BeyinMer / Beyin Dinamiği Araştırma Merkezi
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BeyinMer / Beyin Dinamiği Araştırma Merkezi / Brain Dynamics Research Center
Beyin Dinamiği Araştırma Merkezine ait yayınları içerir.
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- YayınSadece MetadataSub-similarity matching based on data mining with dihedral angles(2013) Berki Çimen, Egemen; Akın, Fatih; Demirer, R. MuratProtein sub-similarity matching remains largely unknown even though it is becoming one of the most important open problems in bioinformatics for drug and vaccine design. Variations in human immune responses to vaccines are, and thus responses, fail. We propose a new matching and protein alignment method based on clustering and Longest Common Subsequence (LCS) techniques. After clustering, we found LCS between a candidate protein and meningitis outer membrane antigen for each candidate. Each similarity was scored, and closest similarities were determined with statistical methods. We located three closely matching proteins among a total of 50 human immune system proteins. Moreover, we selected a HIV-1 related protein from one of scenarios, because it revealed a relationship between HIV and meningitis patients. We also found that Ω main chain torsion angle for atoms CA, C and N is the best angle for determining sub-similarities between meningitis antigen and immune proteins.
- YayınSadece MetadataBrain's Alpha, Beta, Gamma, delta, and theta oscillations in neuropsychiatric diseases: Proposal for biomarker strategies(2013) Başar, Erol; Başar Eroğlu, Canan; Güntekin, Bahar; Gülmen Yener, GörsevBrain oscillations have gained tremendous importance in neuroscience during recent decades as functional building blocks of sensory-cognitive processes. Research also shows that event-related oscillations (EROs) in "alpha," "beta," "gamma," "delta," and "theta" frequency windows are highly modified in pathological brains, especially in patients with cognitive impairment. The strategies and methods applied in the present report reflect the innate organization of the brain: "the whole brain work." The present paper is an account of methods such as evoked/event-related spectra, evoked/ERDs, coherence analysis, and phase-locking. The report does not aim to cover all strategies related to the systems theory applied in brain research literature. However, the essential methods and concepts are applied in several examples from Alzheimer's disease (AD), schizophrenia, and bipolar disorder (BD), and such examples lead to fundamental statements in the search for neurophysiological biomarkers in cognitive impairment. An overview of the results clearly demonstrates that it is obligatory to apply the method of oscillations in multiple electroencephalogram frequency windows in search of functional biomarkers and to detect the effects of drug applications. Again, according to the summary of results in AD patients and BD patients, multiple oscillations and selectively distributed recordings must be analyzed and should include multiple locations. Selective connectivity between selectively distributed neural networks has to be computed by means of spatial coherence. Therefore, by designing a strategy for diagnostics, the differential diagnostics, and application of (preventive) drugs, neurophysiological information should be analyzed within a framework including multiple methods and multiple frequency bands. The application of drugs/neurotransmitters gains a new impact with the analysis of oscillations and coherences. A more clear and differentiated analysis of drug effects can be attained in comparison to the application of the conventional wide-band evoked potential and event-related potential applications.
- YayınSadece MetadataReview of Delta, Theta, Alpha, Beta, and Gamma response oscillations in neuropsychiatric disorders(2013) Başar, Erol; Güntekin, BaharMethod and concepts of brain oscillations pervade the neuroscience literature, especially in cognitive processes. Electrophysiological changes in patients with cognitive impairment will provide fundamental knowledge, not only for clinical studies but also, in turn, for understanding cognitive processes in healthy subjects. This review includes description of brain oscillations in schizophrenia, bipolar disorder, mild cognitive impairment, Alzheimer's disease, and attention deficit hyperactivity disorder. The reviewed publications include several methodological approaches: analysis of spontaneous electroencephalogram (EEG) spectra, evoked oscillations, event-related oscillations, and coherences both in spontaneous EEG and event-related oscillations. The review clearly shows that, in cognitive impairment, fundamental changes are observed in all diseases under study. Accordingly, oscillations can most probably be used as biomarkers in clinical studies. The conclusions of this review include several remarks indicating the nature of brain oscillations, their application to cognitive processes, and the usefulness of recording brain oscillations in memory loss, attention deficit, and learning.
- YayınSadece MetadataBrain oscillations in neuropsychiatric disease(2013-09) Başar, ErolThe term “brain (or neural) oscillations” refers to the rhythmic and/or repetitive electrical activity generated spontaneously and in response to stimuli by neural tissue in the central nervous system. The importance of brain oscillations in sensory-cognitive processes has become increasingly evident. It has also become clear that event-related oscillations are modified in many types of neuropathology, in particular in cognitive impairment. This review discusses methods such as evoked/event-related oscillations and spectra, coherence analysis, and phase locking. It gives examples of applications of essential methods and concepts in bipolar disorder that provide a basis for fundamental notions regarding neurophysiologic biomarkers in cognitive impairment. The take-home message is that in the development of diagnostic and pharmacotherapeutic strategies, neurophysiologic data should be analyzed in a framework that uses a multiplicity of methods and frequency bands.
- YayınSadece MetadataIn memoriam of a great man of neuroscience: Walter J. Freeman(2016-12) Başar, Erol