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SeminarNeuroscience

OpenNeuro FitLins GLM: An Accessible, Semi-Automated Pipeline for OpenNeuro Task fMRI Analysis

Michael Demidenko
Stanford University
Aug 1, 2025

In this talk, I will discuss the OpenNeuro Fitlins GLM package and provide an illustration of the analytic workflow. OpenNeuro FitLins GLM is a semi-automated pipeline that reduces barriers to analyzing task-based fMRI data from OpenNeuro's 600+ task datasets. Created for psychology, psychiatry and cognitive neuroscience researchers without extensive computational expertise, this tool automates what is largely a manual process and compilation of in-house scripts for data retrieval, validation, quality control, statistical modeling and reporting that, in some cases, may require weeks of effort. The workflow abides by open-science practices, enhancing reproducibility and incorporates community feedback for model improvement. The pipeline integrates BIDS-compliant datasets and fMRIPrep preprocessed derivatives, and dynamically creates BIDS Statistical Model specifications (with Fitlins) to perform common mass univariate [GLM] analyses. To enhance and standardize reporting, it generates comprehensive reports which includes design matrices, statistical maps and COBIDAS-aligned reporting that is fully reproducible from the model specifications and derivatives. OpenNeuro Fitlins GLM has been tested on over 30 datasets spanning 50+ unique fMRI tasks (e.g., working memory, social processing, emotion regulation, decision-making, motor paradigms), reducing analysis times from weeks to hours when using high-performance computers, thereby enabling researchers to conduct robust single-study, meta- and mega-analyses of task fMRI data with significantly improved accessibility, standardized reporting and reproducibility.

SeminarNeuroscience

Is it Time for MS Patients to Receive Cognitive Rehabilitation?

John DeLuca
Kessler Foundation, West Orange, New Jersey
Jul 3, 2025
SeminarNeuroscience

“Brain theory, what is it or what should it be?”

Prof. Guenther Palm
University of Ulm
Jun 27, 2025

n the neurosciences the need for some 'overarching' theory is sometimes expressed, but it is not always obvious what is meant by this. One can perhaps agree that in modern science observation and experimentation is normally complemented by 'theory', i.e. the development of theoretical concepts that help guiding and evaluating experiments and measurements. A deeper discussion of 'brain theory' will require the clarification of some further distictions, in particular: theory vs. model and brain research (and its theory) vs. neuroscience. Other questions are: Does a theory require mathematics? Or even differential equations? Today it is often taken for granted that the whole universe including everything in it, for example humans, animals, and plants, can be adequately treated by physics and therefore theoretical physics is the overarching theory. Even if this is the case, it has turned out that in some particular parts of physics (the historical example is thermodynamics) it may be useful to simplify the theory by introducing additional theoretical concepts that can in principle be 'reduced' to more complex descriptions on the 'microscopic' level of basic physical particals and forces. In this sense, brain theory may be regarded as part of theoretical neuroscience, which is inside biophysics and therefore inside physics, or theoretical physics. Still, in neuroscience and brain research, additional concepts are typically used to describe results and help guiding experimentation that are 'outside' physics, beginning with neurons and synapses, names of brain parts and areas, up to concepts like 'learning', 'motivation', 'attention'. Certainly, we do not yet have one theory that includes all these concepts. So 'brain theory' is still in a 'pre-newtonian' state. However, it may still be useful to understand in general the relations between a larger theory and its 'parts', or between microscopic and macroscopic theories, or between theories at different 'levels' of description. This is what I plan to do.

SeminarNeuroscience

Harnessing Big Data in Neuroscience: From Mapping Brain Connectivity to Predicting Traumatic Brain Injury

Franco Pestilli
University of Texas, Austin, USA
May 13, 2025

Neuroscience is experiencing unprecedented growth in dataset size both within individual brains and across populations. Large-scale, multimodal datasets are transforming our understanding of brain structure and function, creating opportunities to address previously unexplored questions. However, managing this increasing data volume requires new training and technology approaches. Modern data technologies are reshaping neuroscience by enabling researchers to tackle complex questions within a Ph.D. or postdoctoral timeframe. I will discuss cloud-based platforms such as brainlife.io, that provide scalable, reproducible, and accessible computational infrastructure. Modern data technology can democratize neuroscience, accelerate discovery and foster scientific transparency and collaboration. Concrete examples will illustrate how these technologies can be applied to mapping brain connectivity, studying human learning and development, and developing predictive models for traumatic brain injury (TBI). By integrating cloud computing and scalable data-sharing frameworks, neuroscience can become more impactful, inclusive, and data-driven..

SeminarNeuroscience

Cognitive maps as expectations learned across episodes – a model of the two dentate gyrus blades

Andrej Bicanski
Max Planck Institute for Human Cognitive and Brain Sciences
Mar 12, 2025

How can the hippocampal system transition from episodic one-shot learning to a multi-shot learning regime and what is the utility of the resultant neural representations? This talk will explore the role of the dentate gyrus (DG) anatomy in this context. The canonical DG model suggests it performs pattern separation. More recent experimental results challenge this standard model, suggesting DG function is more complex and also supports the precise binding of objects and events to space and the integration of information across episodes. Very recent studies attribute pattern separation and pattern integration to anatomically distinct parts of the DG (the suprapyramidal blade vs the infrapyramidal blade). We propose a computational model that investigates this distinction. In the model the two processing streams (potentially localized in separate blades) contribute to the storage of distinct episodic memories, and the integration of information across episodes, respectively. The latter forms generalized expectations across episodes, eventually forming a cognitive map. We train the model with two data sets, MNIST and plausible entorhinal cortex inputs. The comparison between the two streams allows for the calculation of a prediction error, which can drive the storage of poorly predicted memories and the forgetting of well-predicted memories. We suggest that differential processing across the DG aids in the iterative construction of spatial cognitive maps to serve the generation of location-dependent expectations, while at the same time preserving episodic memory traces of idiosyncratic events.

SeminarNeuroscience

What it’s like is all there is: The value of Consciousness

Axel Cleeremans
Université Libre de Bruxelles
Mar 7, 2025

Over the past thirty years or so, cognitive neuroscience has made spectacular progress understanding the biological mechanisms of consciousness. Consciousness science, as this field is now sometimes called, was not only inexistent thirty years ago, but its very name seemed like an oxymoron: how can there be a science of consciousness? And yet, despite this scepticism, we are now equipped with a rich set of sophisticated behavioural paradigms, with an impressive array of techniques making it possible to see the brain in action, and with an ever-growing collection of theories and speculations about the putative biological mechanisms through which information processing becomes conscious. This is all good and fine, even promising, but we also seem to have thrown the baby out with the bathwater, or at least to have forgotten it in the crib: consciousness is not just mechanisms, it’s what it feels like. In other words, while we know thousands of informative studies about access-consciousness, we have little in the way of phenomenal consciousness. But that — what it feels like — is truly what “consciousness” is about. Understanding why it feels like something to be me and nothing (panpsychists notwithstanding) for a stone to be a stone is what the field has always been after. However, while it is relatively easy to study access-consciousness through the contrastive approach applied to reports, it is much less clear how to study phenomenology, its structure and its function. Here, I first overview work on what consciousness does (the "how"). Next, I ask what difference feeling things makes and what function phenomenology might play. I argue that subjective experience has intrinsic value and plays a functional role in everything that we do.

SeminarNeuroscience

Digital Minds: Brain Development in the Age of Technology

Eva Telzer
Winston National Center on Technology Use, Brain and Psychological Development
Feb 17, 2025

Digital Minds: Brain Development in the Age of Technology examines how our increasingly connected world shapes mental and cognitive health. From screen time and social media to virtual interactions, this seminar delves into the latest research on how technology influences brain development, relationships, and emotional well-being. Join us to explore strategies for harnessing technology's benefits while mitigating its potential challenges, empowering you to thrive in a digital age.

SeminarNeuroscience

Vision for perception versus vision for action: dissociable contributions of visual sensory drives from primary visual cortex and superior colliculus neurons to orienting behaviors

Prof. Dr. Ziad M. Hafed
Werner Reichardt Center for Integrative Neuroscience, and Hertie Institute for Clinical Brain Research University of Tübingen
Feb 12, 2025

The primary visual cortex (V1) directly projects to the superior colliculus (SC) and is believed to provide sensory drive for eye movements. Consistent with this, a majority of saccade-related SC neurons also exhibit short-latency, stimulus-driven visual responses, which are additionally feature-tuned. However, direct neurophysiological comparisons of the visual response properties of the two anatomically-connected brain areas are surprisingly lacking, especially with respect to active looking behaviors. I will describe a series of experiments characterizing visual response properties in primate V1 and SC neurons, exploring feature dimensions like visual field location, spatial frequency, orientation, contrast, and luminance polarity. The results suggest a substantial, qualitative reformatting of SC visual responses when compared to V1. For example, SC visual response latencies are actively delayed, independent of individual neuron tuning preferences, as a function of increasing spatial frequency, and this phenomenon is directly correlated with saccadic reaction times. Such “coarse-to-fine” rank ordering of SC visual response latencies as a function of spatial frequency is much weaker in V1, suggesting a dissociation of V1 responses from saccade timing. Consistent with this, when we next explored trial-by-trial correlations of individual neurons’ visual response strengths and visual response latencies with saccadic reaction times, we found that most SC neurons exhibited, on a trial-by-trial basis, stronger and earlier visual responses for faster saccadic reaction times. Moreover, these correlations were substantially higher for visual-motor neurons in the intermediate and deep layers than for more superficial visual-only neurons. No such correlations existed systematically in V1. Thus, visual responses in SC and V1 serve fundamentally different roles in active vision: V1 jumpstarts sensing and image analysis, but SC jumpstarts moving. I will finish by demonstrating, using V1 reversible inactivation, that, despite reformatting of signals from V1 to the brainstem, V1 is still a necessary gateway for visually-driven oculomotor responses to occur, even for the most reflexive of eye movement phenomena. This is a fundamental difference from rodent studies demonstrating clear V1-independent processing in afferent visual pathways bypassing the geniculostriate one, and it demonstrates the importance of multi-species comparisons in the study of oculomotor control.

SeminarNeuroscience

Circuit Mechanisms of Remote Memory

Lauren DeNardo, PhD
Department of Physiology, David Geffen School of Medicine, UCLA
Feb 11, 2025

Memories of emotionally-salient events are long-lasting, guiding behavior from minutes to years after learning. The prelimbic cortex (PL) is required for fear memory retrieval across time and is densely interconnected with many subcortical and cortical areas involved in recent and remote memory recall, including the temporal association area (TeA). While the behavioral expression of a memory may remain constant over time, the neural activity mediating memory-guided behavior is dynamic. In PL, different neurons underlie recent and remote memory retrieval and remote memory-encoding neurons have preferential functional connectivity with cortical association areas, including TeA. TeA plays a preferential role in remote compared to recent memory retrieval, yet how TeA circuits drive remote memory retrieval remains poorly understood. Here we used a combination of activity-dependent neuronal tagging, viral circuit mapping and miniscope imaging to investigate the role of the PL-TeA circuit in fear memory retrieval across time in mice. We show that PL memory ensembles recruit PL-TeA neurons across time, and that PL-TeA neurons have enhanced encoding of salient cues and behaviors at remote timepoints. This recruitment depends upon ongoing synaptic activity in the learning-activated PL ensemble. Our results reveal a novel circuit encoding remote memory and provide insight into the principles of memory circuit reorganization across time.

SeminarNeuroscience

Dimensionality reduction beyond neural subspaces

Alex Cayco Gajic
École Normale Supérieure
Jan 29, 2025

Over the past decade, neural representations have been studied from the lens of low-dimensional subspaces defined by the co-activation of neurons. However, this view has overlooked other forms of covarying structure in neural activity, including i) condition-specific high-dimensional neural sequences, and ii) representations that change over time due to learning or drift. In this talk, I will present a new framework that extends the classic view towards additional types of covariability that are not constrained to a fixed, low-dimensional subspace. In addition, I will present sliceTCA, a new tensor decomposition that captures and demixes these different types of covariability to reveal task-relevant structure in neural activity. Finally, I will close with some thoughts regarding the circuit mechanisms that could generate mixed covariability. Together this work points to a need to consider new possibilities for how neural populations encode sensory, cognitive, and behavioral variables beyond neural subspaces.

SeminarNeuroscience

Decision and Behavior

Sam Gershman, Jonathan Pillow, Kenji Doya
Harvard University; Princeton University; Okinawa Institute of Science and Technology
Nov 29, 2024

This webinar addressed computational perspectives on how animals and humans make decisions, spanning normative, descriptive, and mechanistic models. Sam Gershman (Harvard) presented a capacity-limited reinforcement learning framework in which policies are compressed under an information bottleneck constraint. This approach predicts pervasive perseveration, stimulus‐independent “default” actions, and trade-offs between complexity and reward. Such policy compression reconciles observed action stochasticity and response time patterns with an optimal balance between learning capacity and performance. Jonathan Pillow (Princeton) discussed flexible descriptive models for tracking time-varying policies in animals. He introduced dynamic Generalized Linear Models (Sidetrack) and hidden Markov models (GLM-HMMs) that capture day-to-day and trial-to-trial fluctuations in choice behavior, including abrupt switches between “engaged” and “disengaged” states. These models provide new insights into how animals’ strategies evolve under learning. Finally, Kenji Doya (OIST) highlighted the importance of unifying reinforcement learning with Bayesian inference, exploring how cortical-basal ganglia networks might implement model-based and model-free strategies. He also described Japan’s Brain/MINDS 2.0 and Digital Brain initiatives, aiming to integrate multimodal data and computational principles into cohesive “digital brains.”

SeminarNeuroscience

LLMs and Human Language Processing

Maryia Toneva, Ariel Goldstein, Jean-Remi King
Max Planck Institute of Software Systems; Hebrew University; École Normale Supérieure
Nov 29, 2024

This webinar convened researchers at the intersection of Artificial Intelligence and Neuroscience to investigate how large language models (LLMs) can serve as valuable “model organisms” for understanding human language processing. Presenters showcased evidence that brain recordings (fMRI, MEG, ECoG) acquired while participants read or listened to unconstrained speech can be predicted by representations extracted from state-of-the-art text- and speech-based LLMs. In particular, text-based LLMs tend to align better with higher-level language regions, capturing more semantic aspects, while speech-based LLMs excel at explaining early auditory cortical responses. However, purely low-level features can drive part of these alignments, complicating interpretations. New methods, including perturbation analyses, highlight which linguistic variables matter for each cortical area and time scale. Further, “brain tuning” of LLMs—fine-tuning on measured neural signals—can improve semantic representations and downstream language tasks. Despite open questions about interpretability and exact neural mechanisms, these results demonstrate that LLMs provide a promising framework for probing the computations underlying human language comprehension and production at multiple spatiotemporal scales.

SeminarNeuroscience

Introducing the 'Cognitive Neuroscience & Neurotechnolog' group: From real-time fMRI to layer-fMRI & back

Romy Lorenz
Max Planck Institute for Biological Cybernetics, Tübingen
Nov 28, 2024
SeminarNeuroscience

Understanding the complex behaviors of the ‘simple’ cerebellar circuit

Megan Carey
The Champalimaud Center for the Unknown, Lisbon, Portugal
Nov 14, 2024

Every movement we make requires us to precisely coordinate muscle activity across our body in space and time. In this talk I will describe our efforts to understand how the brain generates flexible, coordinated movement. We have taken a behavior-centric approach to this problem, starting with the development of quantitative frameworks for mouse locomotion (LocoMouse; Machado et al., eLife 2015, 2020) and locomotor learning, in which mice adapt their locomotor symmetry in response to environmental perturbations (Darmohray et al., Neuron 2019). Combined with genetic circuit dissection, these studies reveal specific, cerebellum-dependent features of these complex, whole-body behaviors. This provides a key entry point for understanding how neural computations within the highly stereotyped cerebellar circuit support the precise coordination of muscle activity in space and time. Finally, I will present recent unpublished data that provide surprising insights into how cerebellar circuits flexibly coordinate whole-body movements in dynamic environments.

SeminarNeuroscience

Decomposing motivation into value and salience

Philippe Tobler
University of Zurich
Nov 1, 2024

Humans and other animals approach reward and avoid punishment and pay attention to cues predicting these events. Such motivated behavior thus appears to be guided by value, which directs behavior towards or away from positively or negatively valenced outcomes. Moreover, it is facilitated by (top-down) salience, which enhances attention to behaviorally relevant learned cues predicting the occurrence of valenced outcomes. Using human neuroimaging, we recently separated value (ventral striatum, posterior ventromedial prefrontal cortex) from salience (anterior ventromedial cortex, occipital cortex) in the domain of liquid reward and punishment. Moreover, we investigated potential drivers of learned salience: the probability and uncertainty with which valenced and non-valenced outcomes occur. We find that the brain dissociates valenced from non-valenced probability and uncertainty, which indicates that reinforcement matters for the brain, in addition to information provided by probability and uncertainty alone, regardless of valence. Finally, we assessed learning signals (unsigned prediction errors) that may underpin the acquisition of salience. Particularly the insula appears to be central for this function, encoding a subjective salience prediction error, similarly at the time of positively and negatively valenced outcomes. However, it appears to employ domain-specific time constants, leading to stronger salience signals in the aversive than the appetitive domain at the time of cues. These findings explain why previous research associated the insula with both valence-independent salience processing and with preferential encoding of the aversive domain. More generally, the distinction of value and salience appears to provide a useful framework for capturing the neural basis of motivated behavior.

SeminarNeuroscience

Intrinsic timescales in the visual cortex change with selective attention and reflect spatial connectivity

Attempto Prize Awardee I Roxana Zeraati
IMPRS-MMFD, MPI-BC & University of Tübingen
Oct 31, 2024
SeminarNeuroscience

Animal Research: Time to Talk!

Kirk Leech
European Animal Research Association
Oct 16, 2024
SeminarNeuroscience

Influence of the context of administration in the antidepressant-like effects of the psychedelic 5-MeO-DMT

Romain Hacquet
Université de Toulouse
Aug 29, 2024

Psychedelics like psilocybin have shown rapid and long-lasting efficacy on depressive and anxiety symptoms. Other psychedelics with shorter half-lives, such as DMT and 5-MeO-DMT, have also shown promising preliminary outcomes in major depression, making them interesting candidates for clinical practice. Despite several promising clinical studies, the influence of the context on therapeutic responses or adverse effects remains poorly documented. To address this, we conducted preclinical studies evaluating the psychopharmacological profile of 5-MeO-DMT in contexts previously validated in mice as either pleasant (positive setting) or aversive (negative setting). Healthy C57BL/6J male mice received a single intraperitoneal (i.p.) injection of 5-MeO-DMT at doses of 0.5, 5, and 10 mg/kg, with assessments at 2 hours, 24 hours, and one week post-administration. In a corticosterone (CORT) mouse model of depression, 5-MeO-DMT was administered in different settings, and behavioral tests mimicking core symptoms of depression and anxiety were conducted. In CORT-exposed mice, an acute dose of 0.5 mg/kg administered in a neutral setting produced antidepressant-like effects at 24 hours, as observed by reduced immobility time in the Tail Suspension Test (TST). In a positive setting, the drug also reduced latency to first immobility and total immobility time in the TST. However, these beneficial effects were negated in a negative setting, where 5-MeO-DMT failed to produce antidepressant-like effects and instead elicited an anxiogenic response in the Elevated Plus Maze (EPM).Our results indicate a strong influence of setting on the psychopharmacological profile of 5-MeO-DMT. Future experiments will examine cortical markers of pre- and post-synaptic density to correlate neuroplasticity changes with the behavioral effects of 5-MeO-DMT in different settings.

SeminarNeuroscienceRecording

Reactivation in the human brain connects the past with the present

Avital Hahamy
UCL
Jul 2, 2024
SeminarNeuroscienceRecording

Attending to moments in time

Rachel Denison
Boston University
Jun 25, 2024
SeminarNeuroscienceRecording

There’s more to timing than time: P-centers, beat bins and groove in musical microrhythm

Anne Danielsen
University of Oslo, Norway
Apr 29, 2024

How does the dynamic shape of a sound affect its perceived microtiming? In the TIME project, we studied basic aspects of musical microrhythm, exploring both stimulus features and the participants’ enculturated expertise via perception experiments, observational studies of how musicians produce particular microrhythms, and ethnographic studies of musicians’ descriptions of microrhythm. Collectively, we show that altering the microstructure of a sound (“what” the sound is) changes its perceived temporal location (“when” it occurs). Specifically, there are systematic effects of core acoustic factors (duration, attack) on perceived timing. Microrhythmic features in longer and more complex sounds can also give rise to different perceptions of the same sound. Our results shed light on conflicting results regarding the effect of microtiming on the “grooviness” of a rhythm.

SeminarNeuroscience

Learning representations of specifics and generalities over time

Anna Schapiro
University of Pennsylvania
Apr 12, 2024

There is a fundamental tension between storing discrete traces of individual experiences, which allows recall of particular moments in our past without interference, and extracting regularities across these experiences, which supports generalization and prediction in similar situations in the future. One influential proposal for how the brain resolves this tension is that it separates the processes anatomically into Complementary Learning Systems, with the hippocampus rapidly encoding individual episodes and the neocortex slowly extracting regularities over days, months, and years. But this does not explain our ability to learn and generalize from new regularities in our environment quickly, often within minutes. We have put forward a neural network model of the hippocampus that suggests that the hippocampus itself may contain complementary learning systems, with one pathway specializing in the rapid learning of regularities and a separate pathway handling the region’s classic episodic memory functions. This proposal has broad implications for how we learn and represent novel information of specific and generalized types, which we test across statistical learning, inference, and category learning paradigms. We also explore how this system interacts with slower-learning neocortical memory systems, with empirical and modeling investigations into how the hippocampus shapes neocortical representations during sleep. Together, the work helps us understand how structured information in our environment is initially encoded and how it then transforms over time.

SeminarNeuroscienceRecording

Currents of Hope: how noninvasive brain stimulation is reshaping modern psychiatric care; Adapting to diversity: Integrating variability in brain structure and function into personalized / closed-loop non-invasive brain stimulation for substance use disorders

Colleen Hanlon, PhD & Ghazaleh Soleimani, PhD
Brainsway / University of Minnesota
Mar 28, 2024

In March we will focus on TMS and host Ghazaleh Soleimani and Colleen Hanlon. The talks will talk place on Thursday, March 28th at noon ET – please be aware that this means 5PM CET since Boston already switched to summer time! Ghazaleh Soleimani, PhD, is a postdoctoral fellow in Dr Hamed Ekhtiari’s lab at the University of Minnesota. She is also the executive director of the International Network of tES/TMS for Addiction Medicine (INTAM). She will discuss “Adapting to diversity: Integrating variability in brain structure and function into personalized / closed-loop non-invasive brain stimulation for substance use disorders”. Colleen Hanlon, PhD, currently serves as a Vice President of Medical Affairs for BrainsWay, a company specializing in medical devices for mental health, including TMS. Colleen previously worked at the Medical University of South Carolina and Wake Forest School of Medicine. She received the International Brain Stimulation Early Career Award in 2023. She will discuss “Currents of Hope: how noninvasive brain stimulation is reshaping modern psychiatric care”. As always, we will also get a glimpse at the “Person behind the science”. Please register va talks.stimulatingbrains.org to receive the (free) Zoom link, subscribe to our newsletter, or follow us on Twitter/X for further updates!

SeminarNeuroscienceRecording

Time perception in film viewing as a function of film editing

Lydia Liapi
Panteion University
Mar 27, 2024

Filmmakers and editors have empirically developed techniques to ensure the spatiotemporal continuity of a film's narration. In terms of time, editing techniques (e.g., elliptical, overlapping, or cut minimization) allow for the manipulation of the perceived duration of events as they unfold on screen. More specifically, a scene can be edited to be time compressed, expanded, or real-time in terms of its perceived duration. Despite the consistent application of these techniques in filmmaking, their perceptual outcomes have not been experimentally validated. Given that viewing a film is experienced as a precise simulation of the physical world, the use of cinematic material to examine aspects of time perception allows for experimentation with high ecological validity, while filmmakers gain more insight on how empirically developed techniques influence viewers' time percept. Here, we investigated how such time manipulation techniques of an action affect a scene's perceived duration. Specifically, we presented videos depicting different actions (e.g., a woman talking on the phone), edited according to the techniques applied for temporal manipulation and asked participants to make verbal estimations of the presented scenes' perceived durations. Analysis of data revealed that the duration of expanded scenes was significantly overestimated as compared to that of compressed and real-time scenes, as was the duration of real-time scenes as compared to that of compressed scenes. Therefore, our results validate the empirical techniques applied for the modulation of a scene's perceived duration. We also found interactions on time estimates of scene type and editing technique as a function of the characteristics and the action of the scene presented. Thus, these findings add to the discussion that the content and characteristics of a scene, along with the editing technique applied, can also modulate perceived duration. Our findings are discussed by considering current timing frameworks, as well as attentional saliency algorithms measuring the visual saliency of the presented stimuli.

SeminarNeuroscienceRecording

Distinctive features of experiential time: Duration, speed and event density

Marianna Lamprou Kokolaki
Université Paris-Saclay
Mar 27, 2024

William James’s use of “time in passing” and “stream of thoughts” may be two sides of the same coin that emerge from the brain segmenting the continuous flow of information into discrete events. Departing from that idea, we investigated how the content of a realistic scene impacts two distinct temporal experiences: the felt duration and the speed of the passage of time. I will present you the results from an online study in which we used a well-established experimental paradigm, the temporal bisection task, which we extended to passage of time judgments. 164 participants classified seconds-long videos of naturalistic scenes as short or long (duration), or slow or fast (passage of time). Videos contained a varying number and type of events. We found that a large number of events lengthened subjective duration and accelerated the felt passage of time. Surprisingly, participants were also faster at estimating their felt passage of time compared to duration. The perception of duration heavily depended on objective duration, whereas the felt passage of time scaled with the rate of change. Altogether, our results support a possible dissociation of the mechanisms underlying the two temporal experiences.

SeminarNeuroscienceRecording

Blood-brain barrier dysfunction in epilepsy: Time for translation

Alon Friedman
Dalhousie University
Feb 28, 2024

The neurovascular unit (NVU) consists of cerebral blood vessels, neurons, astrocytes, microglia, and pericytes. It plays a vital role in regulating blood flow and ensuring the proper functioning of neural circuits. Among other, this is made possible by the blood-brain barrier (BBB), which acts as both a physical and functional barrier. Previous studies have shown that dysfunction of the BBB is common in most neurological disorders and is associated with neural dysfunction. Our studies have demonstrated that BBB dysfunction results in the transformation of astrocytes through transforming growth factor beta (TGFβ) signaling. This leads to activation of the innate neuroinflammatory system, changes in the extracellular matrix, and pathological plasticity. These changes ultimately result in dysfunction of the cortical circuit, lower seizure threshold, and spontaneous seizures. Blocking TGFβ signaling and its associated pro-inflammatory pathway can prevent this cascade of events, reduces neuroinflammation, repairs BBB dysfunction, and prevents post-injury epilepsy, as shown in experimental rodents. To further understand and assess BBB integrity in human epilepsy, we developed a novel imaging technique that quantitatively measures BBB permeability. Our findings have confirmed that BBB dysfunction is common in patients with drug-resistant epilepsy and can assist in identifying the ictal-onset zone prior to surgery. Current clinical studies are ongoing to explore the potential of targeting BBB dysfunction as a novel treatment approach and investigate its role in drug resistance, the spread of seizures, and comorbidities associated with epilepsy.

SeminarNeuroscienceRecording

The Role of Spatial and Contextual Relations of real world objects in Interval Timing

Rania Tachmatzidou
Panteion University
Jan 29, 2024

In the real world, object arrangement follows a number of rules. Some of the rules pertain to the spatial relations between objects and scenes (i.e., syntactic rules) and others about the contextual relations (i.e., semantic rules). Research has shown that violation of semantic rules influences interval timing with the duration of scenes containing such violations to be overestimated as compared to scenes with no violations. However, no study has yet investigated whether both semantic and syntactic violations can affect timing in the same way. Furthermore, it is unclear whether the effect of scene violations on timing is due to attentional or other cognitive accounts. Using an oddball paradigm and real-world scenes with or without semantic and syntactic violations, we conducted two experiments on whether time dilation will be obtained in the presence of any type of scene violation and the role of attention in any such effect. Our results from Experiment 1 showed that time dilation indeed occurred in the presence of syntactic violations, while time compression was observed for semantic violations. In Experiment 2, we further investigated whether these estimations were driven by attentional accounts, by utilizing a contrast manipulation of the target objects. The results showed that an increased contrast led to duration overestimation for both semantic and syntactic oddballs. Together, our results indicate that scene violations differentially affect timing due to violation processing differences and, moreover, their effect on timing seems to be sensitive to attentional manipulations such as target contrast.

SeminarNeuroscienceRecording

Measures and models of multisensory integration in reaction times

Hans Colonius
Oldenburg University
Jan 18, 2024

First, a new measure of MI for reaction times is proposed that takes the entire RT distribution into account. Second, we present some recent developments in TWIN modeling, including a new proposal for the sound-induced flash illusion (SIFI).

SeminarNeuroscience

Astrocyte reprogramming / activation and brain homeostasis

Thomaidou Dimitra
Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
Dec 13, 2023

Astrocytes are multifunctional glial cells, implicated in neurogenesis and synaptogenesis, supporting and fine-tuning neuronal activity and maintaining brain homeostasis by controlling blood-brain barrier permeability. During the last years a number of studies have shown that astrocytes can also be converted into neurons if they force-express neurogenic transcription factors or miRNAs. Direct astrocytic reprogramming to induced-neurons (iNs) is a powerful approach for manipulating cell fate, as it takes advantage of the intrinsic neural stem cell (NSC) potential of brain resident reactive astrocytes. To this end, astrocytic cell fate conversion to iNs has been well-established in vitro and in vivo using combinations of transcription factors (TFs) or chemical cocktails. Challenging the expression of lineage-specific TFs is accompanied by changes in the expression of miRNAs, that post-transcriptionally modulate high numbers of neurogenesis-promoting factors and have therefore been introduced, supplementary or alternatively to TFs, to instruct direct neuronal reprogramming. The neurogenic miRNA miR-124 has been employed in direct reprogramming protocols supplementary to neurogenic TFs and other miRNAs to enhance direct neurogenic conversion by suppressing multiple non-neuronal targets. In our group we aimed to investigate whether miR-124 is sufficient to drive direct reprogramming of astrocytes to induced-neurons (iNs) on its own both in vitro and in vivo and elucidate its independent mechanism of reprogramming action. Our in vitro data indicate that miR-124 is a potent driver of the reprogramming switch of astrocytes towards an immature neuronal fate. Elucidation of the molecular pathways being triggered by miR-124 by RNA-seq analysis revealed that miR-124 is sufficient to instruct reprogramming of cortical astrocytes to immature induced-neurons (iNs) in vitro by down-regulating genes with important regulatory roles in astrocytic function. Among these, the RNA binding protein Zfp36l1, implicated in ARE-mediated mRNA decay, was found to be a direct target of miR-124, that be its turn targets neuronal-specific proteins participating in cortical development, which get de-repressed in miR-124-iNs. Furthermore, miR-124 is potent to guide direct neuronal reprogramming of reactive astrocytes to iNs of cortical identity following cortical trauma, a novel finding confirming its robust reprogramming action within the cortical microenvironment under neuroinflammatory conditions. In parallel to their reprogramming properties, astrocytes also participate in the maintenance of blood-brain barrier integrity, which ensures the physiological functioning of the central nervous system and gets affected contributing to the pathology of several neurodegenerative diseases. To study in real time the dynamic physical interactions of astrocytes with brain vasculature under homeostatic and pathological conditions, we performed 2-photon brain intravital imaging in a mouse model of systemic neuroinflammation, known to trigger astrogliosis and microgliosis and to evoke changes in astrocytic contact with brain vasculature. Our in vivo findings indicate that following neuroinflammation the endfeet of activated perivascular astrocytes lose their close proximity and physiological cross-talk with vasculature, however this event is at compensated by the cross-talk of astrocytes with activated microglia, safeguarding blood vessel coverage and maintenance of blood-brain integrity.

SeminarNeuroscienceRecording

Bayesian expectation in the perception of the timing of stimulus sequences

Max De Luca
University of Birmingham
Dec 13, 2023

In the current virtual journal club Dr Di Luca will present findings from a series of psychophysical investigations where he measured sensitivity and bias in the perception of the timing of stimuli. He will present how improved detection with longer sequences and biases in reporting isochrony can be accounted for by optimal statistical predictions. Among his findings was also that the timing of stimuli that occasionally deviate from a regularly paced sequence is perceptually distorted to appear more regular. Such change depends on whether the context these sequences are presented is also regular. Dr Di Luca will present a Bayesian model for the combination of dynamically updated expectations, in the form of a priori probability, with incoming sensory information. These findings contribute to the understanding of how the brain processes temporal information to shape perceptual experiences.

SeminarNeuroscienceRecording

Tracking subjects' strategies in behavioural choice experiments at trial resolution

Mark Humphries
University of Nottingham
Dec 7, 2023

Psychology and neuroscience are increasingly looking to fine-grained analyses of decision-making behaviour, seeking to characterise not just the variation between subjects but also a subject's variability across time. When analysing the behaviour of each subject in a choice task, we ideally want to know not only when the subject has learnt the correct choice rule but also what the subject tried while learning. I introduce a simple but effective Bayesian approach to inferring the probability of different choice strategies at trial resolution. This can be used both for inferring when subjects learn, by tracking the probability of the strategy matching the target rule, and for inferring subjects use of exploratory strategies during learning. Applied to data from rodent and human decision tasks, we find learning occurs earlier and more often than estimated using classical approaches. Around both learning and changes in the rewarded rules the exploratory strategies of win-stay and lose-shift, often considered complementary, are consistently used independently. Indeed, we find the use of lose-shift is strong evidence that animals have latently learnt the salient features of a new rewarded rule. Our approach can be extended to any discrete choice strategy, and its low computational cost is ideally suited for real-time analysis and closed-loop control.

SeminarNeuroscience

Trends in NeuroAI - Meta's MEG-to-image reconstruction

Paul Scotti
Dec 7, 2023

Trends in NeuroAI is a reading group hosted by the MedARC Neuroimaging & AI lab (https://medarc.ai/fmri). This will be an informal journal club presentation, we do not have an author of the paper joining us. Title: Brain decoding: toward real-time reconstruction of visual perception Abstract: In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (≈0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (≈5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that MEG signals primarily contain high-level visual features, whereas the same approach applied to 7T fMRI also recovers low-level features. Overall, these results provide an important step towards the decoding - in real time - of the visual processes continuously unfolding within the human brain. Speaker: Dr. Paul Scotti (Stability AI, MedARC) Paper link: https://arxiv.org/abs/2310.19812

SeminarNeuroscienceRecording

ALBA webinar series - Breaking down the ivory tower: Ep. 4 Maria José Diógenes

Maria José Diógenes
iMM - ULisboa, PT
Dec 4, 2023

With this webinar series, the ALBA Disability & Accessibility Working Group aims to bring down the ivory tower of ableism among the brain research community, one extraordinary neuroscientist at a time. These webinars give a platform to scientists with disabilities across the globe and neuroscience disciplines, while reflecting on how to promote inclusive working environments and accessibility to research. For this 4th episode, Dr. Maria José Diógenes (iMM - ULisboa, PT) will talk about how her personal story changed her professional life: from the pharmacy to the laboratory bench and from ageing to Rett Syndrome.

SeminarNeuroscienceRecording

Event-related frequency adjustment (ERFA): A methodology for investigating neural entrainment

Mattia Rosso
Ghent University, IPEM Institute for Systematic Musicology
Nov 29, 2023

Neural entrainment has become a phenomenon of exceptional interest to neuroscience, given its involvement in rhythm perception, production, and overt synchronized behavior. Yet, traditional methods fail to quantify neural entrainment due to a misalignment with its fundamental definition (e.g., see Novembre and Iannetti, 2018; Rajandran and Schupp, 2019). The definition of entrainment assumes that endogenous oscillatory brain activity undergoes dynamic frequency adjustments to synchronize with environmental rhythms (Lakatos et al., 2019). Following this definition, we recently developed a method sensitive to this process. Our aim was to isolate from the electroencephalographic (EEG) signal an oscillatory component that is attuned to the frequency of a rhythmic stimulation, hypothesizing that the oscillation would adaptively speed up and slow down to achieve stable synchronization over time. To induce and measure these adaptive changes in a controlled fashion, we developed the event-related frequency adjustment (ERFA) paradigm (Rosso et al., 2023). A total of twenty healthy participants took part in our study. They were instructed to tap their finger synchronously with an isochronous auditory metronome, which was unpredictably perturbed by phase-shifts and tempo-changes in both positive and negative directions across different experimental conditions. EEG was recorded during the task, and ERFA responses were quantified as changes in instantaneous frequency of the entrained component. Our results indicate that ERFAs track the stimulus dynamics in accordance with the perturbation type and direction, preferentially for a sensorimotor component. The clear and consistent patterns confirm that our method is sensitive to the process of frequency adjustment that defines neural entrainment. In this Virtual Journal Club, the discussion of our findings will be complemented by methodological insights beneficial to researchers in the fields of rhythm perception and production, as well as timing in general. We discuss the dos and don’ts of using instantaneous frequency to quantify oscillatory dynamics, the advantages of adopting a multivariate approach to source separation, the robustness against the confounder of responses evoked by periodic stimulation, and provide an overview of domains and concrete examples where the methodological framework can be applied.

SeminarNeuroscienceRecording

Circadian modulation by time-restricted feeding rescues brain pathology and improves memory in mouse models of Alzheimer’s disease

Daniel S. Whittaker
UCSD
Nov 9, 2023
SeminarNeuroscience

Effect of nutrient sensing by microglia on mouse behavior

Agnès Nadjar
University of Bordeaux, France
Nov 7, 2023

Microglia are the brain macrophages, eliciting multifaceted functions to maintain brain homeostasis across lifetime. To achieve this, microglia are able to sense a plethora of signals in their close environment. In the lab, we investigate the effect of nutrients on microglia function for several reasons: 1) Microglia express all the cellular machinery required to sense nutrients; 2) Eating habits have changed considerably over the last century, towards diets rich in fats and sugars; 3) This so-called "Western diet" is accompanied by an increase in the occurrence of neuropathologies, in which microglia are known to play a role. In my talk, I will present data showing how variations in nutrient intake alter microglia function, including exacerbation of synaptic pruning, with profound consequences for neuronal activity and behavior. I will also show unpublished data on the mechanisms underlying the effects of nutrients on microglia, notably through the regulation of their metabolic activity.

SeminarNeuroscienceRecording

ALBA webinar series - Breaking down the ivory tower: Ep. 3 Donna Rose Addis

Donna Rose Addis
Rotman Research Institute, Baycrest & University of Toronto, Canada
Oct 23, 2023

With this webinar series, the ALBA Disability & Accessibility Working Group aims to bring down the ivory tower of ableism among the brain research community, one extraordinary neuroscientist at a time. These webinars give a platform to scientists with disabilities across the globe and neuroscience disciplines, while reflecting on how to promote inclusive working environments and accessibility to research. For this 3rd episode, Dr. Donna Rose Addis (Rotman Research Institute, Baycrest & University of Toronto, Canada) will talk about her research and experience.

SeminarNeuroscience

A recurrent network model of planning predicts hippocampal replay and human behavior

Marcelo Mattar
NYU
Oct 20, 2023

When interacting with complex environments, humans can rapidly adapt their behavior to changes in task or context. To facilitate this adaptation, we often spend substantial periods of time contemplating possible futures before acting. For such planning to be rational, the benefits of planning to future behavior must at least compensate for the time spent thinking. Here we capture these features of human behavior by developing a neural network model where not only actions, but also planning, are controlled by prefrontal cortex. This model consists of a meta-reinforcement learning agent augmented with the ability to plan by sampling imagined action sequences drawn from its own policy, which we refer to as `rollouts'. Our results demonstrate that this agent learns to plan when planning is beneficial, explaining the empirical variability in human thinking times. Additionally, the patterns of policy rollouts employed by the artificial agent closely resemble patterns of rodent hippocampal replays recently recorded in a spatial navigation task, in terms of both their spatial statistics and their relationship to subsequent behavior. Our work provides a new theory of how the brain could implement planning through prefrontal-hippocampal interactions, where hippocampal replays are triggered by -- and in turn adaptively affect -- prefrontal dynamics.

SeminarNeuroscienceRecording

How fly neurons compute the direction of visual motion

Axel Borst
Max-Planck-Institute for Biological Intelligence
Oct 9, 2023

Detecting the direction of image motion is important for visual navigation, predator avoidance and prey capture, and thus essential for the survival of all animals that have eyes. However, the direction of motion is not explicitly represented at the level of the photoreceptors: it rather needs to be computed by subsequent neural circuits, involving a comparison of the signals from neighboring photoreceptors over time. The exact nature of this process represents a classic example of neural computation and has been a longstanding question in the field. Much progress has been made in recent years in the fruit fly Drosophila melanogaster by genetically targeting individual neuron types to block, activate or record from them. Our results obtained this way demonstrate that the local direction of motion is computed in two parallel ON and OFF pathways. Within each pathway, a retinotopic array of four direction-selective T4 (ON) and T5 (OFF) cells represents the four Cartesian components of local motion vectors (leftward, rightward, upward, downward). Since none of the presynaptic neurons is directionally selective, direction selectivity first emerges within T4 and T5 cells. Our present research focuses on the cellular and biophysical mechanisms by which the direction of image motion is computed in these neurons.

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