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Kuznetsov, A.

Publications and source records attributed to Kuznetsov, A..

13 recordsLinked to original sources

A piece-wise linear recurrent neural network identifies generalizable dynamics from neural activity during decision-making in rodents

Alterations in impulsivity characterize several neuropsychiatric disorders, however the neural processes that underlie an impulsive choice have not been identified. A recent body of literature suggests that there may be generalizable aspects of neural representations across animals. Whether this is also true for dynamic rather than just static (like geometrical) properties of neural representations, and specifically in the context of impulsive behaviors, is less clear. Therefore, the goal of this study is to characterize generalizable features of latent dynamics that disambiguate an impulsive from non-impulsive choice across many different data sets and animals. A deep learning-based latent factor model was constructed from neural recordings that were acquired in rat anterior cingulate cortex while performing a delay discounting task, which is commonly used to assess impulsivity. Prior work shows this brain region is critical for the performance of this task. We leveraged piecewise linear recurrent neural networks (PLRNNs) to perform a nonlinear latent factor analysis across animals and experimental sessions. Our PLRNN explained a substantially larger percent of variance in fewer dimensions than linear approaches. We cross-validated performance of the model on test data and following the disruption of recurrent connectivity or auto-regressive latent dynamics. These tests confirmed that our fitting procedure consistently embedded generalizable neuronal dynamics within the PLRNN. Further, we found that the latent dynamics exhibited strong rotational features and progressed faster for impulsive choices. In summary, our model captures properties of the latent dynamics that are consistent across multiple data sets and disambiguate impulsive choices.

neuroscience↗

Modeling the Neurocircuitry Involved in Binge Drinking

Binge drinking is characterized by an initial bout of rapid, high-vigor alcohol intake (front-loading) followed by a prolonged period of lower-rate "maintenance" drinking, yet the circuit mechanisms that generate and regulate these phases remain unclear. Here, we develop a systems-level computational model that links the structure of binge drinking to interactions among medial prefrontal cortex (mPFC), insula, striatum, and ventral tegmental area (VTA). The model consists of cortical Seek (mPFC) and Go (insula) populations that form a mutually excitatory loop, a SetPoint population that integrates striatal activity as an internal estimate of effort/consumption, ventral (nucleus accumbens, NAc) and dorsal (dorsolateral striatum, DLS) striatal populations, and a dopaminergic VTA population providing transient reward-prediction signaling. Using a firing-rate formalism with noisy dynamics, we reproduce the canonical two-phase binge pattern and show that: (i) the PFC-insula loop acts as a bistable module that initiates and sustains front-loading; (ii) striato-cortical feedback to the Setpoint population controls the timing of the transition from front-loading to maintenance without altering its vigor; and (iii) the amplitude of the VTA dopamine transient selectively scales front-loading intensity. Sensitivity analyses identify PFC-insula connectivity, VTA-to-NAc modulation, and striato-cortical feedback as key parameters that bifurcate two-phase drinking into regimes with abolished or persistent front-loading. These findings provide a mechanistic framework for interpreting binge-like alcohol intake in terms of identifiable circuit motifs and generate testable predictions for targeting mPFC-insula-striatal-VTA interactions in alcohol use disorder.

neuroscience↗

AI-based separation of malignant cell- and microenvironment-specific gene expression from bulk RNA sequencing enhances biomarker interpretation

Bulk RNA sequencing (RNA-seq)-based gene expression analysis is a promising tool for personalized cancer diagnostics, disease monitoring, and treatment decision-making. However, its clinical utility is limited by interference from non-malignant tumor microenvironment cells, which can dominate transcript data in low-purity tumors. While cell deconvolution methods like Kassandra can predict digital cell percentages from bulk RNA-seq, approaches for delineating the gene expression contribution of tumor compartments remain limited. To overcome this limitation, we developed Helenus, a machine-learning-based tool that separates gene expression between malignant and non-malignant cells. Trained on over 200 million synthetic RNA profiles representing diverse tumor types and purities, Helenus demonstrated high accuracy in separating gene expression origin. Helenus also uncovered true genomic-RNA correlations such as copy number alterations and the expression of therapeutic antibody-drug conjugate targets specifically on tumor cells. Helenus provides critical insights into tumor biology and immunotherapy response by precisely identifying biomarker expressions, paving the way for more effective personalized cancer care. SignificanceHelenus extracts gene expression profiles of cancerous and non-cancerous compartments of tumor biopsies from bulk RNA-seq data, enabling the determination of how the expression of specific genes affects malignancy and tumor immunity.

cancer biology↗

Multi-Model LLM Architectures for Personalized Summarization and Relevance Ranking in Biomedical Literature

ObjectiveTo develop and evaluate a personalized literature review system that efficiently processes and summarizes biomedical literature to provide timely, relevant insights for researchers. MethodsThe system integrates ontology-aware keyword extraction (MeSH/ACM constrained TF-IDF from CV/Research Statement), citation-informed retrieval (PubMed and NIH iCite API), and dual-model large language model (LLM) summarization (Google Gemini 2.0 flash, OpenAI GPT-4o-mini). These LLMs leverage advanced Transformer architectures, building on foundations such as BERT, BART, and BioBERT. A two-stage ranking algorithm combines Relative Citation Ratio (RCR) with cosine similarity. Summary quality was evaluated using ROGUE-1/2/L and BERTScore. The system is deployed as a Streamlit web application. ResultsAcross 20 biomedical queries, the system demonstrated strong average performance (BERT-F1{approx} 0.86), with cosine similarity strongly correlating with summary quality. Human evaluation involving 10 users yielded average scores above 4.5/5 across summary fidelity and keyword relevance. ConclusionHybrid ranking and ensemble LLM summarization significantly accelerate scientific sense-making. These findings suggest broad applicability to various domains beyond biomedicine.

bioinformatics↗

Microbiota metabolized Bile Acids accelerate Gastroesophageal Adenocarcinoma via FXR inhibition

BackgroundThe incidence of Barrett esophagus (BE) and Gastroesophageal Adenocarcinoma (GEAC) correlates with obesity and a diet rich in fat. Bile acids (BA) support fat digestion and undergo microbial metabolization in the gut. The farnesoid X receptor (FXR) is an important modulator of the BA homeostasis. The capacity of inhibiting cancer-related processes when activated, make FXR an appealing therapeutic target. In this work, we assess the role of diet on the microbiota-BA axis and evaluate the role of FXR in disease progression. ResultsHere we show that high fat diet (HFD) accelerated tumorigenesis in L2-IL1B mice (BE- and GEAC- mouse model) while increasing BA levels and enriching gut microbiota that convert primary to secondary BA. While upregulated in BE, expression of FXR was downregulated in GEAC in mice and humans. In L2-IL1B mice, FXR knockout enhanced the dysplastic phenotype and increased Lgr5 progenitor cell numbers. Treatment of murine organoids and L2-IL1B mice with the FXR agonist obeticholic acid (OCA) deacelerated GEAC progression. ConclusionWe provide a novel concept of GEAC carcinogenesis being accelerated via the diet-microbiome-metabolome axis and FXR inhibition on progenitor cells. Further, FXR activation protected with OCA ameliorated the phenotype in vitro and in vivo, suggesting that FXR agonists have potential as differentiation therapy in GEAC prevention. Statement of significanceIf its inhibition is linked to disease progression and its activation to cancer prevention, exploring the potential of FXR as a therapeutic target has great clinical relevance in GEAC context.

cancer biology↗

Cardiomyocyte PGC-1α enables physiological adaptations to endurance exercise through suppression of GDF15 and cardiac atrophy

Exercise training induces physiological cardiac hypertrophy, enhanced mitochondrial biogenesis and myocardial contractility. In skeletal muscle, the transcriptional coactivator PGC-1 is a key orchestrator of these responses. The heart expresses abundant and exercise-responsive PGC-1, but it is unclear whether cardiomyocyte PGC-1 is necessary for cardiac adaptation to endurance training. Here we demonstrate that cardiomyocyte PGC-1 is required for physiological cardiac hypertrophy during exercise training in mice. In the absence of cardiomyocyte PGC-1, voluntary wheel running does not improve exercise capacity and instead confers immune-fibrotic-atrophic heart failure after just 6 weeks of training. We identify cardiomyocyte PGC-1 as a negative regulator of stress-responsive senescence gene expression. The most enriched of these is the myomitokine GDF15. GDF15 is secreted locally but not systemically in PGC-1-deficient mouse hearts and reduces cardiomyocyte size. Cardiomyocyte-specific reduction of GDF15 expression preserves exercise tolerance and cardiac contractility in PGC-1-deficient mice during endurance training. Finally, we show that cardiomyocyte PPARGC1A expression correlates with cardiomyocyte number and negatively with GDF15 expression in human cardiomyopathies through single nucleus RNA sequencing. Our data implicate cardiomyocyte PGC-1 as a vital safeguard against stress-induced atrophy and local GDF15-induced dysfunction during exercise.

physiology↗

Mechanisms of alcohol influence on fear conditioning: a computational model

A connection between stress-related illnesses and alcohol use disorders is extensively documented. Fear conditioning is a standard procedure used to study stress learning and links it to the activation of amygdala circuitry. However, the connection between the changes in amygdala circuit and function induced by alcohol and fear conditioning is not well established. We introduce a computational model to test the mechanistic relationship between amygdala functional and circuit adaptations during fear conditioning and the impact of acute vs. repeated alcohol exposure. In accordance with experiments, both acute and prior repeated alcohol decreases speed and robustness of fear extinction in our simulations. The model predicts that, first, the delay in fear extinction in alcohol is mostly induced by greater activation of the basolateral amygdala (BLA) after fear acquisition due to alcohol-induced modulation of synaptic weights. Second, both acute and prior repeated alcohol shifts the amygdala network away from the robust extinction regime by inhibiting the activity in the central amygdala (CeA). Third, our model predicts that fear memories formed in acute or after chronic alcohol are more connected to the context. Thus, the model suggests how circuit changes induced by alcohol may affect fear behaviors and provides a framework for investigating the involvement of multiple neuromodulators in this neuroadaptive process.

neuroscience↗

ATAT: Automated Tissue Alignment and Traversal in Spatial Transcriptomics with Self-Supervised Learning

Spatial transcriptomics (ST) has enhanced RNA analysis in tissue biopsies, but interpreting these data is challenging without expert input. We present Automated Tissue Alignment and Traversal (ATAT), a novel computational framework designed to enhance ST analysis in the context of multiple and complex tissue architectures and morphologies, such as those found in biopsies of the gastrointestinal tract. ATAT utilizes self-supervised contrastive learning on hematoxylin and eosin (H&E) stained images to automate the alignment and traversal of ST data. This approach addresses a critical gap in current ST analysis methodologies, which rely heavily on manual annotation and pathologist expertise to delineate regions of interest for accurate gene expression modeling. Our framework not only streamlines the alignment of multiple ST samples, but also demonstrates robustness in modeling gene expression transitions across specific regions. Additionally, we highlight the ability of ATAT to traverse complex tissue topologies in real-world cases from various individuals and conditions. Our method successfully elucidates differences in immune infiltration patterns across the intestinal wall, enabling the modeling of transcriptional changes across histological layers. We show that ATAT achieves comparable performance to the state-of-the-art method, while alleviating the burden of manual annotation and enabling alignment of tissue samples with complex morphologies. AvailabilityATAT is available at: https://github.com/StevenSong/tissue-alignment

bioinformatics↗

Beneficial Effects of Moderate Hepatic Activin A Expression on Metabolic pathways, Inflammation, and Atherosclerosis

BACKGROUNDAtherosclerosis is an inflammatory vascular disease marked by hyperlipidemia and hematopoietic stem cell (HSC) expansion. Activin A, a member of the Activin/GDF/TGF{beta}/BMP family is broadly expressed and increases in human atherosclerosis, but its functional effects in vivo in this context remain unclear. METHODSWe studied LDLR-/- mice on a Western diet for 12 weeks and used adeno-associated viral vectors with a liver-specific thyroxine binding globulin (TBG) promoter to express Activin A or GFP (control). Atherosclerotic lesions were analyzed by oil red staining. Blood lipid profiling was performed by HPLC (High Performance Liquid Chromatography), and immune cells were evaluated by flow cytometry. Liver RNA-sequencing was performed to explore the underlying mechanisms. RESULTSActivin A expression decreased in both livers and aortae from LDLR-/- mice fed a Western diet compared with chow. AAV-TBG-Activin A increased Activin A hepatic expression ([~]10-fold at 12-weeks, p<0.0001) and circulating Activin A levels ([~]2000pg/ml vs [~]50pg/ml, p<0.001, compared with controls). Hepatic Activin A expression decreased plasma total and low-density lipoprotein (LDL) cholesterol ([~]60% and [~]40%, respectively), reduced inflammatory cells in aortae and proliferating hematopoietic stem cells (HSC) in bone marrow, and reduced atherosclerotic lesion area in the aortic arch by [~]60%. Activin A also attenuated liver steatosis and expression of the lipogenesis genes, Srebp1 and Srebp2. RNA sequencing revealed Activin A not only blocked expression of genes involved in hepatic de novo lipogenesis but also fatty acid uptake, and liver inflammation. In addition, Activin A expressed in the liver also reduced white fat tissue accumulation, decreased adipocyte size, and improved glucose tolerance. CONCLUSIONSOur studies reveal hepatic Activin A expression reduces inflammation, HSC expansion, liver steatosis, circulating cholesterol, and fat accumulation, which likely all contribute to the observed protection against atherosclerosis. The reduced Activin A observed in LDLR-/- mice on a Western diet appears maladaptive and deleterious for atherogenesis.

pathology↗

Striatal compartments participate in multi-modal and concurrent reward-based learning

Cortical and basal ganglia circuits play a crucial role in the formation of goal-directed and habitual behaviors. In this study, we investigate the cortico-striatal circuitry involved in learning and the role of this circuitry in the emergence of inflexible behaviors such as those observed in addiction. Specifically, we develop a computational model of cortico-striatal interactions that performs concurrent goal-directed and habit learning. The model accomplishes this by distinguishing learning processes in the dorsomedial striatum (DMS) that rely on reward prediction error signals as distinct from the dorsolateral striatum (DLS) where learning is supported by salience signals. These striatal subregions each operate on unique cortical input: the DMS receives input from the prefrontal cortex (PFC) which represents outcomes, and the DLS receives input from the premotor cortex which determines action selection. Following an initial learning of a two-alternative forced choice task, we subjected the model to reversal learning, reward devaluation, and learning a punished outcome. Behavior driven by stimulus-response associations in the DLS resisted goal-directed learning of new reward feedback rules despite devaluation or punishment, indicating the expression of habit. We repeated these simulations after the impairment of executive control, which was implemented as poor outcome representation in the PFC. The degraded executive control reduced the efficacy of goal-directed learning, and stimulus-response associations in the DLS were even more resistant to the learning of new reward feedback rules. In summary, this model describes how circuits of the dorsal striatum are dynamically engaged to control behavior and how the impairment of executive control by the PFC enhances inflexible behavior. Author SummarySubstance abuse changes an animals brain so that it is not able to appropriately respond to new environmental cues such as negative consequences for drug use. It is thought that the transition from adaptive to inflexible responding involves the inappropriate engagement of neural circuitry responsible for habit. In this study, we model neural circuitry that is critical for adaptive responding to changes in reward feedback to animal behavior. We extended previous computational models of the basal ganglia to incorporate detailed biophysical representations of the dorsomedial striatum, which is critical for goal-directed behavior, and the dorsolateral striatum, which is critical for habitual behavior. The model exhibited learning in simulations of reward reversal, devaluation, and punished outcome tasks. Recent work from our group has quantified the impairment of executive control in cortical activity of compulsively drinking rats. Here, we challenged the model in additional simulations by implementing the impairment of executive control as a reduction in the fidelity of prefrontal cortical outcome representations. Our results illustrate how impaired executive control reduces the performance of goal-directed learning and, hence, reduces the models ability to overcome an established habitual response.

neuroscience↗

ACE2 peptide fragment interacts with several sites on the SARS-CoV-2 spike protein S1

The influence of the peptide QAKTFLDKFNHEAEDLFYQ on the kinetics of the SARS-CoV-2 spike protein S1 binding to angiotensin-converting enzyme 2(ACE2) was studied to model the interaction of the virus with its host cell. This peptide corresponds to the sequence 24-42 of the ACE2 1 domain, which is the binding site for the S1 protein. The on-rate and off-rate of S1-ACE2 complex formation were measured in the presence of various peptide concentrations using Bio-Layer Interferometry (BLI). The formation of the S1-ACE2 complex was inhibited when the S1 protein was preincubated with the peptide, however, no significant inhibitory effect was observed in the absence of preincubation. Dissociation kinetics revealed that the peptide remained bound to the S1-ACE2 complex and stabilized this complex. Computational mapping of the S1 protein surface for peptide binding revealed two additional sites, located at some distance from the receptor binding domain (RBD) of S1. These additional binding sites affect the interaction between the peptide, the S1 protein, and ACE2.

biochemistry↗

Basal Ganglia role in learning rewarded actions and executing previously learned choices: healthy and diseased states

The basal ganglia (BG) is a collection of nuclei located deep beneath the cerebral cortex that is involved in learning and selection of rewarded actions. Here, we analyzed BG mechanisms that enable these functions. We implemented a rate model of a BG-thalamo-cortical loop and simulated its performance in a standard action selection task. We have shown that potentiation of corticostriatal synapses enables learning of a rewarded option. However, these synapses became redundant later as direct connections between prefrontal and premotor cortices (PFC-PMC) were potentiated by Hebbian learning. After we switched the reward to the previously unrewarded option (reversal), the BG was again responsible for switching to the new option. Due to the potentiated direct cortical connections, the system was biased to the previously rewarded choice, and establishing the new choice required a greater number of trials. Guided by physiological research, we then modified our model to reproduce pathological states of mild Parkinsons and Huntingtons diseases. We found that in the Parkinsonian state PMC activity levels become extremely variable, which is caused by oscillations arising in the BG-thalamo-cortical loop. The model reproduced severe impairment of learning and predicted that this is caused by these oscillations as well as a reduced reward prediction signal. In the Huntington state, the potentiation of the PFC-PMC connections produced better learning, but altered BG output disrupted expression of the rewarded choices. This resulted in random switching between rewarded and unrewarded choices resembling an exploratory phase that never ended. Our results reconcile the apparent contradiction between the critical involvement of the BG in execution of previously learned actions and yet no impairment of these actions after BG output is ablated by lesions or deep brain stimulation. We predict that the cortico-BG-thalamo-cortical loop conforms to previously learned choice in healthy conditions, but impedes those choices in disease states.\n\nAuthor summaryLearning and selection of a rewarded action, as well as avoiding punishments, are known to involve interaction of cortical and subcortical structures in the brain. The subcortical structure that is included in this interaction is called Basal Ganglia (BG). Accordingly, diseases that damage BG, such as Parkinson and Huntington, disrupt action selection functions. A long-standing puzzle is that abolition of the BG output that disconnects the BG-cortical interaction does not disrupt execution of previously learned actions. This is the principle that is suggested to underlie standard Parkinsonian treatments, such as deep brain stimulation. We model the BG-cortical interaction and reconcile this apparent contradiction. Our simulations show that, while BG is necessary for learning of new rewarded choices, it is not necessary for the expression of previously learned actions. Our model predicts that the BG conforms to previously learned choice in healthy conditions, but impedes those choices in disease states.

neuroscience↗

Circuit-level Mechanisms of EtOH-dependent dopamine release.

Alcoholism is the third leading cause of preventable mortality in the world. In the last decades a large body of experimental data has paved the way to a clearer knowledge of the specific molecular targets through which ethanol (EtOH) acts on brain circuits. Yet how these multiple mechanisms play together to result in a dysregulated dopamine (DA) release under alcohol influence remains unclear. In this manuscript, we delineate potential circuit-level mechanisms responsible for EtOH-dependent increase and dysregulation of DA release from the ventral tegmental area (VTA) into nucleus accumbens (Nac). For this purpose, we build a circuit model of the VTA composed of DA and GABAergic neurons, that integrate external Glutamatergic (Glu) inputs to result in DA release. In particular, we reproduced a non-monotonic dose dependence of DA neurons firing activity on EtOH: an increase in firing at small to intermediate doses and a drop below baseline (alcohol-free) levels at high EtOH concentrations. Our simulations predict that a certain level of synchrony is necessary for the firing rate increase produced by EtOH. Moreover, EtOHs effect on the DA neurons firing rate and, consequently, DA release can reverse depending on the average activity level of the Glu afferents to VTA. Further, we propose a mechanism for emergence of transient (phasic) DA peaks and the increase in their frequency in EtOH. Phasic DA transients result from DA neuron population bursts, and these bursts are enhanced in EtOH. These results suggest the role of synchrony and average activity level of Glu afferents to VTA in shaping the phasic and tonic DA release under the acute influence of EtOH and in normal conditions.

neuroscience↗