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Janak, P. H.

Publications and source records attributed to Janak, P. H..

At least 19 recordsLinked to original sources
bioRxiv2026

Uncovering internal states with a robust shared-state multi-neuron GLM-HMM framework

Neural systems exhibit multiple firing states that reflect an organisms internal state and modulate the relationship between external environmental stimuli and behavior. Several studies have inferred these latent states by supplementing the traditional hidden Markov Model (HMM) with generalized linear models (GLMs) with non-Poisson behavioral observations. However, understanding the relationship between internal brain states and behavior also requires modeling the neural activity. Nonetheless, fitting multi-neuron GLM-HMMs is non-trivial due to high sparsity, collinearity, and low trial counts in neuronal datasets. Therefore, we built a robust multi-neuron GLM-HMM framework that uncovers latent states from population activity while incorporating the influence of time-stamped task variables and spike histories. To obtain reliable model parameters, we employ a modified expectation-maximization procedure. Specifically, we show that incorporating neuron-adaptive penalization in the maximization step overcomes the covariate co-linearity issues typical of time-stamped events and sparse spiking, yielding stable estimates of Poisson GLM coefficients. Furthermore, we incorporate a trust-region algorithm to ensure stable M-step convergence in the presence of ill-conditioned Hessians that can lead to unstable Newton-Raphson updates. We further demonstrate the utility of leave-one-out cross-validation analysis for evaluating model performance on datasets with low trial counts and without breaking their temporal structure. We evaluate our framework on three electrophysiological datasets from primates and rodents as they perform a decision-making task, demonstrate stable model convergence, and discuss the behavioral relevance of the inferred states. Author SummaryNeural systems evolve over time: not only do the individual neurons influence each other across the network, but the network and interconnections themselves change as an animal enters different behaviors (e.g., attentive vs. disengaged) or states (e.g., hungry or tired). Analyzing the neural activity that guides behavior thus must incorporate the time-varying nature of the brain. Recent modeling work has extended the popular Generalized Linear Model, a model that can connect task and behavior to recorded neural action potentials, to incorporate a latent Hidden Markov Model. This extension allows the resulting GLM-HMM to exhibit several different relationships (different GLMs) that are switched between over time to account for the animals changing patterns. While GLM-HMMs have been applied extensively on behavioral data (e.g., task choice in a decision making paradigm), neural data is much more difficult due to the smaller sample sizes, sparser activity, and larger parameter space. Our work presents a new fitting approach and best practices to robustly fit GLM-HMMs to neural data. We demonstrate through numerous applications to a variety of neural datasets that by robustly fitting GLM-HMMs to data, we can identify important features of neural activity that let us better understand its relationship to behavior.

neuroscience↗
bioRxiv2026

The Central Nucleus of the Amygdala Encodes the Motivation to Pursue Ethanol

Prior studies implicate the central nucleus of the amygdala (CeA) in reward motivation, yet how this region encodes motivation for ethanol (EtOH) seeking and consumption-and how this compares to encoding of natural rewards--remains poorly understood. We recorded single-unit neural activity from rats during a cued instrumental task in which lever insertion on each trial indicates the opportunity to lever press for ethanol and post-press lever retraction signals ethanol delivery. We found neurons responsive to multiple trial events (lever insertion and retraction cues, lever press, port entry, and reward licks), including neurons with rhythmic activity entrained to licking during EtOH consumption. Notably, CeA neural responses to the lever insertion cue at trial start encoded both the likelihood and speed of engagement during reward seeking. Using a supervised classifier, we found that trial engagement and motivation level could be decoded from pre-trial and lever insertion response periods. Finally, we assessed whether these effects generalized to natural reward seeking. Sucrose-rewarded rats (both ethanol-exposed and ethanol-naive) showed higher motivation (more rewards earned and shorter first-press latencies) and stronger CeA recruitment and responses at lever insertion than ethanol-rewarded rats, in agreement with the notion that CeA circuits amplify reward-predictive cue signals to facilitate rapid action initiation under high motivational states. Together, these findings indicate that CeA neurons dynamically encode motivational states, with tonic activity and reward-predictive cue responses predicting both engagement in reward seeking and the vigor of action initiation. We suggest these patterns of neural activity drive ethanol and sucrose pursuit. Significance StatementHow motivational states drive reward-seeking is a central question in systems neuroscience, yet the mechanisms linking neural signals to action initiation remain poorly understood. Recording single-unit activity in the amygdala central nucleus (CeA) during cued ethanol self-administration revealed that neural responses to reward-predictive cues encoded both the decision to engage in reward seeking and the vigor of action initiation, and motivational state was decoded from cue-evoked signals and tonic activity even before cue presentation. Consistent with greater motivation for the more palatable sucrose reward, CeA neurons showed stronger cue responses and greater anticipatory firing preceding tongue contact with reward, compared with ethanol-rewarded rats. These findings identify CeA activity patterns that link motivational state to the rapid initiation of goal-directed action.

neuroscience↗
bioRxiv2026

Memory erasure by dopamine-gated retrospective learning

Erasing outdated memories is crucial for adaptive behavior. Yet once a cue-outcome association is learned, repeated cue exposure without outcome suppresses conditioned behavior without erasing the underlying memory. This allows rapid behavioral recovery when outcomes are reintroduced. Here, we confirm this limitation for standard "prospective extinction" protocols that present cues without the associated outcome, but show that true memory erasure is achieved by inverting the paradigm: presenting outcomes without associated cues, i.e., "retrospective extinction". We demonstrate that orbitofrontal cortex activity at outcome is necessary for the rapid behavioral recovery following prospective extinction, and that mesolimbic dopamine activity at outcome is necessary for retrospective extinction. These findings reconceptualize extinction mechanisms and suggest complementary strategies to mitigate relapse and erase maladaptive memories.

neuroscience↗
bioRxiv2025

Transcriptional response to chronic long-access fentanyl self-administration in rat habenula and amygdala

Fentanyl is a potent synthetic opioid associated with overdose. However, little is known about fentanyl-induced molecular adaptations in the habenula and amygdala, two brain regions implicated in opioid use and withdrawal. We performed bulk RNA-sequencing in the rat habenula and amygdala to identify transcriptomic changes associated with fentanyl intake. Rats self-administered intravenous saline or fentanyl over 22-24 days. Ninety minutes following the final session, brains were collected for transcriptomic profiling. In Hb, we identified 453 differentially expressed genes (DEGs) between saline and fentanyl rats, with upregulated genes associated with synaptic transmission and ionic conductance. In amygdala, we identified 3,041 fentanyl-associated DEGs with upregulated genes implicated in metabolic and vesicular functions. Downregulated genes in both regions were enriched for extracellular matrix functions. Integration of DEGs with single-cell RNA-sequencing data from rodents and humans revealed that fentanyl DEGs were enriched in specific habenula and amygdala cell type markers. Furthermore, fentanyl downregulated DEGs in amygdala were enriched in genes associated with risk for substance use disorders. Together, we define how fentanyl intake alters transcriptional programs in the rat habenula and amygdala, and we link these changes to specific human cell types and risk genes for neuropsychiatric disorders and addiction.

neuroscience↗
bioRxiv2025

Uncertainty and reward histories have distinct effects on decisions after wins and losses

Intelligent behavior necessitates an adaptive integration of feedback. It is well-known that animals asymmetrically learn from positive and negative feedback. While asymmetrical learning is a robust behavioral effect, the latent computations behind how animals represent their environments and use this to differentially weight wins and losses is poorly understood. Here we tested whether and how uncertainty and reward histories modulate the weights placed on wins and losses using a behavioral data set collected in rats. We propose a reinforcement learning model that integrates uncertainty history via an unsigned average reward prediction error and a separate subjective reward history component. We showed that in a dynamic probabilistic reversal learning task with blocks of variable reward predictability, ongoing estimation of uncertainty history and reward history both distinctly influenced rats sensitivity to wins and losses. In more predictable environments, and under low uncertainty levels, i.e., when rats were certain in making correct choices, rats weighted wins more than losses, as indicated by a higher win-stay, and lower lose-shift probability. This asymmetrical learning strategy enabled rats to remain with the correct action, while discounting the influence of rare losses. Further, male rats were more impacted by their reward history, i.e., environmental richness, when making lose-shift decisions, but conversely, female rats were more influenced by their uncertainty history. Hence, we found sex-specific contributions of these latent computations in modulating behavior. We overall demonstrate that asymmetrically weighting wins and losses could form an important behavioral strategy when adapting to ongoing changes in reward and uncertainty history.

animal behavior and cognition↗
bioRxiv2024

Optogenetic Central Amygdala Stimulation is Highly Reinforcing and Strongly Outcompetes Fentanyl Self-Administration in Male, but not Female, Rats

The central nucleus of the amygdala plays a key role in many aspects of substance use disorders, in particular biasing behaviors toward one drug or natural reward over another, yet the role of this region in opioid self-administration remains unclear. Here, we report that pharmacological inactivation of the central amygdala reduces fentanyl self-administration, while intra-central amygdala opioid receptor antagonism dose-dependently increases fentanyl self-administration. We tested whether optogenetic activation of the central amygdala would increase motivation for fentanyl in rats with a long fentanyl self-administration history. While pairing fentanyl delivery with optogenetic central amygdala activation increased fentanyl self-administration, optoactivation itself was highly reinforcing and, in choice settings, was pursued over fentanyl despite mounting effort requirements, delays, and sporadic reward availability. Of note, under free response conditions, these effects were limited to male rats; while female rats avidly responded for optogenetic activation of the central amygdala, this activation was less effective in enhancing fentanyl intake, and it was not preferred over fentanyl. In contrast, under discrete trial choice which precluded independent regulation of intake of the two options, both females and males preferred optoactivation to fentanyl. These results demonstrate that optogenetic stimulation of neural activity within the anterior central amygdala does not appear to potentiate the reinforcing effects of fentanyl, but is itself highly reinforcing regardless of sex, and, in male rats can robustly outcompete fentanyl. In contrast, in females, fentanyl intake is relatively insensitive to competing opportunities for optoactivation, except when opportunities to obtain drug or optoactivation are sparse.

neuroscience↗
bioRxiv2024

Role of dopamine in reward expectation and predictability during execution of action sequences

BackgroundMesolimbic dopamine (DA) neurons are central to cue guided reward seeking and action sequence learning. Yet, the mechanisms by which cue-induced DA neural activity drives goal-directed or habitual sequence execution remain unknown. MethodsWe designed two novel tasks to isolate the effect of sequence-delineating cues on DA-driven behavioral strategies and learning. In the lever insertion fixed-ratio 5 task (LI5), the lever insertion marked sequence initiation. In the lever retraction fixed-ratio 5 task (LR5), the lever retraction served as both sequence termination and reward-predictive cue. ResultsWe found that sequence initiation and termination cues differentially affect reward expectation during action sequences, with only the termination cue contributing to greater outcome devaluation insensitivity, automaticity and behavioral chunking. Mesolimbic fiber photometry recording revealed that this habit-like behavior was associated with a rapid backpropagation in DA signals from the reward to the immediately preceding cue and with attenuated DA reward prediction error signals, which reflected greater behavioral inflexibility. Finally, in absence of external cues, brief optogenetic stimulation of VTA DA neurons at sequence termination was sufficient to drive automaticity and, to some extent, behavioral chunking. ConclusionOur results highlight the critical role of cue-evoked DA signals at sequence termination in mediating credit assignment and driving the development of habitual action sequence execution.

neuroscience↗
bioRxiv2024

Fentanyl reinforcement history has sex-specific effects on multi-step decision-making

It is commonly thought that drug addiction involves a transition to habitual control of action, where the choice to consume drugs becomes automatized and reflects a failure to deliberate over possible negative outcomes. Determining whether the pursuit of addictive drugs is habitual is hampered by a lack of behavior assessments suitable for use during a bout of actual drug seeking. Therefore, to understand how variable histories of drug reinforcement might affect goal-directed and habitual pursuit of drug, we trained rats to perform a multi-step decision-making task to earn oral fentanyl and sucrose rewards following extensive pretraining with either fentanyl or sucrose. Importantly, this task allowed for independent measurements of goal-directed and habitual choice characteristics during online pursuit of rewards, and habitual choice could be further categorized into perseverative and reward-guided components. Chronic fentanyl led to a bias for reward-guided habitual choice specifically in females, and a high degree of perseveration in both sexes. These behavioral changes after chronic fentanyl pretraining generalized across fentanyl and sucrose seeking. In contrast, acute fentanyl selectively increased perseveration in females, and blunted the gradual within-session improvement in goal-directed choice in both sexes. These results show that chronic fentanyl reinforcement promotes habits that generalize across drug and non-drug reward seeking, and that female rats are especially susceptible to habitual control induced by both chronic and acute fentanyl reinforcement.

animal behavior and cognition↗
bioRxiv2024

Pavlovian cue-evoked alcohol seeking is disrupted by ventral pallidal inhibition

Cues paired with alcohol can be potent drivers of craving, alcohol-seeking, consumption, and relapse. While the ventral pallidum is implicated in appetitive and consummatory responses across several reward classes and types of behaviors, its role in behavioral responses to Pavlovian alcohol cues has not previously been established. Here, we tested the impact of optogenetic inhibition of ventral pallidum on Pavlovian-conditioned alcohol-seeking in male Long Evans rats. Rats underwent Pavlovian conditioning with an auditory cue predicting alcohol delivery to a reward port and a control cue predicting no alcohol delivery, until they consistently entered the reward port more during the alcohol cue than the control cue. We then tested the within-session effects of optogenetic inhibition during 50% of cue presentations. We found that optogenetic inhibition of ventral pallidum during the alcohol cue reduced port entry likelihood and time spent in the port, and increased port entry latency. Overall, these results suggest that normal ventral pallidum activity is necessary for Pavlovian alcohol-seeking.

neuroscience↗
bioRxiv2024

Chronic Ethanol Exposure Produces Persistent Impairment in Cognitive Flexibility and Decision Signals in the Striatum

Lack of cognitive flexibility is a hallmark of substance use disorders and has been associated with drug-induced synaptic plasticity in the dorsomedial striatum (DMS). Yet the possible impact of altered plasticity on real-time striatal neural dynamics during decision-making is unclear. Here, we identified persistent impairments induced by chronic ethanol (EtOH) exposure on cognitive flexibility and striatal decision signals. After a substantial withdrawal period from prior EtOH vapor exposure, male, but not female, rats exhibited reduced adaptability and exploratory behavior during a dynamic decision-making task. Reinforcement learning models showed that prior EtOH exposure enhanced learning from rewards over omissions. Notably, neural signals in the DMS related to the decision outcome were enhanced, while those related to choice and choice-outcome conjunction were reduced, in EtOH-treated rats compared to the controls. These findings highlight the profound impact of chronic EtOH exposure on adaptive decision-making, pinpointing specific changes in striatal representations of actions and outcomes as underlying mechanisms for cognitive deficits.

neuroscience↗
bioRxiv2024

Basolateral amygdala population coding of a cued reward seeking state depends on orbitofrontal cortex

Basolateral amygdala (BLA) neuronal responses to conditioned stimuli are closely linked to the expression of conditioned behavior. An area of increasing interest is how the dynamics of BLA neurons relate to evolving behavior. Here, we recorded the activity of individual BLA neurons across the acquisition and extinction of conditioned reward seeking and employed population-level analyses to assess ongoing neural dynamics. We found that, with training, sustained cue-evoked activity emerged that discriminated between the CS+ and CS-and correlated with conditioned responding. This sustained population activity continued until reward receipt and rapidly extinguished along with conditioned behavior during extinction. To assess the contribution of orbitofrontal cortex (OFC), a major reciprocal partner to BLA, to this component of BLA neural activity, we inactivated OFC while recording in BLA and found blunted sustained cue-evoked activity in BLA that accompanied reduced reward seeking. Optogenetic disruption of BLA activity and OFC terminals in BLA also reduced reward seeking. Our data suggest that sustained cue-driven activity in BLA, which in part depends on OFC input, underlies conditioned reward-seek-ing states.

neuroscience↗
bioRxiv2023

Contexts facilitate dynamic value encoding in the mesolimbic dopamine system

Adaptive behavior in a dynamic environment often requires rapid revaluation of stimuli that deviates from well-learned associations. The divergence between stable value-encoding and appropriate behavioral output remains a critical test to theories of dopamines function in learning, motivation, and motor control. Yet how dopamine neurons are involved in the revaluation of cues when the world changes to alter our behavior remains unclear. Here we make use of pharmacology, in vivo electrophysiology, fiber photometry, and optogenetics to resolve the contributions of the mesolimbic dopamine system to the dynamic reorganization of reward-seeking. Male and female rats were trained to discriminate when a conditioned stimulus would be followed by sucrose reward by exploiting the prior, non-overlapping presentation of a separate discrete cue - an occasion setter. Only when the occasion setters presentation preceded the conditioned stimulus did the conditioned stimulus predict sucrose delivery. As a result, in this task we were able to dissociate the average value of the conditioned stimulus from its immediate expected value on a trial-to-trial basis. Both the activity of ventral tegmental area dopamine neurons and dopamine signaling in the nucleus accumbens were essential for rats to successfully update behavioral responding in response to the occasion setter. Moreover, dopamine release in the nucleus accumbens following the conditioned stimulus only occurred when the occasion setter indicated it would predict reward. Downstream of dopamine release, we found that single neurons in the nucleus accumbens dynamically tracked the value of the conditioned stimulus. Together these results reveal a novel mechanism within the mesolimbic dopamine system for the rapid revaluation of motivation.

neuroscience↗
bioRxiv2023

Encoding and context-dependent control of reward consumption within the central nucleus of the amygdala

The ability to evaluate and select a preferred option among a variety of available offers is an essential aspect of goal-directed behavior. Dysregulation of this valuation process is characteristic of alcohol use disorder, with the central amygdala being implicated in persistent alcohol pursuit. However, the mechanism by which the central amygdala encodes and promotes the motivation to seek and consume alcohol remains unclear. We recorded single-unit activity in male Long-Evans rats as they consumed 10% ethanol or 14.2% sucrose. We observed significant activity at the time of approach to alcohol or sucrose, as well as lick-entrained activity during the ongoing consumption of both alcohol and sucrose. We then evaluated the ability of central amygdala optogenetic manipulation time-locked to consumption to alter ongoing intake of alcohol or sucrose, a preferred non-drug reward. In closed two-choice scenarios where rats could drink only sucrose, alcohol, or quinine-adulterated alcohol with or without central amygdala stimulation, rats drank more of stimulation-paired options. Microstructural analysis of licking patterns suggests these effects were mediated by changes in motivation, not palatability. Given a choice among different options, central amygdala stimulation enhanced consumption if the stimulation was associated with the preferred reward while closed-loop inhibition only decreased consumption if the options were equally valued. However, optogenetic stimulation during consumption of the less-preferred option, alcohol, was unable to enhance overall alcohol intake while sucrose was available. Collectively, these findings indicate that the central amygdala processes the motivational value of available offers to promote pursuit of the most preferred available option.

neuroscience↗
bioRxiv2023

Mesostriatal dopamine is sensitive to specific cue-reward contingencies

Learning causal relationships relies on understanding how often one event precedes another. To gain an understanding of how dopamine neuron activity and neurotransmitter release change when a retrospective relationship is degraded for a specific pair of events, we used outcome-selective Pavlovian contingency degradation in rats. Two cues were paired with distinct food rewards, one of which was also delivered in the absence of either cue. Conditioned approach was attenuated for the cue-reward contingency that was degraded. Dopamine neuron activity in the midbrain and dopamine release in the ventral striatum showed a profile of changes in cue- and reward-evoked responding that was not easily explained by a standard reinforcement learning model. An alternative model based on learning causal relationships was better able to capture evoked dopamine responses during contingency degradation, as well as conditioned behavior following optogenetic manipulations of dopamine during noncontingent rewards. Our results suggest that mesostriatal dopamine encodes the contingencies between meaningful events during learning.

neuroscience↗
bioRxiv2023

Nucleus accumbens and dorsal medial striatal dopamine and neural activity are essential for action sequence performance

Separable striatal circuits have unique functions in Pavlovian and instrumental behaviors but how these roles relate to performance of sequences of actions with and without associated cues is less clear. Here we tested whether dopamine release and neural activity more generally in three striatal subdomains are necessary for performance of an action chain leading to reward delivery. Male and female Long-Evans rats were trained to press a series of three spatially-distinct levers to receive reward. We assessed the contribution of neural activity or dopamine release within each striatal subdomain when progression through the action sequence was explicitly cued and in the absence of cues. Behavior in both task variations was substantially impacted following microinfusion of the dopamine antagonist, flupenthixol, into nucleus accumbens core (NAc) or dorsomedial striatum (DMS), with impairments in sequence timing and a strong impact on motivation after NAc flupenthixol. In contrast, after pharmacological inactivation to suppress overall activity, there was minimal impact on motivation, except within the uncued task after DMS inactivation. Inactivation of both NAc and DMS impaired sequence timing and led to sequence errors in the uncued, but not cued task. There was virtually no impact of dopamine antagonism or reversible inactivation of dorsolateral striatum on either cued or uncued action sequence completion. These results highlight an essential contribution of NAc and DMS dopamine systems in motivational and performance aspects of chains of actions, whether cued or internally generated, as well as the impact of intact NAc and DMS function for correct sequence performance.

neuroscience↗
bioRxiv2023

Pramipexole restores behavioral inhibition in highly impulsive rats through a paradoxical modulation of frontostriatal networks

Impulse control disorders (ICDs), a wide spectrum of maladaptive behaviors which includes pathological gambling, hypersexuality and compulsive buying, have been recently suggested to be triggered or aggravated by treatments with dopamine D2/3 receptor agonists, such as pramipexole (PPX). Despite evidence showing that impulsivity is associated with functional alterations in corticostriatal networks, the neural basis of the exacerbation of impulsivity by PPX has not been elucidated. Here we used a hotspot analysis to assess the functional recruitment of several corticostriatal structures by PPX in male rats identified as highly (HI), moderately impulsive (MI) or with low levels of impulsivity (LI) in the 5-choice serial reaction time task (5-CSRTT). PPX dramatically reduced impulsivity in HI rats. Assessment of the expression pattern of the two immediate early genes C-fos and Zif268 by in situ hybridization subsequently revealed that PPX resulted in a decrease in Zif268 mRNA levels in different striatal regions of both LI and HI rats accompanied by a high impulsivity specific reduction of Zif268 mRNA levels in prelimbic and cingulate cortices. PPX also decreased C-fos mRNA levels in all striatal regions of LI rats, but only in the dorsolateral striatum and nucleus accumbens core (NAc Core) of HI rats. Structural equation modelling further suggested that the anti-impulsive effect of PPX was mainly attributable to the specific downregulation of Zif268 mRNA in the NAc Core. Altogether, our results show that PPX restores impulse control in highly impulsive rats by modulation of limbic frontostriatal circuits.

neuroscience↗
bioRxiv2022

From Prediction to Action: Dissociable Roles of Ventral Tegmental Area and Substantia Nigra Dopamine Neurons in Instrumental Reinforcement

Reward-seeking requires the coordination of motor programs to achieve goals. Midbrain dopamine neurons are critical for reinforcement and their activation is sufficient for learning about cues, actions, and outcomes. Here we examine in detail the mechanisms underlying the ability of ventral tegmental area (VTA) and substantia nigra (SNc) dopamine neurons to support instrumental learning. By exploiting numerous behavioral tasks in combination with time-limited optogenetic manipulations, we reveal that VTA and SNc dopamine neurons generate reinforcement through separable psychological processes. VTA dopamine neurons imbue actions and their associated cues with motivational value that allows flexible and persistent pursuit whereas SNc dopamine neurons support time-limited, precise, action-specific learning that is non-scalable and inflexible. This architecture is reminiscent of actor-critic reinforcement learning models with VTA and SNc instructing the critic and actor, respectively. Our findings indicate that heterogeneous dopamine systems support unique forms of instrumental learning that ultimately result in disparate reward-seeking strategies.

neuroscience↗