Computational neuroscience and neuroinformatics: Recent progress and resources

Relationships and representations of brain structures, connectivity, dynamics and functions

The review explores the complex interplay between brain structures and their associated functions, presenting a diversity of hierarchical models that enhances our understanding of these relationships. Central to this approach are structure-function flow diagrams, which offer a visual representation of how specific neuroanatomical structures are linked to their functional roles. These diagrams are instrumental in mapping the intricate connections between different brain regions, providing a clearer understanding of how functions emerge from the underlying neural architecture. The study details innovative attempts to develop new functional hierarchies that integrate structural and functional data. These efforts leverage recent advancements in neuroimaging techniques such as fMRI, EEG, MEG, and PET, as well as computational models that simulate neural dynamics. By combining these approaches, the study seeks to create a more refined and dynamic hierarchy that can accommodate the brain's complexity, including its capacity for plasticity and adaptation. A significant focus is placed on the overlap of structures and functions within the brain. The manuscript acknowledges that many brain regions are multifunctional, contributing to different cognitive and behavioral processes depending on the context. This overlap highlights the need for a flexible, non-linear hierarchy that can capture the brain's intricate functional landscape. Moreover, the study examines the interdependence of these functions, emphasizing how the loss or impairment of one function can impact others. Another crucial aspect discussed is the brain's ability to compensate for functional deficits following neurological diseases or injuries. The investigation explores how the brain reorganizes itself, often through the recruitment of alternative neural pathways or the enhancement of existing ones, to maintain functionality despite structural damage. This compensatory mechanism underscores the brain's remarkable plasticity, demonstrating its ability to adapt and reconfigure itself in response to injury, thereby ensuring the continuation of essential functions. In conclusion, the study presents a system of brain functions that integrates structural, functional, and dynamic perspectives. It offers a robust framework for understanding how the brain's complex network of structures supports a wide range of cognitive and behavioral functions, with significant implications for both basic neuroscience and clinical applications.

Targeting Ferroptosis in Rare Neurological Disorders Including Pediatric Conditions: Innovations and Therapeutic Challenges

Ferroptosis, characterized by iron dependency and lipid peroxidation, has emerged as a key mechanism underlying neurodegeneration in rare neurological disorders. These conditions, often marked by significant therapeutic gaps and high unmet medical needs, present unique challenges for intervention development. This review examines the involvement of ferroptosis in rare neurological disease pathogenesis, focusing on its role in oxidative damage and neuronal dysfunction. We explore recent pharmacological advancements, including iron chelators, lipid peroxidation blockers, and antioxidant-based strategies, designed to target ferroptosis. While these approaches show promise, challenges such as disease heterogeneity, limited diagnostic tools, and small patient cohorts hinder progress. Furthermore, we discuss the translational and regulatory barriers to implementing ferroptosis-based therapies in clinical practice. By addressing these obstacles and fostering innovative solutions, this review underscores the potential of ferroptosis-targeting strategies to revolutionize treatment paradigms for rare neurological disorders.

The Roles of Potassium and Calcium Currents in the Bistable Firing Transition

Healthy brains display a wide range of firing patterns, from synchronized oscillations during slow-wave sleep to desynchronized firing during movement. These physiological activities coexist with periods of pathological hyperactivity in the epileptic brain, where neurons can fire in synchronized bursts. Most cortical neurons are pyramidal regular spiking (RS) cells with frequency adaptation and do not exhibit bursts in current-clamp experiments (in vitro). In this work, we investigate the transition mechanism of spike-to-burst patterns due to slow potassium and calcium currents, considering a conductance-based model of a cortical RS cell. The joint influence of potassium and calcium ion channels on high synchronous patterns is investigated for different synaptic couplings (gsyn) and external current inputs (I). Our results suggest that slow potassium currents play an important role in the emergence of high-synchronous activities, as well as in the spike-to-burst firing pattern transitions. This transition is related to the bistable dynamics of the neuronal network, where physiological asynchronous states coexist with pathological burst synchronization. The hysteresis curve of the coefficient of variation of the inter-spike interval demonstrates that a burst can be initiated by firing states with neuronal synchronization. Furthermore, we notice that high-threshold (IL) and low-threshold (IT) ion channels play a role in increasing and decreasing the parameter conditions (gsyn and I) in which bistable dynamics occur, respectively. For high values of IL conductance, a synchronous burst appears when neurons are weakly coupled and receive more external input. On the other hand, when the conductance IT increases, higher coupling and lower I are necessary to produce burst synchronization. In light of our results, we suggest that channel subtype-specific pharmacological interactions can be useful to induce transitions from pathological high bursting states to healthy states.

The Role of Potassium and Calcium Currents in the Bistable Firing Transition

Healthy brains display a wide range of firing patterns, from synchronized oscillations during slowwave sleep to desynchronized firing during movement. These physiological activities coexist with periods of pathological hyperactivity in the epileptic brain, where neurons can fire in synchronized bursts. Most cortical neurons are pyramidal regular spiking cells (RS) with frequency adaptation and do not exhibit bursts in current-clamp experiments ( in vitro ). In this work, we investigate the transition mechanism of spike-to-burst patterns due to slow potassium and calcium currents, considering a conductance-based model of a cortical RS cell. The joint influence of potassium and calcium ion channels on high synchronous patterns is investigated for different synaptic couplings ( g syn ) and external current inputs ( I ). Our results suggest that slow potassium currents play an important role in the emergence of high-synchronous activities, as well as in the spike-to-burst firing pattern transitions. This transition is related to bistable dynamics of the neuronal network, where physiological asynchronous states coexist with pathological burst synchronization. The hysteresis curve of the coefficient of variation of the inter-spike interval demonstrates that a burst can be initiated by firing states with neuronal synchronization. Furthermore, we notice that high-threshold ( I L ) and low-threshold ( I T ) ion channels play a role in increasing and decreasing the parameter conditions ( g syn and I ) in which bistable dynamics occur, respectively. For high values of I L conductance, a synchronous burst appears when neurons are weakly coupled and receive more external input. On the other hand, when the conductance I T increases, higher coupling and lower I are necessary to produce burst synchronization. In light of our results, we suggest that channel subtype-specific pharmacological interactions can be useful to induce transitions from pathological high bursting states to healthy states.

Data management strategy for a collaborative research center

The importance of effective research data management (RDM) strategies to support the generation of Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience data grows with each advance in data acquisition techniques and research methods. To maximize the impact of diverse research strategies, multidisciplinary, large-scale neuroscience research consortia face a number of unsolved challenges in RDM. While open science principles are largely accepted, it is practically difficult for researchers to prioritize RDM over other pressing demands. The implementation of a coherent, executable RDM plan for consortia spanning animal, human, and clinical studies is becoming increasingly challenging. Here, we present an RDM strategy implemented for the Heidelberg Collaborative Research Consortium. Our consortium combines basic and clinical research in diverse populations (animals and humans) and produces highly heterogeneous and multimodal research data (e.g., neurophysiology, neuroimaging, genetics, behavior). We present a concrete strategy for initiating early-stage RDM and FAIR data generation for large-scale collaborative research consortia, with a focus on sustainable solutions that incentivize incremental RDM while respecting research-specific requirements.

Italian, European, and international neuroinformatics efforts: An overview

Neuroinformatics is a research field that focusses on software tools capable of identifying, analysing, modelling, organising and sharing multiscale neuroscience data. Neuroinformatics has exploded in the last two decades with the emergence of the Big Data phenomenon, characterised by the so-called 3Vs (volume, velocity and variety), which provided neuroscientists with an improved ability to acquire and process data faster and more cheaply thanks to technical improvements in clinical, genomic and radiological technologies. This situation has led to a 'data deluge', as neuroscientists can routinely collect more study data in a few days than they could in a year just a decade ago. To address this phenomenon, several neuroimaging-focussed neuroinformatics platforms have emerged, funded by national or transnational agencies, with the following goals: (i) development of tools for archiving and organising analytical data (XNAT, REDCap and LabKey); (ii) development of data-driven models evolving from reductionist approaches to multidimensional models (RIN, IVN, HBD, EuroPOND, E-DADS and GAAIN BRAIN); and (iii) development of e-infrastructures to provide sufficient computational power and storage resources (neuGRID, HBP-EBRAINS, LONI and CONP). Although the scenario is still fragmented, there are technological and economical attempts at both national and international levels to introduce high standards for open and Findable, Accessible, Interoperable and Reusable (FAIR) neuroscience worldwide.

Optical Imaging in Brainsmatics

When neuroscience’s focus moves from molecular and cellular level to systems level, information technology mixes in and cultivates a new branch neuroinformatics. Especially under the investments of brain initiatives all around the world, brain atlases and connectomics are identified as the substructure to understand the brain. We think it is time to call for a potential interdisciplinary subject, brainsmatics, referring to brain-wide spatial informatics science and emphasizing on precise positioning information affiliated to brain-wide connectome, genome, proteome, transcriptome, metabolome, etc. Brainsmatics methodology includes tracing, surveying, visualizing, and analyzing brain-wide spatial information. Among all imaging techniques, optical imaging is the most appropriate solution to achieve whole-brain connectome in consistent single-neuron resolution. This review aims to introduce contributions of optical imaging to brainsmatics studies, especially the major strategies applied in tracing and surveying processes. After discussions on the state-of-the-art technology, the development objectives of optical imaging in brainsmatics field are suggested. We call for a global contribution to the brainsmatics field from all related communities such as neuroscientists, biologists, engineers, programmers, chemists, mathematicians, physicists, clinicians, pharmacists, etc. As the leading approach, optical imaging will, in turn, benefit from the prosperous development of brainsmatics.