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Three different computed tomography (CT) reconstruction algorithms: Filtered Back Projection (FBP), Unified Tomographic Reconstruction (UTR) and customized Simultaneous Algebraic Reconstruction Technique (cSART), have been systematically compared and evaluated using experimental data from CT scans of ten fresh mastectomy samples collected at the Imaging and Medical beamline of the Australian Synchrotron. All the scans were collected at the mean glandular dose of 2 mGy, using monochromatic X-rays with 32 keV energy, flat-panel detectors with 0.1 mm pixels and 6 meter distance between the rotation stage and the detector. Paganin's phase retrieval method was used in conjunction with all three CT reconstruction algorithms. The reconstructed images were compared in terms of the objective image quality characteristics, including spatial resolution, contrast, signal-to-noise, and contrast-to-noise ratios. The images were also evaluated by seven experienced medical imaging specialists, rating perceptible contrast, sharpness of tissue interfaces, image noise, calcification visibility and overall image quality. Of the three compared algorithms, cSART was clearly superior to UTR and FBP in terms of most measured objective image quality characteristics. At the same time, the results of the subjective quality evaluation consistently favoured the images reconstructed by FBP, followed by UTR, with cSART receiving lower scores on average. We argue that this apparent disagreement between the objective and subjective assessments of image quality can be explained by the importance assigned to image contrast in the subjective assessment, while the signal-to-noise ratio seemed to receive relatively low weighting. This study was conducted in preparation for phase-contrast breast CT imaging of live patients at Australian Synchrotron (Melbourne, Australia)., Comment: 21 pages, 5 figures, 2 tables

A growing body of research indicates that structural plasticity mechanisms are crucial for learning and memory consolidation. Starting from a simple phenomenological model, we exploit a mean-field approach to develop a theoretical framework of learning through this kind of plasticity, capable of taking into account several features of the connectivity and pattern of activity of biological neural networks, including probability distributions of neuron firing rates, selectivity of the responses of single neurons to multiple stimuli, probabilistic connection rules and noisy stimuli. More importantly, it describes the effects of stabilization, pruning and reorganization of synaptic connections. This framework is used to compute the values of some relevant quantities used to characterize the learning and memory capabilities of the neuronal network in training and testing procedures as the number of training patterns and other model parameters vary. The results are then compared with those obtained through simulations with firing-rate-based neuronal network models.

Simulation speed matters for neuroscientific research: this includes not only how quickly the simulated model time of a large-scale spiking neuronal network progresses, but also how long it takes to instantiate the network model in computer memory. On the hardware side, acceleration via highly parallel GPUs is being increasingly utilized. On the software side, code generation approaches ensure highly optimized code, at the expense of repeated code regeneration and recompilation after modifications to the network model. Aiming for a greater flexibility with respect to iterative model changes, here we propose a new method for creating network connections interactively, dynamically, and directly in GPU memory through a set of commonly used high-level connection rules. We validate the simulation performance with both consumer and data center GPUs on two neuroscientifically relevant models: a cortical microcircuit of about 77,000 leaky-integrate-and-fire neuron models and 300 million static synapses, and a two-population network recurrently connected using a variety of connection rules. With our proposed ad hoc network instantiation, both network construction and simulation times are comparable or shorter than those obtained with other state-of-the-art simulation technologies, while still meeting the flexibility demands of explorative network modeling., Comment: 29 pages, 9 figures

Sleep is essential for learning and cognition, but the mechanisms by which it stabilizes learning, supports creativity, and manages the energy consumption of networks engaged in post-sleep task have not been yet modelled. During sleep, the brain cycles between non-rapid eye movement (NREM), a mainly unconscious state characterized by collective oscillations, and rapid eye movement (REM), associated with the integrated experience of dreaming. We propose a biologically grounded two-area thalamo-cortical plastic spiking neural network model and investigate the role of NREM - REM cycles on its awake performance. We demonstrate that sleep has a positive effect on energy consumption and cognitive performance during the post-sleep awake classification task of handwritten digits. NREM and REM simulated dynamics modify the synaptic structure into a sharper representation of training experiences. Sleep-induced synaptic modifications reduce firing rates and synaptic activity without reducing cognitive performance. Also, it creates novel multi-area associations. The model leverages the apical amplification, isolation and drive experimentally grounded principles and the combination of contextual and perceptual information. In summary, the main novelty is the proposal of a multi-area plastic model that also expresses REM and integrates information during a plastic dream-like state, with cognitive and energetic benefits during post-sleep awake classification., Comment: 22 pages, 9 figures

Over the past decade there has been a growing interest in the development of parallel hardware systems for simulating large-scale networks of spiking neurons. Compared to other highly-parallel systems, GPU-accelerated solutions have the advantage of a relatively low cost and a great versatility, thanks also to the possibility of using the CUDA-C/C++ programming languages. NeuronGPU is a GPU library for large-scale simulations of spiking neural network models, written in the C++ and CUDA-C++ programming languages, based on a novel spike-delivery algorithm. This library includes simple LIF (leaky-integrate-and-fire) neuron models as well as several multisynapse AdEx (adaptive-exponential-integrate-and-fire) neuron models with current or conductance based synapses, user definable models and different devices. The numerical solution of the differential equations of the dynamics of the AdEx models is performed through a parallel implementation, written in CUDA-C++, of the fifth-order Runge-Kutta method with adaptive step-size control. In this work we evaluate the performance of this library on the simulation of a cortical microcircuit model, based on LIF neurons and current-based synapses, and on a balanced network of excitatory and inhibitory neurons, using AdEx neurons and conductance-based synapses. On these models, we will show that the proposed library achieves state-of-the-art performance in terms of simulation time per second of biological activity. In particular, using a single NVIDIA GeForce RTX 2080 Ti GPU board, the full-scale cortical-microcircuit model, which includes about 77,000 neurons and $3 \cdot 10^8$ connections, can be simulated at a speed very close to real time, while the simulation time of a balanced network of 1,000,000 AdEx neurons with 1,000 connections per neuron was about 70 s per second of biological activity.

The brain exhibits capabilities of fast incremental learning from few noisy examples, as well as the ability to associate similar memories in autonomously-created categories and to combine contextual hints with sensory perceptions. Together with sleep, these mechanisms are thought to be key components of many high-level cognitive functions. Yet, little is known about the underlying processes and the specific roles of different brain states. In this work, we exploited the combination of context and perception in a thalamo-cortical model based on a soft winner-take-all circuit of excitatory and inhibitory spiking neurons. After calibrating this model to express awake and deep-sleep states with features comparable with biological measures, we demonstrate the model capability of fast incremental learning from few examples, its resilience when proposed with noisy perceptions and contextual signals, and an improvement in visual classification after sleep due to induced synaptic homeostasis and association of similar memories.

The occurrence of sleep passed through the evolutionary sieve and is widespread in animal species. Sleep is known to be beneficial to cognitive and mnemonic tasks, while chronic sleep deprivation is detrimental. Despite the importance of the phenomenon, a complete understanding of its functions and underlying mechanisms is still lacking. In this paper, we show interesting effects of deep-sleep-like slow oscillation activity on a simplified thalamo-cortical model which is trained to encode, retrieve and classify images of handwritten digits. During slow oscillations, spike-timing-dependent-plasticity (STDP) produces a differential homeostatic process. It is characterized by both a specific unsupervised enhancement of connections among groups of neurons associated to instances of the same class (digit) and a simultaneous down-regulation of stronger synapses created by the training. This hierarchical organization of post-sleep internal representations favours higher performances in retrieval and classification tasks. The mechanism is based on the interaction between top-down cortico-thalamic predictions and bottom-up thalamo-cortical projections during deep-sleep-like slow oscillations. Indeed, when learned patterns are replayed during sleep, cortico-thalamo-cortical connections favour the activation of other neurons coding for similar thalamic inputs, promoting their association. Such mechanism hints at possible applications to artificial learning systems., Comment: 11 pages, 5 figures, v5 is the final version published on Scientific Reports journal

Communicative interactions involve a kind of procedural knowledge that is used by the human brain for processing verbal and nonverbal inputs and for language production. Although considerable work has been done on modeling human language abilities, it has been difficult to bring them together to a comprehensive tabula rasa system compatible with current knowledge of how verbal information is processed in the brain. This work presents a cognitive system, entirely based on a large-scale neural architecture, which was developed to shed light on the procedural knowledge involved in language elaboration. The main component of this system is the central executive, which is a supervising system that coordinates the other components of the working memory. In our model, the central executive is a neural network that takes as input the neural activation states of the short-term memory and yields as output mental actions, which control the flow of information among the working memory components through neural gating mechanisms. The proposed system is capable of learning to communicate through natural language starting from tabula rasa, without any a priori knowledge of the structure of phrases, meaning of words, role of the different classes of words, only by interacting with a human through a text-based interface, using an open-ended incremental learning process. It is able to learn nouns, verbs, adjectives, pronouns and other word classes, and to use them in expressive language. The model was validated on a corpus of 1587 input sentences, based on literature on early language assessment, at the level of about 4-years old child, and produced 521 output sentences, expressing a broad range of language processing functionalities., Comment: The source code of the software, the User Guide and the datasets used for its validation are available in the ANNABELL web site at https://github.com/golosio/annabell/wiki