Quantitative Biology

Recently, visual perception (VP) and visual imagery (VI) paradigms are investigated in several brain-computer interface (BCI) studies. VP and VI are defined as a changing of brain signals when perceiving and memorizing visual information, respectively. These paradigms could be alternatives to the previous visual-based paradigms which have limitations such as fatigue and low information transfer rates (ITR). In this study, we analyzed VP and VI to investigate the possibility to control BCI. First, we conducted a time-frequency analysis with event-related spectral perturbation. In addition, two types of decoding accuracies were obtained with convolutional neural network to verify whether the brain signals can be distinguished from each class in the VP and whether they can be differentiated with VP and VI paradigms. As a result, the 6-class classification performance in VP was 32.56% and the binary classification performance which classifies two paradigms was 90.16%.

The evolution of biological brains has always been contingent on their embodiment within their respective environments, in which survival required appropriate navigation and manipulation skills. Studying such interactions thus represents an important aspect of computational neuroscience and, by extension, a topic of interest for neuromorphic engineering. Here, we present three examples of embodiment on the BrainScaleS-2 architecture, in which dynamical timescales of both agents and environment are accelerated by several orders of magnitude with respect to their biological archetypes.

The human brains are organized into hierarchically modular networks facilitating efficient and stable information processing and supporting diverse cognitive processes during the course of development. While the remarkable reconfiguration of functional brain network has been firmly established in early life, all these studies investigated the network development from a "single-scale" perspective, which ignore the richness engendered by its hierarchical nature. To fill this gap, this paper leveraged a longitudinal infant resting-state functional magnetic resonance imaging dataset from birth to 2 years of age, and proposed an advanced methodological framework to delineate the multi-scale reconfiguration of functional brain network during early development. Our proposed framework is consist of two parts. The first part developed a novel two-step multi-scale module detection method that could uncover efficient and consistent modular structure for longitudinal dataset from multiple scales in a completely data-driven manner. The second part designed a systematic approach that employed the linear mixed-effect model to four global and nodal module-related metrics to delineate scale-specific age-related changes of network organization. By applying our proposed methodological framework on the collected longitudinal infant dataset, we provided the first evidence that, in the first 2 years of life, the brain functional network is co-evolved at different scales, where each scale displays the unique reconfiguration pattern in terms of modular organization.

Wright and Bourkes compelling article rightly points out that existing models of embryogenesis fail to explain the mechanisms and functional significance of the dynamic connections among neurons. We pursue their account of Dynamic Logic by appealing to the Markov blanket formalism that underwrites the Free Energy Principle. We submit that this allows one to model embryogenesis as self-organisation in a dynamical system that minimises free-energy. The ensuing formalism may be extended to also explain the autonomous emergence of cognition, specifically in the brain, as a dynamic self-assembling process.

Cognitive states are involving in our daily life, which motivates us to explore them and understand them by a vast variety of perspectives. Among these perspectives, brain connectivity is increasingly receiving attention in recent years. It is the right time to summarize the past achievements, serving as a cornerstone for the upcoming progress in the field. In this chapter, the definition of the cognitive state is first given and the cognitive states that are frequently investigated are then outlined. The introduction of the methods for estimating connectivity strength and graph theoretical metrics is followed. Subsequently, each cognitive state is separately described and the progress in cognitive state investigation is summarized, including analysis, understanding, and decoding. We concentrate on the literature ascertaining macro-scale representations of cognitive states from the perspective of brain connectivity and give an overview of achievements related to cognitive states to date, especially within the past ten years. The discussions and future prospects are stated at the end of the chapter.

Memory for the past makes use of a record of what happened when---a function over past time. Time cells in the hippocampus and temporal context cells in the entorhinal cortex both code for events as a function of past time, but with very different receptive fields. Time cells in the hippocampus can be understood as a compressed estimate of events as a function of the past. Temporal context cells in the entorhinal cortex can be understood as the Laplace transform of that function, respectively. Other functional cell types in the hippocampus and related regions, including border cells, place cells, trajectory coding, splitter cells, can be understood as coding for functions over space or past movements or their Laplace transforms. More abstract quantities, like distance in an abstract conceptual space or numerosity could also be mapped onto populations of neurons coding for the Laplace transform of functions over those variables. Quantitative cognitive models of memory and evidence accumulation can also be specified in this framework allowing constraints from both behavior and neurophysiology. More generally, the computational power of the Laplace domain could be important for efficiently implementing data-independent operators, which could serve as a basis for neural models of a very broad range of cognitive computations.

The auto feature extraction capability of deep neural networks (DNN) endows them the potentiality for analysing complicated electroencephalogram (EEG) data captured from brain functionality research. This work investigates the potential coherent correspondence between the region-of-interest (ROI) for DNN to explore, and ROI for conventional neurophysiological oriented methods to work with, exemplified in the case of working memory study. The attention mechanism induced by global average pooling (GAP) is applied to a public EEG dataset of working memory, to unveil these coherent ROIs via a classification problem. The result shows the alignment of ROIs from different research disciplines. This work asserts the confidence and promise of utilizing DNN for EEG data analysis, albeit in lack of the interpretation to network operations.

The idealisation of neuronal pulses as δ -spikes is a convenient approach in neuroscience but can sometimes lead to erroneous conclusions. We investigate the effect of a finite pulse-width on the dynamics of balanced neuronal networks. In particular, we study two populations of identical excitatory and inhibitory neurons in a random network of phase oscillators coupled through exponential pulses with different widths. We consider three coupling functions, inspired by leaky integrate-and-fire neurons with delay and type-I phase-response curves. By exploring the role of the pulse-widths for different coupling strengths we find a robust collective irregular dynamics, which collapses onto a fully synchronous regime if the inhibitory pulses are sufficiently wider than the excitatory ones. The transition to synchrony is accompanied by hysteretic phenomena (i.e. the co-existence of collective irregular and synchronous dynamics). Our numerical results are supported by a detailed scaling and stability analysis of the fully synchronous solution. A conjectured first-order phase transition emerging for δ -spikes is smoothed out for finite-width pulses.

The advancement of single cell RNA-sequencing technologies has led to an explosion of cell type definitions across multiple organs and organisms. While standards for data and metadata intake are arising, organization of cell types has largely been left to individual investigators, resulting in widely varying nomenclature and limited alignment between taxonomies. To facilitate cross-dataset comparison, the Allen Institute created the Common Cell type Nomenclature (CCN) for matching and tracking cell types across studies that is qualitatively similar to gene transcript management across different genome builds. The CCN can be readily applied to new or established taxonomies and was applied herein to diverse cell type datasets derived from multiple quantifiable modalities. The CCN facilitates assigning accurate yet flexible cell type names in the mammalian cortex as a step towards community-wide efforts to organize multi-source, data-driven information related to cell type taxonomies from any organism.

How can memories be maintained from days to a lifetime, given turnover of proteins that underlie expression of long-term synaptic potentiation (LTP)? One likely solution relies on synaptic positive feedback loops, prominently including persistent activation of CaM kinase II (CaMKII) and self-activated synthesis of protein kinase M zeta (PKM). Recent studies also suggest positive feedback based on recurrent synaptic reactivation within neuron assemblies, or engrams, is necessary to maintain memories. The relative importance of these feedback mechanisms is controversial. To explore the likelihood that each mechanism is necessary or sufficient, we simulated LTP maintenance with a simplified model incorporating persistent kinase activation, synaptic tagging, and preferential reactivation of strong synapses, and analyzed implications of recent data. We simulated three model variants, each maintaining LTP with one feedback loop: self-activated PKM synthesis (variant I); self-activated CamKII (variant II); and recurrent reactivation of strengthened synapses (variant III). Variant I requires and predicts that PKM must contribute to synaptic tagging. Variant II maintains LTP and suggests persistent CaMKII activation could maintain PKM activity, a feedforward interaction not previously considered. However we note data challenging this feedback loop. In variant III synaptic reactivation drives, and thus predicts, recurrent or persistent activity elevations of CamKII and other necessary kinases, plausibly contributing to empirically persistent elevation of PKM levels. Reactivation is thus predicted to sustain recurrent rounds of synaptic tagging and incorporation of plasticity-related proteins. We also suggest (model variant IV) that synaptic reactivation and autonomous kinase activation could synergistically maintain LTP. We propose experiments that could discriminate these maintenance mechanisms.