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      A cognitive neural circuit biotype of depression showing functional and behavioral improvement after transcranial magnetic stimulation in the B-SMART-fMRI trial

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          Abstract

          We previously identified a cognitive biotype of depression characterized by treatment resistance, impaired cognitive control behavioral performance and dysfunction in the cognitive control circuit, comprising the dorsolateral prefrontal cortex (dLPFC) and dorsal anterior cingulate cortex (dACC). Therapeutic transcranial magnetic stimulation (TMS) to the left dLPFC is a promising option for individuals whose depression does not respond to pharmacotherapy. Here, 43 veterans with treatment-resistant depression were assessed before TMS, after early TMS and post-TMS using functional magnetic resonance imaging during a Go–NoGo paradigm, behavioral cognitive control tests and symptom questionnaires. Stratifying veterans at baseline based on task-evoked dLPFC–dACC connectivity, we demonstrate that TMS-related improvement in cognitive control circuit connectivity and behavioral performance is specific to individuals with reduced connectivity at baseline (cognitive biotype +), whereas individuals with intact connectivity at baseline (cognitive biotype −) did not demonstrate significant changes. Our findings show that dLPFC–dACC connectivity during cognitive control is both a promising diagnostic biomarker for a cognitive biotype of depression and a response biomarker for cognitive improvement after TMS applied to the dLPFC.

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          FSL.

          FSL (the FMRIB Software Library) is a comprehensive library of analysis tools for functional, structural and diffusion MRI brain imaging data, written mainly by members of the Analysis Group, FMRIB, Oxford. For this NeuroImage special issue on "20 years of fMRI" we have been asked to write about the history, developments and current status of FSL. We also include some descriptions of parts of FSL that are not well covered in the existing literature. We hope that some of this content might be of interest to users of FSL, and also maybe to new research groups considering creating, releasing and supporting new software packages for brain image analysis. Copyright © 2011 Elsevier Inc. All rights reserved.
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            Adjusting batch effects in microarray expression data using empirical Bayes methods.

            Non-biological experimental variation or "batch effects" are commonly observed across multiple batches of microarray experiments, often rendering the task of combining data from these batches difficult. The ability to combine microarray data sets is advantageous to researchers to increase statistical power to detect biological phenomena from studies where logistical considerations restrict sample size or in studies that require the sequential hybridization of arrays. In general, it is inappropriate to combine data sets without adjusting for batch effects. Methods have been proposed to filter batch effects from data, but these are often complicated and require large batch sizes ( > 25) to implement. Because the majority of microarray studies are conducted using much smaller sample sizes, existing methods are not sufficient. We propose parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples. We illustrate our methods using two example data sets and show that our methods are justifiable, easy to apply, and useful in practice. Software for our method is freely available at: http://biosun1.harvard.edu/complab/batch/.
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              Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion.

              Here, we demonstrate that subject motion produces substantial changes in the timecourses of resting state functional connectivity MRI (rs-fcMRI) data despite compensatory spatial registration and regression of motion estimates from the data. These changes cause systematic but spurious correlation structures throughout the brain. Specifically, many long-distance correlations are decreased by subject motion, whereas many short-distance correlations are increased. These changes in rs-fcMRI correlations do not arise from, nor are they adequately countered by, some common functional connectivity processing steps. Two indices of data quality are proposed, and a simple method to reduce motion-related effects in rs-fcMRI analyses is demonstrated that should be flexibly implementable across a variety of software platforms. We demonstrate how application of this technique impacts our own data, modifying previous conclusions about brain development. These results suggest the need for greater care in dealing with subject motion, and the need to critically revisit previous rs-fcMRI work that may not have adequately controlled for effects of transient subject movements. Copyright © 2011 Elsevier Inc. All rights reserved.
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                Author and article information

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                Journal
                Nature Mental Health
                Nat. Mental Health
                Springer Science and Business Media LLC
                2731-6076
                July 05 2024
                Article
                10.1038/s44220-024-00271-9
                61f9391e-6a39-4af1-bf10-6e7a3b67b930
                © 2024

                https://creativecommons.org/licenses/by/4.0

                https://creativecommons.org/licenses/by/4.0

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