Browsing by Author "Karakas, Cemal"

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    Inferring metabolic networks using the Bayesian adaptive graphical lasso with informative priors
    (International Press, 2013) Peterson, Christine; Vannucci, Marina; Karakas, Cemal; Choi, William; Ma, Lihua; Maletic-Savatic, Mirjana
    Metabolic processes are essential for cellular function and survival. We are interested in inferring a metabolic network in activated microglia, a major neuroimmune cell in the brain responsible for the neuroinflammation associated with neurological diseases, based on a set of quantified metabolites. To achieve this, we apply the Bayesian adaptive graphical lasso with informative priors that incorporate known relationships between covariates. To encourage sparsity, the Bayesian graphical lasso places double exponential priors on the off-diagonal entries of the precision matrix. The Bayesian adaptive graphical lasso allows each double exponential prior to have a unique shrinkage parameter. These shrinkage parameters share a common gamma hyperprior. We extend this model to create an informative prior structure by formulating tailored hyperpriors on the shrinkage parameters. By choosing parameter values for each hyperprior that shift probability mass toward zero for nodes that are close together in a reference network, we encourage edges between covariates with known relationships. This approach can improve the reliability of network inference when the sample size is small relative to the number of parameters to be estimated. When applied to the data on activated microglia, the inferred network includes both known relationships and associations of potential interest for further investigation.
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    Sub-scalp electroencephalography: A next-generation technique to study human neurophysiology
    (Elsevier, 2022) Haneef, Zulfi; Yang, Kaiyuan; Sheth, Sameer A.; Aloor, Fuad Z.; Aazhang, Behnaam; Krishnan, Vaishnav; Karakas, Cemal
    Sub-scalp electroencephalography (ssEEG) is emerging as a promising technology in ultra-long-term electroencephalography (EEG) recordings. Given the diversity of devices available in this nascent field, uncertainty persists about its utility in epilepsy evaluation. This review critically dissects the many proposed utilities of ssEEG devices including (1) seizure quantification, (2) seizure characterization, (3) seizure lateralization, (4) seizure localization, (5) seizure alarms, (6) seizure forecasting, (7) biomarker discovery, (8) sleep medicine, and (9) responsive stimulation. The different ssEEG devices in development have individual design philosophies with unique strengths and limitations. There are devices offering primarily unilateral recordings (24/7 EEGTM SubQ, NeuroviewTM, Soenia® UltimateEEG™), bilateral recordings (Minder™, Epios™), and even those with responsive stimulation capability (EASEE®). We synthesize the current knowledge of these ssEEG systems. We review the (1) ssEEG devices, (2) use case scenarios, (3) challenges and (4) suggest a roadmap for ideal ssEEG designs.