R-3 Repository :: Browsing by Author "Dabaghian, Yuri"

Browsing by Author "Dabaghian, Yuri"

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25th Annual Computational Neuroscience Meeting: CNS-2016
(BioMed Central, 2016) Sharpee, Tatyana O.; Destexhe, Alain; Kawato, Mitsuo; Sekulić, Vladislav; Skinner, Frances K.; Wójcik, Daniel K.; Chintaluri, Chaitanya; Cserpán, Dorottya; Somogyvári, Zoltán; Kim, Jae K.; Kilpatrick, Zachary P.; Bennett, Matthew R.; Josić, Kresimir; Elices, Irene; Arroyo, David; Levi, Rafael; Rodriguez, Francisco B.; Varona, Pablo; Hwang, Eunjin; Kim, Bowon; Han, Hio-Been; Kim, Tae; McKenna, James T.; Brown, Ritchie E.; McCarley, Robert W.; Choi, Jee H.; Rankin, James; Popp, Pamela O.; Rinzel, John; Tabas, Alejandro; Rupp, André; Balaguer-Ballester, Emili; Maturana, Matias I.; Grayden, David B.; Cloherty, Shaun L.; Kameneva, Tatiana; Ibbotson, Michael R.; Meffin, Hamish; Koren, Veronika; Lochmann, Timm; Dragoi, Valentin; Obermayer, Klaus; Psarrou, Maria; Schilstra, Maria; Davey, Neil; Torben-Nielsen, Benjamin; Steuber, Volker; Ju, Huiwen; Yu, Jiao; Hines, Michael L.; Chen, Liang; Yu, Yuguo; Kim, Jimin; Leahy, Will; Shlizerman, Eli; Birgiolas, Justas; Gerkin, Richard C.; Crook, Sharon M.; Viriyopase, Atthaphon; Memmesheimer, Raoul-Martin; Gielen, Stan; Dabaghian, Yuri; DeVito, Justin; Perotti, Luca; Kim, Anmo J.; Fenk, Lisa M.; Cheng, Cheng; Maimon, Gaby; Zhao, Chang; Widmer, Yves; Sprecher, Simon; Senn, Walter; Halnes, Geir; Mäki-Marttunen, Tuomo; Keller, Daniel; Pettersen, Klas H.; Andreassen, Ole A.; Einevoll, Gaute T.; Yamada, Yasunori; Steyn-Ross, Moira L.; Alistair Steyn-Ross, D.; Mejias, Jorge F.; Murray, John D.; Kennedy, Henry; Wang, Xiao-Jing; Kruscha, Alexandra; Grewe, Jan; Benda, Jan; Lindner, Benjamin; Badel, Laurent; Ohta, Kazumi; Tsuchimoto, Yoshiko; Kazama, Hokto; Kahng, B.; Tam, Nicoladie D.; Pollonini, Luca; Zouridakis, George; Soh, Jaehyun; Kim, DaeEun; Yoo, Minsu; Palmer, S.E.; Culmone, Viviana; Bojak, Ingo; Ferrario, Andrea; Merrison-Hort, Robert; Borisyuk, Roman; Kim, Chang S.; Tezuka, Taro; Joo, Pangyu; Rho, Young-Ah; Burton, Shawn D.; Bard Ermentrout, G.; Jeong, Jaeseung; Urban, Nathaniel N.; Marsalek, Petr; Kim, Hoon-Hee; Moon, Seok-hyun; Lee, Do-won; Lee, Sung-beom; Lee, Ji-yong; Molkov, Yaroslav I.; Hamade, Khaldoun; Teka, Wondimu; Barnett, William H.; Kim, Taegyo; Markin, Sergey; Rybak, Ilya A.; Forro, Csaba; Dermutz, Harald; Demkó, László; Vörös, János; Babichev, Andrey; Huang, Haiping; Verduzco-Flores, Sergio; Dos Santos, Filipa; Andras, Peter; Metzner, Christoph; Schweikard, Achim; Zurowski, Bartosz; Roach, James P.; Sander, Leonard M.; Zochowski, Michal R.; Skilling, Quinton M.; Ognjanovski, Nicolette; Aton, Sara J.; Zochowski, Michal; Wang, Sheng-Jun; Ouyang, Guang; Guang, Jing; Zhang, Mingsha; Michael Wong, K.Y.; Zhou, Changsong; Robinson, Peter A.; Sanz-Leon, Paula; Drysdale, Peter M.; Fung, Felix; Abeysuriya, Romesh G.; Rennie, Chris J.; Zhao, Xuelong; Choe, Yoonsuck; Yang, Huei-Fang; Mi, Yuanyuan; Lin, Xiaohan; Wu, Si; Liedtke, Joscha; Schottdorf, Manuel; Wolf, Fred; Yamamura, Yoriko; Wickens, Jeffery R.; Rumbell, Timothy; Ramsey, Julia; Reyes, Amy; Draguljić, Danel; Hof, Patrick R.; Luebke, Jennifer; Weaver, Christina M.; He, Hu; Yang, Xu; Ma, Hailin; Xu, Zhiheng; Wang, Yuzhe; Baek, Kwangyeol; Morris, Laurel S.; Kundu, Prantik; Voon, Valerie; Agnes, Everton J.; Vogels, Tim P.; Podlaski, William F.; Giese, Martin; Kuravi, Pradeep; Vogels, Rufin; Seeholzer, Alexander; Podlaski, William; Ranjan, Rajnish; Vogels, Tim; Torres, Joaquin J.; Baroni, Fabiano; Latorre, Roberto; Gips, Bart; Lowet, Eric; Roberts, Mark J.; de Weerd, Peter; Jensen, Ole; van der Eerden, Jan; Goodarzinick, Abdorreza; Niry, Mohammad D.; Valizadeh, Alireza; Pariz, Aref; Parsi, Shervin S.; Warburton, Julia M.; Marucci, Lucia; Tamagnini, Francesco; Brown, Jon; Tsaneva-Atanasova, Krasimira; Kleberg, Florence I.; Triesch, Jochen; Moezzi, Bahar; Iannella, Nicolangelo; Schaworonkow, Natalie; Plogmacher, Lukas; Goldsworthy, Mitchell R.; Hordacre, Brenton; McDonnell, Mark D.; Ridding, Michael C.; Zapotocky, Martin; Smit, Daniel; Fouquet, Coralie; Trembleau, Alain; Dasgupta, Sakyasingha; Nishikawa, Isao; Aihara, Kazuyuki; Toyoizumi, Taro; Robb, Daniel T.; Mellen, Nick; Toporikova, Natalia; Tang, Rongxiang; Tang, Yi-Yuan; Liang, Guangsheng; Kiser, Seth A.; Howard, James H.; Goncharenko, Julia; Voronenko, Sergej O.; Ahamed, Tosif; Stephens, Greg; Yger, Pierre; Lefebvre, Baptiste; Spampinato, Giulia L.B.; Esposito, Elric; et Olivier Marre, Marcel S.; Choi, Hansol; Song, Min-Ho; Chung, SueYeon; Lee, Dan D.; Sompolinsky, Haim; Phillips, Ryan S.; Smith, Jeffrey; Chatzikalymniou, Alexandra P.; Ferguson, Katie; Alex Cayco Gajic, N.; Clopath, Claudia; Angus Silver, R.; Gleeson, Padraig; Marin, Boris; Sadeh, Sadra; Quintana, Adrian; Cantarelli, Matteo; Dura-Bernal, Salvador; Lytton, William W.; Davison, Andrew; Li, Luozheng; Zhang, Wenhao; Wang, Dahui; Song, Youngjo; Park, Sol; Choi, Ilhwan; Shin, Hee-sup; Choi, Hannah; Pasupathy, Anitha; Shea-Brown, Eric; Huh, Dongsung; Sejnowski, Terrence J.; Vogt, Simon M; Kumar, Arvind; Schmidt, Robert; Van Wert, Stephen; Schiff, Steven J.; Veale, Richard; Scheutz, Matthias; Lee, Sang W.; Gallinaro, Júlia; Rotter, Stefan; Rubchinsky, Leonid L.; Cheung, Chung C.; Ratnadurai-Giridharan, Shivakeshavan; Shomali, Safura R.; Ahmadabadi, Majid N.; Shimazaki, Hideaki; Nader Rasuli, S.; Zhao, Xiaochen; Rasch, Malte J.; Wilting, Jens; Priesemann, Viola; Levina, Anna; Rudelt, Lucas; Lizier, Joseph T.; Spinney, Richard E.; Rubinov, Mikail; Wibral, Michael; Bak, Ji H.; Pillow, Jonathan; Zaho, Yuan; Park, Il M.; Kang, Jiyoung; Park, Hae-Jeong; Jang, Jaeson; Paik, Se-Bum; Choi, Woochul; Lee, Changju; Song, Min; Lee, Hyeonsu; Park, Youngjin; Yilmaz, Ergin; Baysal, Veli; Ozer, Mahmut; Saska, Daniel; Nowotny, Thomas; Chan, Ho K.; Diamond, Alan; Herrmann, Christoph S.; Murray, Micah M.; Ionta, Silvio; Hutt, Axel; Lefebvre, Jérémie; Weidel, Philipp; Duarte, Renato; Morrison, Abigail; Lee, Jung H.; Iyer, Ramakrishnan; Mihalas, Stefan; Koch, Christof; Petrovici, Mihai A.; Leng, Luziwei; Breitwieser, Oliver; Stöckel, David; Bytschok, Ilja; Martel, Roman; Bill, Johannes; Schemmel, Johannes; Meier, Karlheinz; Esler, Timothy B.; Burkitt, Anthony N.; Kerr, Robert R.; Tahayori, Bahman; Nolte, Max; Reimann, Michael W.; Muller, Eilif; Markram, Henry; Parziale, Antonio; Senatore, Rosa; Marcelli, Angelo; Skiker, K.; Maouene, M.; Neymotin, Samuel A.; Seidenstein, Alexandra; Lakatos, Peter; Sanger, Terence D.; Menzies, Rosemary J.; McLauchlan, Campbell; van Albada, Sacha J.; Kedziora, David J.; Neymotin, Samuel; Kerr, Cliff C.; Suter, Benjamin A.; Shepherd, Gordon M.G.; Ryu, Juhyoung; Lee, Sang-Hun; Lee, Joonwon; Lee, Hyang J.; Lim, Daeseob; Wang, Jisung; Lee, Heonsoo; Jung, Nam; Anh Quang, Le; Maeng, Seung E.; Lee, Tae H.; Lee, Jae W.; Park, Chang-hyun; Ahn, Sora; Moon, Jangsup; Choi, Yun S.; Kim, Juhee; Jun, Sang B.; Lee, Seungjun; Lee, Hyang W.; Jo, Sumin; Jun, Eunji; Yu, Suin; Goetze, Felix; Lai, Pik-Yin; Kim, Seonghyun; Kwag, Jeehyun; Jang, Hyun J.; Filipović, Marko; Reig, Ramon; Aertsen, Ad; Silberberg, Gilad; Bachmann, Claudia; Buttler, Simone; Jacobs, Heidi; Dillen, Kim; Fink, Gereon R.; Kukolja, Juraj; Kepple, Daniel; Giaffar, Hamza; Rinberg, Dima; Shea, Steven; Koulakov, Alex; Bahuguna, Jyotika; Tetzlaff, Tom; Kotaleski, Jeanette H.; Kunze, Tim; Peterson, Andre; Knösche, Thomas; Kim, Minjung; Kim, Hojeong; Park, Ji S.; Yeon, Ji W.; Kim, Sung-Phil; Kang, Jae-Hwan; Lee, Chungho; Spiegler, Andreas; Petkoski, Spase; Palva, Matias J.; Jirsa, Viktor K.; Saggio, Maria L.; Siep, Silvan F.; Stacey, William C.; Bernar, Christophe; Choung, Oh-hyeon; Jeong, Yong; Lee, Yong-il; Kim, Su H.; Jeong, Mir; Lee, Jeungmin; Kwon, Jaehyung; Kralik, Jerald D.; Jahng, Jaehwan; Hwang, Dong-Uk; Kwon, Jae-Hyung; Park, Sang-Min; Kim, Seongkyun; Kim, Hyoungkyu; Kim, Pyeong S.; Yoon, Sangsup; Lim, Sewoong; Park, Choongseok; Miller, Thomas; Clements, Katie; Ahn, Sungwoo; Ji, Eoon H.; Issa, Fadi A.; Baek, JeongHun; Oba, Shigeyuki; Yoshimoto, Junichiro; Doya, Kenji; Ishii, Shin; Mosqueiro, Thiago S.; Strube-Bloss, Martin F.; Smith, Brian; Huerta, Ramon; Hadrava, Michal; Hlinka, Jaroslav; Bos, Hannah; Helias, Moritz; Welzig, Charles M.; Harper, Zachary J.; Kim, Won S.; Shin, In-Seob; Baek, Hyeon-Man; Han, Seung K.; Richter, René; Vitay, Julien; Beuth, Frederick; Hamker, Fred H.; Toppin, Kelly; Guo, Yixin; Graham, Bruce P.; Kale, Penelope J.; Gollo, Leonardo L.; Stern, Merav; Abbott, L.F.; Fedorov, Leonid A.; Giese, Martin A.; Ardestani, Mohammad H.; Faraji, Mohammad J.; Preuschoff, Kerstin; Gerstner, Wulfram; van Gendt, Margriet J.; Briaire, Jeroen J.; Kalkman, Randy K.; Frijns, Johan H.M.; Lee, Won H.; Frangou, Sophia; Fulcher, Ben D.; Tran, Patricia H.P.; Fornito, Alex; Gliske, Stephen V.; Lim, Eugene; Holman, Katherine A.; Fink, Christian G.; Kim, Jinseop S.; Mu, Shang; Briggman, Kevin L.; Sebastian Seung, H.; Wegener, Detlef; Bohnenkamp, Lisa; Ernst, Udo A.; Devor, Anna; Dale, Anders M.; Lines, Glenn T.; Edwards, Andy; Tveito, Aslak; Hagen, Espen; Senk, Johanna; Diesmann, Markus; Schmidt, Maximilian; Bakker, Rembrandt; Shen, Kelly; Bezgin, Gleb; Hilgetag, Claus-Christian; van Albada, Sacha J.; Sun, Haoqi; Sourina, Olga; Huang, Guang-Bin; Klanner, Felix; Denk, Cornelia; Glomb, Katharina; Ponce-Alvarez, Adrián; Gilson, Matthieu; Ritter, Petra; Deco, Gustavo; Witek, Maria A.G.; Clarke, Eric F.; Hansen, Mads; Wallentin, Mikkel; Kringelbach, Morten L.; Vuust, Peter; Klingbeil, Guido; De Schutter, Erik; Chen, Weiliang; Zang, Yunliang; Hong, Sungho; Takashima, Akira; Zamora, Criseida; Gallimore, Andrew R.; Goldschmidt, Dennis; Manoonpong, Poramate; Karoly, Philippa J.; Freestone, Dean R.; Soundry, Daniel; Kuhlmann, Levin; Paninski, Liam; Cook, Mark; Lee, Jaejin; Fishman, Yonatan I.; Cohen, Yale E.; Roberts, James A.; Cocchi, Luca; Sweeney, Yann; Lee, Soohyun; Jung, Woo-Sung; Kim, Youngsoo; Jung, Younginha; Song, Yoon-Kyu; Chavane, Frédéric; Soman, Karthik; Muralidharan, Vignesh; Srinivasa Chakravarthy, V.; Shivkumar, Sabyasachi; Mandali, Alekhya; Pragathi Priyadharsini, B.; Mehta, Hima; Davey, Catherine E.; Brinkman, Braden A.W.; Kekona, Tyler; Rieke, Fred; Buice, Michael; De Pittà, Maurizio; Berry, Hugues; Brunel, Nicolas; Breakspear, Michael; Marsat, Gary; Drew, Jordan; Chapman, Phillip D.; Daly, Kevin C.; Bradle, Samual P.; Seo, Sat B.; Su, Jianzhong; Kavalali, Ege T.; Blackwell, Justin; Shiau, LieJune; Buhry, Laure; Basnayake, Kanishka; Lee, Sue-Hyun; Levy, Brandon A.; Baker, Chris I; Leleu, Timothée; Philips, Ryan T.; Chhabria, Karishma
Applying the Short-Time Direct Directed Transfer Function to Human Electrocorticographic Recordings from a Language Task
(2013-06-28) Whaley, Meagan; Cox, Steven J.; Embree, Mark; Tandon, Nitin; Dabaghian, Yuri
This thesis applied the short-time direct directed transfer function (SdDTF) to time series data recordings from intracranial electrodes that measure the brain's electrical activity to determine the causal influences that occurred between brain regions during a speech production task. The combination of high temporal and spatial resolution of the electrocorticography (ECoG) recordings directly from the cortex render these measurements of brain activity desirable, particularly when analyzing the fine cognitive dynamics involved in word generation. This research applied a new method to characterize the SdDTF results by compressing across time and high gamma frequencies, generating adjacency matrices, and graphing them to visualize the influences between anatomical regions over the duration of the entire task. This consolidated SdDTF analysis technique allowed for data from a total of seven patients to be combined, generating results which were consistent with current speech production models. The results from this thesis contribute to the expansion of language research by identifying areas relevant to word generation, providing information that will help surgeons avoid irreparable damage to crucial cortex during brain surgery.
Cytoplasmic sphingosine-1-phosphate pathway modulates neuronal autophagy
(Springer Nature, 2015) Manchon, Jose Felix Moruno; Uzor, Ndidi-Ese; Dabaghian, Yuri; Furr-Stimming, Erin E.; Finkbeiner, Steven; Tsvetkov, Andrey S.
Autophagy is an important homeostatic mechanism that eliminates long-lived proteins, protein aggregates and damaged organelles. Its dysregulation is involved in many neurodegenerative disorders. Autophagy is therefore a promising target for blunting neurodegeneration. We searched for novel autophagic pathways in primary neurons and identified the cytosolic sphingosine-1-phosphate (S1P) pathway as a regulator of neuronal autophagy. S1P, a bioactive lipid generated by sphingosine kinase 1 (SK1) in the cytoplasm, is implicated in cell survival. We found that SK1 enhances flux through autophagy and that S1P-metabolizing enzymes decrease this flux. When autophagy is stimulated, SK1 relocalizes to endosomes/autophagosomes in neurons. Expression of a dominant-negative form of SK1 inhibits autophagosome synthesis. In a neuron model of Huntington's disease, pharmacologically inhibiting S1P-lyase protected neurons from mutant huntingtin-induced neurotoxicity. These results identify the S1P pathway as a novel regulator of neuronal autophagy and provide a new target for developing therapies for neurodegenerative disorders.
Dynamics of brain networks during reading
(2015-10-05) Whaley, Meagan; Cox, Steven J; Dabaghian, Yuri; Kemere, Caleb; Tandon, Nitin
We recorded electrocorticographic (ECoG) data from 15 patients with intractable epilepsy during a word completion task to precisely describe the spatiotemporal brain dynamics underlying word reading. Using a novel technique of analyzing grouped ECoG, cortical regions distributed throughout the left hemisphere were identified as significantly active versus baseline during our word stem completion task. Regions of activity spread from fusiform to frontal regions, including pars opercularis, pars triangularis, and pre, post, and subcentral gyri during the time period approaching articulation onset. The ECoG data recorded from electrodes within these regions were fit into linear multivariate autoregressive models, which precisely reveal the time, frequency, and magnitude of information flow between localized brain regions. Grouped network dynamics were quantified with two metrics of evaluating statistical significance of post-stimulus interactions compared to baseline. Results from both methods reveal bidirectional exchanges between frontal regions with fusiform, supporting theories which incorporate top-down and bottom-up processing during single word reading.
Functional inference of conductances in the LGMD neuron
(2013-08-27) Ackermann, Etienne; Cox, Steven J.; Embree, Mark; Sorensen, Danny C.; Dabaghian, Yuri
This thesis develops an approach to determine spatially-varying ionic channel conductances throughout the dendrites of the LGMD neuron from distal transmembrane potential recordings in response to distributed subthreshold current injections. In particular this approach is demonstrated on a straight cable approximation to the LGMD neuron with leak and hyperpolarization-activated h-currents. Knowledge of the underlying channel conductances can help neuroscientists to characterize, better understand, and predict neuronal behavior---and topographic integration in the LGMD neuron in particular---but it is extremely difficult to measure these conductances directly. As a consequence, these conductances are commonly estimated by searching for several parameters that lead to simulated responses that are consistent with recorded behavior. In contrast, the approach presented here uses the method of moments to directly recover the underlying conductances, eliminating the need to simulate responses, making this approach both faster and more robust than typical optimization approaches since the solution cannot get trapped in local minima.
Identifying ECG Clusters in Congenital Heart Disease
(2015-04-23) Hendryx, Emily; Riviere, Beatrice M.; Rusin, Craig; Cox, Steven; Dabaghian, Yuri
This thesis presents a method of clustering ECG morphologies for the identification of individual ECG features in congenital heart disease. Clustering is performed on the computed heart dipole moment magnitude using k-medoids clustering with variants of dynamic time warping. The method is applied to both synthetic data and patient data with different parameter values for classic and derivative dynamic time warping. A deterministic k-medoids algorithm demonstrates poor clustering results on both data sets, but an iterative approach with random initialization shows marked improvement. The synthetic data clusters are generally well-defined with the expected number of clusters. Though the patient data derivative results are inconclusive, upon closer examination, the clustering results from classic dynamic time warping with a small warping window seem sensible. Through this project, the groundwork is laid for the future classification of ECG recordings and the development of predictive models in patients with congenital heart disease.
Levetiracetam mitigates doxorubicin-induced DNA and synaptic damage in neurons
(Springer Nature, 2016) Manchon, Jose Felix Moruno; Dabaghian, Yuri; Uzor, Ndidi-Ese; Kesler, Shelli R.; Wefel, Jeffrey S.; Tsvetkov, Andrey S.
Neurotoxicity may occur in cancer patients and survivors during or after chemotherapy. Cognitive deficits associated with neurotoxicity can be subtle or disabling and frequently include disturbances in memory, attention, executive function and processing speed. Searching for pathways altered by anti-cancer treatments in cultured primary neurons, we discovered that doxorubicin, a commonly used anti-neoplastic drug, significantly decreased neuronal survival. The drug promoted the formation of DNA double-strand breaks in primary neurons and reduced synaptic and neurite density. Pretreatment of neurons with levetiracetam, an FDA-approved anti-epileptic drug, enhanced survival of chemotherapy drug-treated neurons, reduced doxorubicin-induced formation of DNA double-strand breaks, and mitigated synaptic and neurite loss. Thus, levetiracetam might be part of a valuable new approach for mitigating synaptic damage and, perhaps, for treating cognitive disturbances in cancer patients and survivors.
The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map
(Public Library of Science, 2014) Arai, Mamiko; Brandt, Vicky; Dabaghian, Yuri
Learning arises through the activity of large ensembles of cells, yet most of the data neuroscientists accumulate is at the level of individual neurons; we need models that can bridge this gap. We have taken spatial learning as our starting point, computationally modeling the activity of place cells using methods derived from algebraic topology, especially persistent homology. We previously showed that ensembles of hundreds of place cells could accurately encode topological information about different environments (?learn? the space) within certain values of place cell firing rate, place field size, and cell population; we called this parameter space the learning region. Here we advance the model both technically and conceptually. To make the model more physiological, we explored the effects of theta precession on spatial learning in our virtual ensembles. Theta precession, which is believed to influence learning and memory, did in fact enhance learning in our model, increasing both speed and the size of the learning region. Interestingly, theta precession also increased the number of spurious loops during simplicial complex formation. We next explored how downstream readout neurons might define co-firing by grouping together cells within different windows of time and thereby capturing different degrees of temporal overlap between spike trains. Our model's optimum coactivity window correlates well with experimental data, ranging from ~150-200 msec. We further studied the relationship between learning time, window width, and theta precession. Our results validate our topological model for spatial learning and open new avenues for connecting data at the level of individual neurons to behavioral outcomes at the neuronal ensemble level. Finally, we analyzed the dynamics of simplicial complex formation and loop transience to propose that the simplicial complex provides a useful working description of the spatial learning process.

Browsing by Author "Dabaghian, Yuri"

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