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Information-based methods for neuroimaging: analyzing structure, function and dynamics

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195022 Year: Pages: 191 DOI: 10.3389/978-2-88919-502-2 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Science (General)
Added to DOAB on : 2015-12-03 13:02:24
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The aim of this Research Topic is to discuss the state of the art on the use of Information-based methods in the analysis of neuroimaging data. Information-based methods, typically built as extensions of the Shannon Entropy, are at the basis of model-free approaches which, being based on probability distributions rather than on specific expectations, can account for all possible non-linearities present in the data in a model-independent fashion.Mutual Information-like methods can also be applied on interacting dynamical variables described by time-series, thus addressing the uncertainty reduction (or information) in one variable by conditioning on another set of variables.In the last years, different Information-based methods have been shown to be flexible and powerful tools to analyze neuroimaging data, with a wide range of different methodologies, including formulations-based on bivariate vs multivariate representations, frequency vs time domains, etc. Apart from methodological issues, the information bit as a common unit represents a convenient way to open the road for comparison and integration between different measurements of neuroimaging data in three complementary contexts: Structural Connectivity, Dynamical (Functional and Effective) Connectivity, and Modelling of brain activity. Applications are ubiquitous, starting from resting state in healthy subjects to modulations of consciousness and other aspects of pathophysiology.Mutual Information-based methods have provided new insights about common-principles in brain organization, showing the existence of an active default network when the brain is at rest. It is not clear, however, how this default network is generated, the different modules are intra-interacting, or disappearing in the presence of stimulation. Some of these open-questions at the functional level might find their mechanisms on their structural correlates. A key question is the link between structure and function and the use of structural priors for the understanding of the functional connectivity measures. As effective connectivity is concerned, recently a common framework has been proposed for Transfer Entropy and Granger Causality, a well-established methodology originally based on autoregressive models. This framework can open the way to new theories and applications.This Research Topic brings together contributions from researchers from different backgrounds which are either developing new approaches, or applying existing methodologies to new data, and we hope it will set the basis for discussing the development and validation of new Information-based methodologies for the understanding of brain structure, function, and dynamics.

Neural Circuits Revealed

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195619 Year: Pages: 181 DOI: 10.3389/978-2-88919-561-9 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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Deciphering anatomical and functional maps in the nervous system is a main challenge for both clinical and basic neuroscience. Modern approaches to mark and manipulate neurons are bringing us closer than ever to better understand nervous system wiring diagrams. Here we present both original research and review material on current work in this area. Together, this eBook aims to provide a comprehensive snapshot of some of the tools and technologies currently available to investigate brain wiring and function, as well as discuss ongoing challenges the field will be confronted with in the future.

Wiring Principles of Cerebral Cortex

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196920 Year: Pages: 171 DOI: 10.3389/978-2-88919-692-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2016-08-16 10:34:25
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Cerebral cortex is probably the most complex biological network. Here many millions of individual neurons, the functional units of cortex, are interconnected through a massive yet highly organized pattern of axonal and dendritic wiring. This wiring enables both near and distant cells to coordinate their responses and generate a rich variety of cognitions and behaviours. When the wiring is damaged through disease or trauma it may reorganize but this may lead to characteristic pathological behaviours. While there have been significant advances in mapping cortical connectivity, the organizing principles and function of this connectivity are not well understood. On the one hand, there appears to be general design constraints governing cortical wiring, as first recognised by Rámon y Cajal's in his laws of conduction, material, and volume conservation. Yet on the other hand, particular patterns of cortical wiring exist to serve specific functions. There is a wide gap in understanding how the response and connectivity properties of a single neuron contribute to emergent network functions such as in detecting perceptually relevant features. Unravelling this intimate causal relationship represents one of the major challenges in neuroscience. This Research Topic will examine progress in understanding cortical wiring principles. This Research Topic aims to draw together recent advances in methods and understanding as well as recent challenges to existing ideas about how cerebral cortex is wired. This is particularly timely because new automated techniques may soon yield huge datasets in need of explanation. Recent studies have, for instance, empirically evaluated Rámon y Cajal's conservation laws for cerebral cortex, while others have shown some unexpected connectivity features that may refine the traditional view of how corticocortical connections are organised with regard to functional representations of auditory, somatosensory and visual cortices. Understanding these data will help improve the fidelity of neural models of cerebral cortical function and take into account the diversity of connections at both micro- and mesoscopic scales not seen at such a depth before.

Neuroanatomy of Human Brain Development

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889451203 Year: Pages: 221 DOI: 10.3389/978-2-88945-120-3 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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The human brain is extraordinary complex and yet its origin is a simple tubular structure. Rapid and dramatic structural growth takes place during the fetal and perinatal period. By the time of birth, a repertoire of major cortical, subcortical and white matter structures resembling the adult pattern has emerged, however there are continued maturational changes of the gray matter and white matter throughout childhood and adolescence and into adulthood. The maturation of neuronal structures provides the neuroanatomical basis for the acquisition and refinement of cognitive functions during postnatal development. Histological imaging has been traditionally dominant in understanding neuroanatomy of early brain development and still plays an unparalleled role in this field. Modern magnetic resonance imaging (MRI) techniques including diffusion MRI, as noninvasive tools readily applied to in vivo brains, have become an important complementary approach in revealing the detailed brain anatomy, including the structural connectivity between brain regions. In this research topic, we presented the most recent investigations on understanding the neuroanatomy and connectivity of human brain development using both histology and MRI. Modern advances in mapping normal developmental brain anatomy and connectivity should elucidate many neurodevelopmental disorders, ranging from rare congenital malformations to common disorders such as autism and attention deficit hyperactivity disorder (ADHD), which is a prerequisite for better diagnosis and treatment of these currently poorly understood diseases.

New Insights on Basic and Clinical Aspects of EEG and MEG Connectome

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455317 Year: Pages: 97 DOI: 10.3389/978-2-88945-531-7 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2019-01-23 14:53:42
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Recent advances in the neuroimaging field areas allow us to visualize the aggregate of neural connections at the macroscopic level within the brain, the so-called “connectome”. In order to promote the development of the neurophysiological investigation of connectome of brain oscillations, this eBook aims at bringing together contributions from researchers in basic and clinical neuroscience using EEG and MEG connectome analysis. The most important focal point will be to address the functional roles of connectome of brain oscillations in contributing to understandings of higher cognitive processes in normal subjects and pathophysiology of psychiatric diseases. This Research Topic presented novel methodologies and various applications of neurophysiological connectome analysis. As a result, these papers were cited more than 120 times in these four years in total and threw light and impact on new directions for investigating the connectome of human brain.

Producing and Analyzing Macro-Connectomes: Current State and Challenges

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199815 Year: Pages: 139 DOI: 10.3389/978-2-88919-981-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2016-01-19 14:05:46
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Construction of comprehensive and detailed brain regions neuroanatomical connections matrices (macro-connectomes) is necessary to understand how the nervous system is organized and to elucidate how its different parts interact. Macro-connectomes also are the structural foundation of any finer granularity approaches at the neuron classes and types (meso-connectomes) or individual neuron (micro-connectomes) levels. The advent of novel neuroanatomical methods, as well as combinations of classic techniques, form the basis of several large scale projects with the ultimate goal of producing publicly available connectomes at different levels. A parallel approach, that of systematic and comprehensive collation of connectivity data from the published literature and from publicly accessible neuroinformatics platforms, has produced macro-connectomes of different parts of the central nervous system (CNS) in several mammalian species. The emergence of these public platforms that allow for the manipulation of rich connectivity data sets and enable the construction of CNS macro-connectomes in different species may have significant and long lasting implications. Moreover, when these efforts are leveraged by novel statistical methods, they may influence our way of thinking about the brain. Hence, the present brain region-centric paradigm may be challenged by a network-centric one. Ultimately, these projects will provide the information and knowledge for understanding how different neuronal parts communicate and function, developing novel approaches to diseases and disorders, and facilitating translational efforts in neurosciences. With this Research Topic we bring together the current state of macro-connectome related projects including the large scale production of thousands of publicly available neuronatomical experiments, databases with tens of thousands of connectivity records collated from the published literature, and the newest methods for displaying and analyzing this information. This topic also includes a wide range of challenges and how they are addressed - from platforms designed to integrate connectivity data across different sources, species and CNS levels of organization, to languages specifically designed to use these data in models at different scales of resolution, to efforts of 3D reconstruction and data integration, and to approaches for extraction and representation of this knowledge. Finally, we address the present state of different efforts of meso-connectomes construction, and of computational modeling in the context of the

Information Theory in Neuroscience

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ISBN: 9783038976646 Year: Pages: 280 DOI: 10.3390/books978-3-03897-665-3 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Mathematics --- Science (General)
Added to DOAB on : 2019-03-21 15:50:41
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As the ultimate information processing device, the brain naturally lends itself to being studied with information theory. The application of information theory to neuroscience has spurred the development of principled theories of brain function, and has led to advances in the study of consciousness, as well as to the development of analytical techniques to crack the neural code—that is, to unveil the language used by neurons to encode and process information. In particular, advances in experimental techniques enabling the precise recording and manipulation of neural activity on a large scale now enable for the first time the precise formulation and the quantitative testing of hypotheses about how the brain encodes and transmits the information used for specific functions across areas. This Special Issue presents twelve original contributions on novel approaches in neuroscience using information theory, and on the development of new information theoretic results inspired by problems in neuroscience.

Neuroproteomics

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ISBN: 9783039281060 9783039281077 Year: Pages: 318 DOI: 10.3390/books978-3-03928-107-7 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Neurology
Added to DOAB on : 2020-04-07 23:07:08
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The Neuroproteomics Special Issue overviews the unique challenges that must be addressed to carry out meaningful MS/proteomics analyses on neural tissues and the technologies that are available to meet these challenges. The articles on Alzheimer’s disease, addiction, and schizophrenia illustrate how MS/proteomics technologies can be used to improve our ability to diagnose and understand the molecular basis for neurological diseases. Several articles will be of interest to investigators beyond the field of neurological disorders. The review on the discovery of biofluid biomarkers of neurodegenerative dementias will be of interest to investigators searching for other disease biomarkers. Similarly, the review on the role of neuroproteomics in elucidating mechanisms of drug addiction provides an overview of the utility of MS/proteomics approaches for addressing critical questions in addiction neuroscience that should be applicable to investigators involved in virtually any area of biomedical research. Likewise, the article on developing targeted MS approaches for quantifying postsynaptic density proteins will be useful for any investigator who wishes to design targeted assays for virtually any protein. Finally, the peroxidase-mediated proximity labeling technology, described in the article on mapping the proteome of the synaptic cleft, will be of interest to investigators interested in mapping other spatially restricted proteomes.

Keywords

proteomics --- basal ganglia --- synapses --- synapse specificity --- neuronal circuits --- axons --- dendrites --- neurodegeneration --- synapse --- postsynaptic --- proteome --- mass spectrometry --- protein interaction networks --- connectome --- neurodegeneration --- Alzheimer’s disease --- cerebrospinal fluid --- plasma --- serum --- proteomics --- biomarkers --- LC-MS/MS --- cocaine --- addiction --- cytokine --- neuroimmune --- ventral tegmental area --- peptidylglycine ?-amidating monooxygenase --- cilia --- mating --- signal peptide --- prohormone convertase --- carboxypeptidase --- matrix metalloproteinase --- subtilisin --- pherophorin --- morphine --- opioid receptors --- conformational antibody --- analgesia --- GPCR signaling --- phosphorylation --- AMPA receptor complex --- transmembrane AMPA receptor regulatory protein --- synaptic plasticity --- adolescence --- corticosterone --- proteomics --- yohimbine --- progressive ratio --- reinstatement --- ethanol --- nicotinic receptor --- CaMKII --- PKA --- quantitative phosphoproteomics --- mouse --- phosphorylation --- nicotine --- proteomics --- proteome --- mass spectrometry --- Alzheimer’s disease --- protein aggregation --- laser capture microdissection --- splicing --- U1 snRNP --- synapse --- synaptic cleft --- trans-synaptic adhesion --- proximity labeling --- SynCAM --- Cadm --- Receptor-type tyrosine-protein phosphatase zeta --- R-PTP-zeta --- Ptprz1 --- neuroproteome --- drug abuse --- neuropeptidomics --- phosphorylation --- interactome --- cell type --- neuroscience --- proteomics --- mass spectrometry --- neuron --- proximity labeling --- affinity chromatography --- neuroproteomics --- biotinylation --- amphetamine --- spinophilin --- protein phosphatase-1 --- dopamine --- striatum --- mass spectroscopy --- bioinformatics --- FGF14 --- voltage gated channels --- schizophrenia --- autism --- Alzheimer’s Disease --- sex-specific differences --- synaptic plasticity --- cognitive impairment --- excitatory/inhibitory tone --- n/a --- postsynaptic density --- PSD --- parallel reaction monitoring --- PRM --- targeted proteomics --- data-independent acquisition --- DIA --- quantitative mass spectrometry --- n/a

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