhibitory control is crucial for survival. Traditionally, this control in mammals was attributed solely to the hyperdirect pathway, with cortical control signals flowing unidirectionally from the subthalamic nucleus (STN) to basa…
View article: Distinct dopaminergic spike-timing-dependent plasticity rules are suited to different functional roles
Distinct dopaminergic spike-timing-dependent plasticity rules are suited to different functional roles Open
Various mathematical models have been formulated to describe the changes in synaptic strengths resulting from spike-timing-dependent plasticity (STDP). A subset of these models include a third factor, dopamine, which interacts with spike t…
View article: A novel mechanism for ramping bursts based on slow negative feedback in model respiratory neurons
A novel mechanism for ramping bursts based on slow negative feedback in model respiratory neurons Open
Recordings from pre-Bötzinger complex neurons responsible for the inspiratory phase of the respiratory rhythm reveal a ramping burst pattern, starting around the time that the transition from expiration to inspiration begins, in which the …
View article: How cortico-basal ganglia-thalamic subnetworks can shift decision policies to maximize reward rate
How cortico-basal ganglia-thalamic subnetworks can shift decision policies to maximize reward rate Open
All mammals exhibit flexible decision policies that depend, at least in part, on the cortico-basal ganglia-thalamic (CBGT) pathways. Yet understanding how the complex connectivity, dynamics, and plasticity of CBGT circuits translate into e…
View article: Arkypallidal neurons in the external globus pallidus can mediate inhibitory control by altering competition in the striatum
Arkypallidal neurons in the external globus pallidus can mediate inhibitory control by altering competition in the striatum Open
Reactive inhibitory control is crucial for survival. Traditionally, this control in mammals was attributed solely to the hyperdirect pathway, with cortical control signals flowing unidirectionally from the subthalamic nucleus (STN) to basa…
View article: Rethinking the external globus pallidus and information flow in cortico‐basal ganglia‐thalamic circuits
Rethinking the external globus pallidus and information flow in cortico‐basal ganglia‐thalamic circuits Open
For decades, the external globus pallidus (GPe) has been viewed as a passive way‐station in the indirect pathway of the cortico‐basal ganglia‐thalamic (CBGT) circuit, sandwiched between striatal inputs and basal ganglia outputs. According …
View article: Rethinking the external globus pallidus and information flow in cortico-basal ganglia-thalamic circuits
Rethinking the external globus pallidus and information flow in cortico-basal ganglia-thalamic circuits Open
For decades the external globus pallidus (GPe) has been viewed as a passive way-station in the indirect pathway of the cortico-basal ganglia-thalamic (CBGT) circuit, sandwiched between striatal inputs and basal ganglia outputs. According t…
View article: Diagnostically distinct resting state fMRI energy distributions: A subject-specific maximum entropy modeling study
Diagnostically distinct resting state fMRI energy distributions: A subject-specific maximum entropy modeling study Open
Objective Existing neuroimaging studies of psychotic and mood disorders have reported brain activation differences (first-order properties) and altered pairwise correlation based functional connectivity (second-order properties). However, …
View article: Exploring the role of the Kölliker–Fuse nucleus in breathing variability by mathematical modelling
Exploring the role of the Kölliker–Fuse nucleus in breathing variability by mathematical modelling Open
The Kölliker–Fuse nucleus (KF), which is part of the parabrachial complex, participates in the generation of eupnoea under resting conditions and the control of active abdominal expiration when increased ventilation is required. Moreover, …
View article: Energy of functional brain states correlates with cognition in adolescent-onset schizophrenia and healthy persons
Energy of functional brain states correlates with cognition in adolescent-onset schizophrenia and healthy persons Open
Adolescent-onset schizophrenia (AOS) is rare, under-studied, and associated with more severe cognitive impairments and poorer outcomes than adult-onset schizophrenia. Neuroimaging has shown altered regional activations (first-order effects…
View article: Competing neural representations of choice shape evidence accumulation in humans
Competing neural representations of choice shape evidence accumulation in humans Open
Making adaptive choices in dynamic environments requires flexible decision policies. Previously, we showed how shifts in outcome contingency change the evidence accumulation process that determines decision policies. Using in silico experi…
View article: CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making
CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making Open
Here we introduce CBGTPy, a virtual environment for designing and testing goal-directed agents with internal dynamics that are modeled on the cortico-basal-ganglia-thalamic (CBGT) pathways in the mammalian brain. CBGTPy enables researchers…
View article: The role of Kölliker-Fuse nucleus in breathing variability
The role of Kölliker-Fuse nucleus in breathing variability Open
The Kölliker-Fuse nucleus (KF), which is part of the parabrachial complex, participates in the generation of eupnea under resting conditions and the control of active abdominal expiration when increased ventilation is required. Moreover, d…
View article: Author response: Competing neural representations of choice shape evidence accumulation in humans
Author response: Competing neural representations of choice shape evidence accumulation in humans Open
Full text Figures and data Side by side Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Making …