Transmission delays and frequency detuning can regulate information flow between brain regions

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, it is hypothesized that these sites must be in proximity. Inverted repeat sequences, such as Alu elements, in the upstream and downstream introns are predicted to base-pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the human HIPK3 gene at exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing techniques, including the recently developed SHAPE- JuMP strategy, to characterize secondary and tertiary interactions in the pre- mRNA that govern backsplicing. Our data confirm that the antisense Alu elements, AluSz(-) and AluSq2(+) in the upstream and downstream introns, form a highly- paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data identified multiple long-range interactions between non-pairing nucleotides. Genome-wide analysis of inverted repeats flanking circular RNAs confirm that their presence favors circularization, but the overall effect is modest. Together these results suggest that secondary structure considerations alone cannot fully explain backsplicing and additional interactions are key.

How Distributed Subcortical Integration of Reward and Threat May Inform Subsequent Approach-Avoidance Decisions

Healthy and successful living involves carefully navigating rewarding and threatening situations by balancing approach and avoidance behaviors. Excessive avoidance to evade potential threats often leads to forfeiting potential rewards. However, little is known about how reward and threat information is integrated neurally to inform approach or avoidance. In this preregistered study, participants (N behavior = 31, 17F; N MRI = 28, 15F) made approach-avoidance decisions under varying reward (monetary gains) and threat (electrical stimulations) prospects during functional MRI scanning. In contrast to theorized parallel subcortical processing of reward and threat information before cortical integration, Bayesian multivariate multilevel analyses revealed subcortical reward and threat integration prior to indicating approach-avoidance decisions. This integration occurred in the ventral striatum, thalamus, and bed nucleus of the stria terminalis (BNST). When reward was low, risk-diminishing avoidance decisions dominated, which was linked to more positive tracking of threat magnitude prior to indicating avoidance than approach decisions. In contrast, the amygdala exhibited dual sensitivity to reward and threat. While anticipating outcomes of risky approach decisions, we observed positive tracking of threat magnitude within the salience network (dorsal anterior cingulate cortex, thalamus, periaqueductal gray, BNST). Conversely, after risk-diminishing avoidance, characterized by reduced reward prospects, we observed more negative tracking of reward magnitude in the ventromedial prefrontal cortex and ventral striatum. These findings shed light on the temporal dynamics of approach-avoidance decision-making. Importantly, they demonstrate the role of subcortical integration of reward and threat information in balancing approach and avoidance, challenging theories positing predominantly separate subcortical processing prior to cortical integration.

Volumetric imaging and computation to explore contractile function in zebrafish hearts

Despite advancements in cardiovascular engineering, heart diseases remain a leading cause of mortality. The limited understanding of the underlying mechanisms of cardiac dysfunction at the cellular level restricts the development of effective screening and therapeutic methods. To address this, we have developed a framework that incorporates light field detection and individual cell tracking to capture real-time volumetric data in zebrafish hearts, which share structural and electrical similarities with the human heart and generate 120 to 180 beats per minute. Our results indicate that the in-house system achieves an acquisition speed of 200 volumes per second, with resolutions of up to 5.02 ± 0.54 µm laterally and 9.02 ± 1.11 µm axially across the entire depth, using the estimated-maximized-smoothed deconvolution method. The subsequent deep learning-based cell trackers enable further investigation of contractile dynamics, including cellular displacement and velocity, followed by volumetric tracking of specific cells of interest from end-systole to end-diastole in an interactive environment. Collectively, our strategy facilitates real-time volumetric imaging and assessment of contractile dynamics across the entire ventricle at the cellular resolution over multiple cycles, providing significant potential for exploring intercellular interactions in both health and disease.

Research on brain functional network property analysis and recognition methods targeting brain fatigue

At present, researches on brain fatigue recognition are still in the stage of single task and simple brain region network features, while researches on high-order brain functional network features and brain region state mechanisms during fatigue in multi-task scenarios are still insufficient, making it difficult to meet the needs of fatigue recognition under complex conditions. Therefore, this study utilized functional near-infrared spectroscopy (fNIRS) technology to explore the correlation and differences in the low-order and high-order brain functional network attributes of three task induced mental fatigue, and to explore the brain regions that have a major impact on mental fatigue. Self-training algorithms were used to identify the three levels of brain fatigue. The results showed that during the fatigue development, the overall connection strength of the endothelial cell metabolic activity and neural activity frequency bands of the low-order brain functional network first decreased and then increased, while the myogenic activity and heart rate activity frequency bands showed the opposite pattern. Network topology analysis indicated that from no fatigue to mild fatigue, the clustering coefficient of endothelial cell metabolic activity and myogenic activity frequency bands significantly decreased, while the characteristic path length of myogenic activity significantly increased; when experiencing severe fatigue, the small-world attribute of the neural frequency band significantly weakened. However, each frequency band maintained its small-world attribute, reflecting the self-optimization and adaptability of the network during the fatigue process. During mild fatigue, neuronal activity bands' node degree, cluster coefficient, and efficiency rose in high-order brain networks, while low-order networks showed no significant changes. As fatigue progressed, the myogenic activity bands of high-order network properties dominated, but neural bands gained prominence in mild fatigue, approaching the level of myogenic bands in severe fatigue, indicating that brain fatigue orchestrated a shift from myogenic to neural dominance in frequency bands. In addition, during the process of fatigue, the four network attributes of the high-order network cluster composed of low-order nodes related to the prefrontal cortex region, left anterior motor region, motor assist region, and left frontal lobe eye movement region significantly increased, indicating that these brain regions had a significant impact on brain fatigue status. The accuracy of using both high-order and low-order features to identify fatigue levels reached 88.095%, indicating that the combined network features of both high-order and low-order fNIRS signals could effectively detect multi-level mental fatigue, providing innovative ideas for fatigue warning.

Emergence of complex oscillatory dynamics in the neuronal networks with long activity time of inhibitory synapses

The brain displays complex dynamics, including collective oscillations, and extensive research has been conducted to understand their generation. However, our understanding of how biological constraints influence these oscillations is incomplete. This study investigates the essential properties of neuronal networks needed to generate oscillations resembling those in the brain. A simple discrete-time model of interconnected excitable elements is developed, capable of closely resembling the complex oscillations observed in biological neural networks. In the model, synaptic connections remain active for a duration exceeding individual neuron activity. We show that the inhibitory synapses must exhibit longer activity than excitatory synapses to produce a diverse range of the dynamical states, including biologically plausible oscillations. Upon meeting this condition, the transition between different dynamical states can be controlled by external stochastic input to the neurons. The study provides a comprehensive explanation for the emergence of distinct dynamical states in neural networks based on specific parameters.

Developing Cardiac Digital Twins at Scale: Insights from Personalised Myocardial Conduction Velocity

Large-cohort studies using cardiovascular imaging and diagnostic datasets have assessed cardiac anatomy, function, and outcomes, but typically do not reveal underlying biological mechanisms. Cardiac digital twins (CDTs) provide personalized physics- and physiology-constrained in-silico representations, enabling inference of multi-scale properties tied to these mechanisms. We constructed 3464 anatomically-accurate CDTs using cardiac magnetic resonance images from UK biobank and personalised their myocardial conduction velocities (CVs) from electrocardiograms (ECG), through an automated framework. We found well-known sex-specific differences in QRS duration were fully explained by myocardial anatomy, as CV remained consistent across sexes. Conversely, significant associations of CV with ageing and increased BMI suggest myocardial tissue remodelling. Novel associations were observed with left ventricular ejection fraction and mental-health phenotypes, through a phenome-wide association study, and CV was also linked with adverse clinical outcomes. Our study highlights the utility of population-based CDTs in assessing intersubject variability and uncovering strong links with mental health.

Genome-wide QTL mapping across three tissues highlights several Alzheimer's and Parkinson's disease loci potentially acting via DNA methylation

DNA methylation (DNAm) is an epigenetic mark with essential roles in disease development and predisposition. Here, we created genome-wide maps of methylation quantitative trait loci (meQTL) in three peripheral tissues and used Mendelian randomization (MR) analyses to assess the potential causal relationships between DNAm and risk for two common neurodegenerative disorders, i.e. Alzheimer's disease (AD) and Parkinson's disease (PD). Genome-wide single nucleotide polymorphism (SNP; ~5.5M sites) and DNAm (~850K CpG sites) data were generated from whole blood (n=1,058), buccal (n=1,527) and saliva (n=837) specimens. We identified between 11 and 15 million genome-wide significant (p<10-14) SNP-CpG associations in each tissue. Combining these meQTL GWAS results with recent AD/PD GWAS summary statistics by MR strongly suggests that the previously described associations between PSMC3, PICALM, and TSPAN14 and AD may be founded on differential DNAm in or near these genes. In addition, there is strong, albeit less unequivocal, support for causal links between DNAm at PRDM7 in AD as well as at KANSL1/MAPT in AD and PD. Our study adds valuable insights on AD/PD pathogenesis by combining two high-resolution "omics" domains, and the meQTL data shared along with this publication will allow like-minded analyses in other diseases.

Altered dynamical integration/segregation balance during anesthesia-induced loss of consciousness

In recent years, brain imaging studies have begun to shed light on the neural correlates of physiologically-reversible altered states of consciousness such as deep sleep, anesthesia, and psychedelic experiences. The emerging consensus is that normal waking consciousness requires the exploration of a dynamical repertoire enabling both global integration i.e., long-distance interactions between brain regions, and segregation, i.e., local processing in functionally specialized clusters. Altered states of consciousness have notably been characterized by a tipping of the integration/segregation balance away from this equilibrium. Historically, functional MRI (fMRI) has been the modality of choice for such investigations. However, fMRI does not enable characterization of the integration/segregation balance at sub-second temporal resolution. Here, we investigated global brain spatiotemporal patterns in electrocorticography (ECoG) data of a monkey (Macaca fuscata) under either ketamine or propofol general anesthesia. We first studied the effects of these anesthetics from the perspective of band-specific synchronization across the entire ECoG array, treating individual channels as oscillators. We further aimed to determine whether synchrony within spatially localized clusters of oscillators was differently affected by the drugs in comparison to synchronization over spatially distributed subsets of ECoG channels, thereby quantifying changes in integration/segregation balance on physiologically-relevant time scales. The findings reflect global brain dynamics characterized by a loss of long-range integration in multiple frequency bands under both ketamine and propofol anesthesia, most pronounced in the beta (13-30 Hz) and low-gamma bands (30-80 Hz), and with strongly preserved local synchrony in all bands.

Neural network extrapolation to distant regions of the protein fitness landscape

Machine learning (ML) has transformed protein engineering by constructing models of the underlying sequence-function landscape to accelerate the discovery of new biomolecules. ML-guided protein design requires models, trained on local sequence-function information, to accurately predict distant fitness peaks. In this work, we evaluate neural networks' capacity to extrapolate beyond their training data. We perform model-guided design using a panel of neural network architectures trained on protein G (GB1)-Immunoglobulin G (IgG) binding data and experimentally test thousands of GB1 designs to systematically evaluate the models' extrapolation. We find each model architecture infers markedly different landscapes from the same data, which give rise to unique design preferences. We find simpler models excel in local extrapolation to design high fitness proteins, while more sophisticated convolutional models can venture deep into sequence space to design proteins that fold but are no longer functional. Our findings highlight how each architecture's inductive biases prime them to learn different aspects of the protein fitness landscape.

A supervised data-driven spatial filter denoising method for speech artifacts in intracranial electrophysiological recordings

Neurosurgical procedures that enable direct brain recordings in awake patients offer unique opportunities to explore the neurophysiology of human speech. The scarcity of these opportunities and the altruism of participating patients compel us to apply the highest rigor to signal analysis. Intracranial electroencephalography (iEEG) signals recorded during overt speech can contain a speech artifact that tracks the fundamental frequency (F0) of the participant's voice, involving the same high-gamma frequencies that are modulated during speech production and perception. To address this artifact, we developed a spatial-filtering approach to identify and remove acoustic-induced contaminations of the recorded signal. We found that traditional reference schemes jeopardized signal quality, whereas our data-driven method denoised the recordings while preserving underlying neural activity.

Understanding the effects of cortical gyrification in tACS: insights from experiments and computational models

The alpha rhythm is often associated with relaxed wakefulness or idling and is altered by various factors. Abnormalities in the alpha rhythm have been linked to several neurological and psychiatric disorders, including Alzheimer's disease. Transcranial alternating current stimulation (tACS) has been proposed as a potential tool to restore a disrupted alpha rhythm in the brain by stimulating at the individual alpha frequency (IAF), although some research has produced contradictory results. In this study, we applied an IAF-tACS protocol over parieto-occipital areas to a sample of healthy subjects and measured its effects over the power spectra. Additionally, we used computational models to get a deeper understanding of the results observed in the experiment. Both experimental and numerical results showed an increase in alpha power of 8.02% with respect to the sham condition in a widespread set of regions in the cortex, excluding some expected parietal regions. This result could be partially explained by taking into account the orientation of the electric field with respect to the columnar structures of the cortex, showing that the gyrification in parietal regions could generate effects in opposite directions (hyper-/depolarization) at the same time in specific brain regions. Additionally, we used a network model of spiking neuronal populations to explore the effects that these opposite polarities could have on neural activity, and we found that the best predictor of alpha power was the average of the normal components of the electric field. To sum up, our study sheds light on the mechanisms underlying tACS brain activity modulation, using both empirical and computational approaches. Non-invasive brain stimulation techniques hold promise for treating brain disorders, but further research is needed to fully understand and control their effects on brain dynamics and cognition. Our findings contribute to this growing body of research and provide a foundation for future studies aimed at optimizing the use of non-invasive brain stimulation in clinical settings.

Editorial to the Special Issue “Information Processing in Neuronal Circuits and Systems”

The nervous system processes sensory information through a hierarchical structure with multiple processing stages [...]

Phase response approaches to neural activity models with distributed delay

In weakly coupled neural oscillator networks describing brain dynamics, the coupling delay is often distributed. We present a theoretical framework to calculate the phase response curve of distributed-delay induced limit cycles with infinite-dimensional phase space. Extending previous works, in which non-delayed or discrete-delay systems were investigated, we develop analytical results for phase response curves of oscillatory systems with distributed delay using Gaussian and log-normal delay distributions. We determine the scalar product and normalization condition for the linearized adjoint of the system required for the calculation of the phase response curve. As a paradigmatic example, we apply our technique to the Wilson-Cowan oscillator model of excitatory and inhibitory neuronal populations under the two delay distributions. We calculate and compare the phase response curves for the Gaussian and log-normal delay distributions. The phase response curves obtained from our adjoint calculations match those compiled by the direct perturbation method, thereby proving that the theory of weakly coupled oscillators can be applied successfully for distributed-delay-induced limit cycles. We further use the obtained phase response curves to derive phase interaction functions and determine the possible phase locked states of multiple inter-coupled populations to illuminate different synchronization scenarios. In numerical simulations, we show that the coupling delay distribution can impact the stability of the synchronization between inter-coupled gamma-oscillatory networks.

Youth ice hockey COVID-19 protocols and prevention of sport-related transmission

OBJECTIVES

This observational study evaluated the impact of return-to-play protocols to prevent transmission of SARS-CoV-2 in a youth ice hockey programme in Virginia Beach, Virginia.

METHODS

Following an outbreak of SARS-CoV-2 in November 2020, a COVID-19 Response Team evaluated the epidemiological data to identify transmission dynamics and develop enhanced protocols to prevent transmission. During the subsequent 18-week study period, incident cases were investigated to identify the likely transmission source; testing, quarantine and isolation recommendations were provided to families in accordance with Centers for Disease Control and Prevention guidelines.

RESULTS

Simple but stringent protocols were implemented among 148 youth ice hockey players ages 6-18. Players were required to arrive at the rink in full gear; locker rooms were closed, building entry was limited to one parent per player, and masks were required at all times except for players on the ice. Following implementation of the enhanced protocols, more than 500 practices and games were completed with at least 15 858 athlete-hours of exposure and no within-programme COVID-19 transmission was detected despite high community incidence and sporadic household exposures.

CONCLUSION

This study suggests indoor youth sports can operate safely with appropriate protocols in place, even within communities of high COVID-19 transmission, even when athletes are not yet vaccinated or wearing masks during play. Transmission appears to be more likely in congested indoor areas involving adults than on the ice during play. Protocols should be developed in collaboration with programme participants. Strong collaboration in the interest of youth sports can motivate adoption of protocols which prevent within-team transmission.

Mechanisms of Flexible Information Sharing through Noisy Oscillations

Simple Summary

To properly interact with our environment, the brain must be able to identify external stimuli, process them, and make the right decisions all in a short time. This may involve several brain regions interacting together by sharing information birectionally via rhythmic activity. Such flexibility requires the functional connectivity between the areas to be dynamic, and a key question is the relevant parameter and operating regimes that make this possible in spite of fixed structural connectivity. Working towards this goal, we consider two coupled brain regions, each of which exhibits a noisy rhythm, a commonly observed type of neural activity. Such rhythms can be induced by the stochasticity in the neural circuitry, or be autonomously generated through nonlinearities and not necessitating noise. For these two types of rhythms, we computed the amount of information shared between the brain areas and the preferred direction(s) of sharing. We found that without the coupling delay, the flexibility needed by the brain to perform cognitive tasks requires the rhythms to be autogenerated rather than noise-induced. This is the case even with asymmetry or heterogeneity. This suggests that the importance of the dynamical regime has to be taken into account when modeling interacting neural rhythms from an information theoretical point of view.

Abstract

Brain areas must be able to interact and share information in a time-varying, dynamic manner on a fast timescale. Such flexibility in information sharing has been linked to the synchronization of rhythm phases between areas. One definition of flexibility is the number of local maxima in the delayed mutual information curve between two connected areas. However, the precise relationship between phase synchronization and information sharing is not clear, nor is the flexibility in the face of the fixed structural connectivity and noise. Here, we consider two coupled oscillatory excitatory-inhibitory networks connected through zero-delay excitatory connections, each of which mimics a rhythmic brain area. We numerically compute phase-locking and delayed mutual information between the phases of excitatory local field potential (LFPs) of the two networks, which measures the shared information and its direction. The flexibility in information sharing is shown to depend on the dynamical origin of oscillations, and its properties in different regimes are found to persist in the presence of asymmetry in the connectivity as well as system heterogeneity. For coupled noise-induced rhythms (quasi-cycles), phase synchronization is robust even in the presence of asymmetry and heterogeneity. However, they do not show flexibility, in contrast to noise-perturbed rhythms (noisy limit cycles), which are shown here to exhibit two local information maxima, i.e., flexibility. For quasi-cycles, phase difference and information measures for the envelope-phase dynamics obtained from previous analytical work using the Stochastic Averaging Method (SAM) are found to be in good qualitative agreement with those obtained from the original dynamics. The relation between phase synchronization and communication patterns is not trivial, particularly in the noisy limit cycle regime. There, complex patterns of information sharing can be observed for a single value of the phase difference. The mechanisms reported here can be extended to I-I networks since their phase synchronizations are similar. Our results set the stage for investigating information sharing between several connected noisy rhythms in neural and other complex biological networks.

Information Transmission in Delay-Coupled Neuronal Circuits in the Presence of a Relay Population

Synchronization between neuronal populations is hypothesized to play a crucial role in the communication between brain networks. The binding of features, or the association of computations occurring in spatially segregated areas, is supposed to take place when a stable synchronization between cortical areas occurs. While a direct cortico-cortical connection typically fails to support this mechanism, the participation of a third area, a relay element, mediating in the communication was proposed to overcome this limitation. Among the different structures that could play the role of coordination during the binding process, the thalamus is the best placed region to carry out this task. In this paper we study how information flows in a canonical motif that mimics a cortico-thalamo-cortical circuit composed by three mutually coupled neuronal populations (also called the V-motif). Through extensive numerical simulations, we found that the amount of information transferred between the oscillating neuronal populations is determined by the delay in their connections and the mismatch in their oscillation frequencies (detuning). While the transmission from a cortical population is mostly restricted to positive detuning, transmission from the relay (thalamic) population to the cortical populations is robust for a broad range of detuning values, including negative values, while permitting feedback communication from the cortex at high frequencies, thus supporting robust bottom up and top down interaction. In this case, a strong feedback transmission between the cortex to thalamus supports the possibility of robust bottom-up and top-down interactions in this motif. Interestingly, adding a cortico-cortical bidirectional connection to the V-motif (C-motif) expands the dynamics of the system with distinct operation modes. While overall transmission efficiency is decreased, new communication channels establish cortico-thalamo-cortical association loops. Switching between operation modes depends on the synaptic strength of the cortico-cortical connections. Our results support a role of the transthalamic V-motif in the binding of spatially segregated cortical computations, and suggest an important regulatory role of the direct cortico-cortical connection.