Neural Networks as Cybernetic Systems (3rd and revised edition) - Part I

Neural Networks as Cybernetic Systems is a textbox that combines classical systems theory with artificial neural network technology. This third edition essentially compares with the 2nd one, but has been improved by correction of errors and by a rearrangement and minor expansion of the sections referring to recurrent networks. These changes hopefully allow for an easier comprehension of the essential aspects of this important domain that has received growing attention during the last years.

Neural Networks as Cybernetic Systems (3rd and revised edition) - Part 2

eural Networks as Cybernetic Systems is a textbox that combines classical systems theory with artificial neural network technology. This third edition essentially compares with the 2nd one, but has been improved by correction of errors and by a rearrangement and minor expansion of the sections referring to recurrent networks. These changes hopefully allow for an easier comprehension of the essential aspects of this important domain that has received growing attention during the last years.

Brain systems underlying encounter expectancy bias in spider phobia.

Spider-phobic individuals are characterized by exaggerated expectancies to be faced with spiders (so-called encounter expectancy bias). Whereas phobic responses have been linked to brain systems mediating fear, little is known about how the recruitment of these systems relates to exaggerated expectancies of threat. We used fMRI to examine spider-phobic and control participants while they imagined visiting different locations in a forest after having received background information about the likelihood of encountering different animals (spiders, snakes, and birds) at these locations. Critically, imagined encounter expectancies modulated brain responses differently in phobics as compared with controls. Phobics displayed stronger negative modulation of activity in the lateral prefrontal cortex, precuneus, and visual cortex by encounter expectancies for spiders, relative to snakes or birds (within-participants analysis); these effects were not seen in controls. Between-participants correlation analyses within the phobic group further corroborated the hypothesis that these phobia-specific modulations may underlie irrationality in encounter expectancies (deviations of encounter expectancies from objective background information) in spider phobia; the greater the negative modulation a phobic participant displayed in the lateral prefrontal cortex, precuneus, and visual cortex, the stronger was her bias in encounter expectancies for spiders. Interestingly, irrationality in expectancies reflected in frontal areas relied on right rather than left hemispheric deactivations. Our data accord with the idea that expectancy biases in spider phobia may reflect deficiencies in cognitive control and contextual integration that are mediated by right frontal and parietal areas.

Illusory memories: A cognitive neuroscience analysis

Memory illusions and distortions have long been of interest to psychology researchers studying memory, but neuropsychologists and neuroscientists have paid relatively little attention to them. This article attempts to lay the foundation for a cognitive neuroscience analysis of memory illusions and distortions by reviewing relevant evidence from a patient with a right frontal lobe lesion, patients with amnesia produced by damage to the medial temporal lobes, normal aging, and healthy young volunteers studied with functional neuroimaging techniques. Particular attention is paid to the contrasting roles of prefrontal cortex and medial temporal lobe structures in accurate and illusory remembering. Converging evidence suggests that the study of illusory memories can provide a useful tool for delineating the brain processes and systems involved in constructive aspects of remembering.

Biology of sensory systems

Since publication of the first edition, huge developments have taken place in sensory biology research and new insights have been provided in particular by molecular biology. These show the similarities in the molecular architecture and in the physiology of sensory cells across species and across sensory modality and often indicate a common ancestry dating back over half a billion years. Biology of Sensory Systems has thus been completely revised and takes a molecular, evolutionary and comparative approach, providing an overview of sensory systems in vertebrates, invertebrates and prokaryotes, with a strong focus on human senses. Written by a renowned author with extensive teaching experience, the book covers, in six parts, the general features of sensory systems, the mechanosenses, the chemosenses, the senses which detect electromagnetic radiation, other sensory systems including pain, thermosensitivity and some of the minority senses and, finally, provides an outline and discussion of philosophical implications. New in this edition: - Greater emphasis on molecular biology and intracellular mechanisms - New chapter on genomics and sensory systems - Sections on TRP channels, synaptic transmission, evolution of nervous systems, arachnid mechanosensitive sensilla and photoreceptors, electroreception in the Monotremata, language and the FOXP2 gene, mirror neurons and the molecular biology of pain - Updated passages on human olfaction and gustation. Over four hundred illustrations, boxes containing supplementary material and self-assessment questions and a full bibliography at the end of each part make Biology of Sensory Systems essential reading for undergraduate students of biology, zoology, animal physiology, neuroscience, anatomy and physiological psychology. The book is also suitable for postgraduate students in more specialised courses such as vision sciences, optometry, neurophysiology, neuropathology, developmental biology.

Biology of sensory systems

A comprehensive and highly illustrated text providing a broad and invaluable overview of sensory systems at the molecular, cellular and neurophysiological level of vertebrates, invertebrates and prokaryotes. It retains a strong focus on human systems, and takes an evolutionary and comparative approach to review the mechanosenses, chemosenses, photosenses, and other sensory systems including those for detecting pain, temperature electric and magnetic fields etc. It incorporates exciting and significant new insights provided by molecular biology which demonstrate how similar the molecular architecture and physiology of sensory cells are across species and across sensory modality, often indicationg a common ancestry dating back over half a billion years. Written by a renowned author, with extensive teaching experience in the biology of sensory systems, this book includes: - Over 400 illustrations - Self–assessment questions - Full bibliography preceded by short bibliographical essays - Boxes containing useful supplementary material. It will be invaluable for undergraduates and postgraduates studying biology, zoology, animal physiology, neuroscience, anatomy, molecular biology, physiological psychology and related courses.

Synchronization processes in nonlinear systems and their relation to cortical oscillatory dynamics

This thesis was focused on theoretical models of synchronization to cortical dynamics as measured by magnetoencephalography (MEG). Dynamical systems theory was used in both identifying relevant variables for brain coordination and also in devising methods for their quantification. We presented a method for studying interactions of linear and chaotic neuronal sources using MEG beamforming techniques. We showed that such sources can be accurately reconstructed in terms of their location, temporal dynamics and possible interactions. Synchronization in low-dimensional nonlinear systems was studied to explore specific correlates of functional integration and segregation. In the case of interacting dissimilar systems, relevant coordination phenomena involved generalized and phase synchronization, which were often intermittent. Spatially-extended systems were then studied. For locally-coupled dissimilar systems, as in the case of cortical columns, clustering behaviour occurred. Synchronized clusters emerged at different frequencies and their boundaries were marked through oscillation death. The macroscopic mean field revealed sharp spectral peaks at the frequencies of the clusters and broader spectral drops at their boundaries. These results question existing models of Event Related Synchronization and Desynchronization. We re-examined the concept of the steady-state evoked response following an AM stimulus. We showed that very little variability in the AM following response could be accounted by system noise. We presented a methodology for detecting local and global nonlinear interactions from MEG data in order to account for residual variability. We found crosshemispheric nonlinear interactions of ongoing cortical rhythms concurrent with the stimulus and interactions of these rhythms with the following AM responses. Finally, we hypothesized that holistic spatial stimuli would be accompanied by the emergence of clusters in primary visual cortex resulting in frequency-specific MEG oscillations. Indeed, we found different frequency distributions in induced gamma oscillations for different spatial stimuli, which was suggestive of temporal coding of these spatial stimuli. Further, we addressed the bursting character of these oscillations, which was suggestive of intermittent nonlinear dynamics. However, we did not observe the characteristic-3/2 power-law scaling in the distribution of interburst intervals. Further, this distribution was only seldom significantly different to the one obtained in surrogate data, where nonlinear structure was destroyed. In conclusion, the work presented in this thesis suggests that advances in dynamical systems theory in conjunction with developments in magnetoencephalography may facilitate a mapping between levels of description int he brain. this may potentially represent a major advancement in neuroscience.

Understanding Ten-Eleven Translocation-2 in Hematological and Nervous Systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.

Machine learning and data decompositions for complex networked dynamical systems

Thesis (Ph.D.)--University of Washington, 2016-08

Sparse Signal Representation in Digital and Biological Systems

Theories of sparse signal representation, wherein a signal is decomposed as the sum of a small number of constituent elements, play increasing roles in both mathematical signal processing and neuroscience. This happens despite the differences between signal models in the two domains. After reviewing preliminary material on sparse signal models, I use work on compressed sensing for the electron tomography of biological structures as a target for exploring the efficacy of sparse signal reconstruction in a challenging application domain. My research in this area addresses a topic of keen interest to the biological microscopy community, and has resulted in the development of tomographic reconstruction software which is competitive with the state of the art in its field. Moving from the linear signal domain into the nonlinear dynamics of neural encoding, I explain the sparse coding hypothesis in neuroscience and its relationship with olfaction in locusts. I implement a numerical ODE model of the activity of neural populations responsible for sparse odor coding in locusts as part of a project involving offset spiking in the Kenyon cells. I also explain the validation procedures we have devised to help assess the model's similarity to the biology. The thesis concludes with the development of a new, simplified model of locust olfactory network activity, which seeks with some success to explain statistical properties of the sparse coding processes carried out in the network.

On the zeros of the Abelian integrals for a class of Liénard systems

A planar polynomial differential system has a finite number of limit cycles. However, finding the upper bound of the number of limit cycles is an open problem for the general nonlinear dynamical systems. In this paper, we investigated a class of Liénard systems of the form x'=y, y'=f(x)+y g(x) with deg f=5 and deg g=4. We proved that the related elliptic integrals of the Liénard systems have at most three zeros including multiple zeros, which implies that the number of limit cycles bifurcated from the periodic orbits of the unperturbed system is less than or equal to 3.