BeyinMer / Beyin Dinamiği Araştırma Merkezi
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BeyinMer / Beyin Dinamiği Araştırma Merkezi / Brain Dynamics Research Center
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Publication Metadata only Sub-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.Publication Metadata only Brain's Alpha, Beta, Gamma, delta, and theta oscillations in neuropsychiatric diseases: Proposal for biomarker strategies(2013) Başar Eroğlu, Canan; Güntekin, Bahar; Gülmen Yener, Görsev; BAŞAR, EROLBrain 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.Publication Metadata only Review of Delta, Theta, Alpha, Beta, and Gamma response oscillations in neuropsychiatric disorders(2013) Güntekin, Bahar; BAŞAR, EROLMethod 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.Publication Metadata only Brain 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.Publication Metadata only In memoriam of a great man of neuroscience: Walter J. Freeman(2016-12) BAŞAR, EROLPublication Metadata only Lithium monotherapy increases beta oscillatory responses in euthymic patients with bipolar disorder(2011-06) Tan, D.; Özerdem, A.; Güntekin, B.; Atagün, I.; Tülay, E.; Karadağ, F.; BAŞAR, EROLPublication Metadata only Views of hayek, hebb, and heiisenberg:Toward an approach to brain functioning(2011) BAŞAR, EROLPurpose - The conceptual ideas of Hebb, Heisenberg, and Feynman are embedded in the framework Hayek's so-called New Psychology. The present survey tries to bridge these concepts. Methodology - A theoretical and empirical informed approach. Findings - The theory of D. O. Hebb opened the way to "Neurobiology of Learning" in the past century. The S-Matrix theory of Werner Heisenberg and the so-called Feynman Diagrams that consider everything in the path-history of particles opened up new avenues to predict production of elementary particles. This as Hayek proposed or assumed in his theoretical monograph The Sensory Order. Originality/value of paper - Besides Fuster and Edelman few (if any) currently practicing neuroscientists have any knowledge of or appreciation of Hayek's philosophical psychology.Publication Metadata only Brain-Body-Mind in the nebulous cartesian system: A holistic approach by oscillations(SPRINGER, 233 SPRING STREET, NEW YORK, NY 10013, UNITED STATES, 2011) BAŞAR, EROLPublication Open Access How is the brain working? Research on brain oscillations and connectivities in a new "Take-Off" state(2016-05) Düzgün, Aysel; BAŞAR, EROLThe present report is a trial to survey analysis and applications of brain oscillations in cognitive impairment for opening the way to a new take off in research on brain oscillation. Although the number of papers related to brain oscillations rapidly increases, it is important to indicate the common principles governing the functioning of brain oscillations in the brain and body. Research scientists need a global view on the types of analysis, applications and existing oscillations. Further, scientists dealing with brain oscillations must have some knowledge from theoretical physics, system theory, and also general philosophy. The neuroscientists working on brain oscillations can mentally integrate several papers in the present report, and try to discover new avenues to augment knowledge on brain functions. A new take off in the search of brain oscillations indicates the strong need to survey this brunch of neuroscience in a broad panoply of science. (C) 2016 The Authors. Published by Elsevier B.V.Publication Metadata only Long distance gamma (28-48 Hz) coherence decreases under cognitive load in drug free euthymic patients with bipolar disorder(Wiley-Blackwell Publishing, Inc, Commerce Place, 350 Main St, Malden 02148, Ma USA, 2010-03) Özerdem, Ayşegül; Güntekin, Bahar; Atagün, Murat İlhan; Turp, Bilge; Oral, Esat Timuçin; BAŞAR, EROL; 140995; 204666; 25145; 22231; 142226Publication Metadata only Significant decrease of EEG alpha activity and alpha response in bipolar patients(Wiley-Blackwell Publishing, Inc, Commerce Place, 350 Main St, Malden 02148, Ma USA, 2010-03) Güntekin, Bahar; Atagün, Murat İlhan; Oral, Esat Timuçin; Özerdem, Ayşegül; BAŞAR, EROL; 142226; 204666; 25145; 22231; 140995Publication Metadata only Decrease of Long Distance Gamma (28-48 Hz) Coherence in Euthymic Drug Free Bipolar Patients upon Cognitive Load(Elsevier Science Inc, 360 Park Ave South, New York, Ny 10010-1710 USA, 2010-05-01) Özerdem, Ayşegül; Güntekin, Bahar; Atagün, Murat İlhan; Turp, Bilge; Oral, Esat Timuçin; BAŞAR, EROL; 140995; 204666; 25145; 22231; 142226Publication Metadata only Significant Reduction of EEG Alpha Activity and Sensory Alpha Response in Bipolar Patients(Elsevier Science Inc, 360 Park Ave South, New York, Ny 10010-1710 USA, 2010-05-01) Güntekin, Bahar; Atagün, Murat İlhan; Özerdem, Ayşegül; BAŞAR, EROL; 142226; 204666; 25145; 140995Publication Metadata only Event Related Coherence of Healthy Subjects upon Application of an Auditory Oddball Paradigm(Elsevier Science Inc, 360 Park Ave South, New York, Ny 10010-1710 USA, 2010-05-01) Güntekin, Bahar; BAŞAR, EROL; 142226; 204666Publication Metadata only Decrease of long distance event related gamma coherence in bipolar patients(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2010-09) Özerdem, Ayşegül; Güntekin, Bahar; Atagün, Murat İlhan; Turp, Bilge; Oral, Esat Timuçin; BAŞAR, EROL; 140995; 204666; 25145; 22231; 142226Publication Metadata only Enhanced event-related delta and theta response coherence upon cognitive stimulation(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2010-09) Güntekin, Bahar; BAŞAR, EROL; 204666; 142226Publication Metadata only Significant decrease of EEG alpha activity and visual-evoked alpha response in bipolar patients(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2010-09) Güntekin, Bahar; Atagün, Murat İlhan; Tülay, Elif; Özerdem, Ayşegül; BAŞAR, EROL; Erol Başar 142226; 204666; 25145; 140995Publication Metadata only Brain's beta response is strongly enhanced upon negative emotion eliciting stimuli(Elsevier Science Bv, Po Box 211, 1000 AE Amsterdam, Netherlands, 2010-09) Güntekin, Bahar; Elif, Tülay; Turp, Bilge; BAŞAR, EROL; 204666; 142226Publication Metadata only Increase of Beta Response upon Application of Lithium in Euthymic Bipolar Patients(Elsevier Science Inc, 360 Park Ave South, New York, Ny 10010-1710 USA, 2011-05-01) Tan, Devran; Özerdem, Ayşegül; Güntekin, Bahar; Atagün, Murat İlhan; Tülay, Elif; Karadağ, Figen; BAŞAR, EROL; 103606; 140995; 204666; 25145; 111061; Erol Başar 142226Publication Metadata only Evoked and Event Related Theta Oscillations are Decreased in Drug-Free Euthymic Bipolar Patients(Elsevier Science Inc, 360 Park Ave South, New York, Ny 10010-1710 USA, 2011-05-01) Atagün, Murat İlhan; Özerdem, Ayşegül; Güntekin, Bahar; BAŞAR, EROL; 25145; 140995; 204666; Erol Başar 142226