39 research outputs found
Measuring Neuronal Branching Patterns Using Model-Based Approach
Neurons have complex branching systems which allow them to communicate with thousands of other neurons. Thus understanding neuronal geometry is clearly important for determining connectivity within the network and how this shapes neuronal function. One of the difficulties in uncovering relationships between neuronal shape and its function is the problem of quantifying complex neuronal geometry. Even by using multiple measures such as: dendritic length, distribution of segments, direction of branches, etc, a description of three dimensional neuronal embedding remains incomplete. To help alleviate this problem, here we propose a new measure, a shape diffusiveness index (SDI), to quantify spatial relations between branches at the local and global scale. It was shown that growth of neuronal trees can be modeled by using diffusion limited aggregation (DLA) process. By measuring “how easy” it is to reproduce the analyzed shape by using the DLA algorithm it can be measured how “diffusive” is that shape. Intuitively, “diffusiveness” measures how tree-like is a given shape. For example shapes like an oak tree will have high values of SDI. This measure is capturing an important feature of dendritic tree geometry, which is difficult to assess with other measures. This approach also presents a paradigm shift from well-defined deterministic measures to model-based measures, which estimate how well a model with specific properties can account for features of analyzed shape
Spatial embedding of neuronal trees modeled by diffusive growth
The relative importance of the intrinsic and extrinsic factors determining
the variety of geometric shapes exhibited by dendritic trees remains unclear.
This question was addressed by developing a model of the growth of dendritic
trees based on diffusion-limited aggregation process. The model reproduces
diverse neuronal shapes (i.e., granule cells, Purkinje cells, the basal and
apical dendrites of pyramidal cells, and the axonal trees of interneurons) by
changing only the size of the growth area, the time span of pruning, and the
spatial concentration of 'neurotrophic particles'. Moreover, the presented
model shows how competition between neurons can affect the shape of the
dendritic trees. The model reveals that the creation of complex (but
reproducible) dendrite-like trees does not require precise guidance or an
intrinsic plan of the dendrite geometry. Instead, basic environmental factors
and the simple rules of diffusive growth adequately account for the spatial
embedding of different types of dendrites observed in the cortex. An example
demonstrating the broad applicability of the algorithm to model diverse types
of tree structures is also presented. Key words: Diffusion-limited aggregation;
Neuronal morphology; Dendrites; Growth model; tree; dendritic geometry.Comment: 9 pages, 6 figure
Creation of a Deep Convolutional Auto-Encoder in Caffe
The development of a deep (stacked) convolutional auto-encoder in the Caffe
deep learning framework is presented in this paper. We describe simple
principles which we used to create this model in Caffe. The proposed model of
convolutional auto-encoder does not have pooling/unpooling layers yet. The
results of our experimental research show comparable accuracy of dimensionality
reduction in comparison with a classic auto-encoder on the example of MNIST
dataset.Comment: 9 pages, 7 figures, 5 tables, 34 references in the list; Added
references, corrected Table 3, changed several paragraphs in the tex
Default activity patterns at the neocortical microcircuit level
Even in absence of sensory stimuli cortical networks exhibit complex, self-organized activity patterns. While the function of those spontaneous patterns of activation remains poorly understood, recent studies both in vivo and in vitro have demonstrated that neocortical neurons activate in a surprisingly similar sequential order both spontaneously and following input into cortex. For example, neurons that tend to fire earlier within spontaneous bursts of activity also fire earlier than other neurons in response to sensory stimuli. These “default patterns” can last hundreds of milliseconds and are strongly conserved under a variety of conditions. In this paper, we will review recent evidence for these default patterns at the local cortical level. We speculate that cortical architecture imposes common constraints on spontaneous and evoked activity flow, which result in the similarity of the patterns
Computational Properties of the Hippocampus Increase the Efficiency of Goal-Directed Foraging through Hierarchical Reinforcement Learning
Sherpa Romeo green journal; open accessThe mammalian brain is thought to use a version of Model-based Reinforcement Learning (MBRL) to guide “goal-directed” behavior, wherein animals consider goals and make plans to acquire desired outcomes. However, conventional MBRL algorithms do not fully explain animals’ ability to rapidly adapt to environmental changes, or learn multiple complex tasks. They also require extensive computation, suggesting that goal-directed behavior is cognitively expensive. We propose here that key features of processing in the hippocampus support a flexible MBRL mechanism for spatial navigation that is computationally efficient and can adapt quickly to change. We investigate this idea by implementing a computational MBRL framework that incorporates features inspired by computational properties of the hippocampus: a hierarchical representation of space, “forward sweeps” through future spatial trajectories, and context-driven remapping of place cells. We find that a hierarchical abstraction of space greatly reduces the computational load (mental effort) required for adaptation to changing environmental conditions, and allows efficient scaling to large problems. It also allows abstract knowledge gained at high levels to guide adaptation to new obstacles. Moreover, a context-driven remapping mechanism allows learning and memory of multiple tasks. Simulating dorsal or ventral hippocampal lesions in our computational framework qualitatively reproduces behavioral deficits observed in rodents with analogous lesions. The framework may thus embody key features of how the brain organizes model-based RL to efficiently solve navigation and other difficult tasks.Ye
Anodal transcranial direct current stimulation with monopolar pulses improves limb use after stroke by enhancing inter-hemispheric coherence
UP-DOWN cortical dynamics reflect state transitions in a bistable network
In the idling brain, neuronal circuits transition between periods of sustained firing (UP state) and quiescence (DOWN state), a pattern the mechanisms of which remain unclear. Here we analyzed spontaneous cortical population activity from anesthetized rats and found that UP and DOWN durations were highly variable and that population rates showed no significant decay during UP periods. We built a network rate model with excitatory (E) and inhibitory (I) populations exhibiting a novel bistable regime between a quiescent and an inhibition-stabilized state of arbitrarily low rate. Fluctuations triggered state transitions, while adaptation in E cells paradoxically caused a marginal decay of E-rate but a marked decay of I-rate in UP periods, a prediction that we validated experimentally. A spiking network implementation further predicted that DOWN-to-UP transitions must be caused by synchronous high-amplitude events. Our findings provide evidence of bistable cortical networks that exhibit non-rhythmic state transitions when the brain rests
Involvement of fast-spiking cells in ictal sequences during spontaneous seizures in rats with chronic temporal lobe epilepsy
Epileptic seizures represent altered neuronal network dynamics, but the temporal evolution and cellular substrates of the neuronal activity patterns associated with spontaneous seizures are not fully understood. We used simultaneous recordings from multiple neurons in the hippocampus and neocortex of rats with chronic temporal lobe epilepsy to demonstrate that subsets of cells discharge in a highly stereotypical sequential pattern during ictal events, and that these stereotypical patterns were reproducible across consecutive seizures. In contrast to the canonical view that principal cell discharges dominate ictal events, the ictal sequences were predominantly composed of fast-spiking, putative inhibitory neurons, which displayed unusually strong coupling to local field potential even before seizures. The temporal evolution of activity was characterized by unique dynamics where the most correlated neuronal pairs before seizure onset displayed the largest increases in correlation strength during the seizures. These results demonstrate the selective involvement of fast spiking interneurons in structured temporal sequences during spontaneous ictal events in hippocampal and neocortical circuits in experimental models of chronic temporal lobe epilepsy