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Principal Investigator: Govind Nair
Organization: NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE
Fiscal Year: 2024
Award: $867,749
Funding agency: National Institute of Neurological Disorders and Stroke
- Brain segmentation algorithms: Neurological diseases can alter the brain volumes, and the core has focused on robust automated brain segmentation and volumetric methods. Machine learning based brain segmentation technique developed in-house (Classification using DErivative-based Features or C-DEF) used to analyze brain volumes from people living with HIV (PLWH) in comparison with socio-economically matched control subjects found a greater decline of grey matter volumes with age in PLWH, and a greater increase in white matter hyperintensities with age in black participants of the study. These changes were correlated with various neuropsychological and clinical metrics (McMahan et. al., Neurology 100, e2466-e2476; Chien et. al., Ann Neurol 95, 941). Using C-DEF, we are also currently investigating brain volumetric changes in other neurological disorders such as multiple sclerosis (MS), cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), and a clinical trial on safety of drug pembrolizumab in HIV-positive people. We have also used MRI to better understand the “neurologic phenotypes of post-acute sequelae of SARS-CoV-2 infection” (Mina et. al., Neurol Neuroimmunol Neuroinflamm 2023;10:e200097). In addition, conventional brain segmentation algorithms such as FreeSurfer are used for finer parcellations in studies such as long-term effects in the brain of people who have recovered from COVID-19 infections. Furthermore, a transfer-learning based brain segmentation method was developed for images acquired on 7T scanners (called Pseudo-Label Assisted nnU-Net or PLAn, Donnay et. al., Front Neuroimaging 2, 1252261).
- Imaging of postmortem brain tissue: We have previously developed high-resolution imaging techniques for the postmortem fixed brain. The core also has expertise to implement MRI-guided histopathology utilizing sample-specific or individualized 3D-printed cutting boxes (Galbusera et. al., Brain Pathol 33, e13136). These are widely used in collaborative projects, such as identifying regions of brain metastasis in small-cell lung cancer (Desai et. al., Cell Rep Med 5, 101610), identifying pathological features in various brain regions of progressive multifocal leukoencephalopathy (PML), and locating lesions in MS. The core is also working on collaborative projects to perform MR-Microscopy (imaging at finer than 100-micron isotropic resolution) in various regions of the human brain to better understand the cytoarchitectural contributions to MRI contrast. We are preparing to extend the postmortem imaging techniques to study the spinal cord in various neurological disorders. We have recently developed cold-tissue imaging method for MRI of tissue frozen at extraction, while preserving RNA and tissue integrity during scanning (Nair et. al., Neuroimage 296, 120680). We are working on a generic cutting box that can be used in autopsy suits to produce homogenous standard sections.
- In-vivo spinal cord imaging: The core has previously developed high resolution spinal cord imaging techniques at 3T and 7T. In collaboration with researchers at University of Florence, we have found that spinal cord cross-sectional area at the time of hematopoietic stem cell transplantation in multiple sclerosis patients is a promising marker for treatment outcome (Mariottini et. al., Mult Scler Relat Disord 88, 105745). In addition, we evaluated software to measure spinal cord atrophy in pre- and post-operative syrinx (Kohut et. al., J. Clin. Med. 2023, 12(21), 6725).
- In-vivo imaging at ultra-low fields: Core is involved with developing and applying imaging techniques on the ultra-low field MRI scanners, including better visualization of MRI contrast agent (CA) and improving imaging resolution of routine sequences. We have developed a k-space based super-resolution method for doubling the resolution with only 1.6 times increase in scan time (Donnay et. al., Front Neurol 15, 1330203). We are also working closely with other NINDS groups to evaluate MRI-contrast enhancement in various neurological diseases and stroke.
Terms: <3-D print><3-D printer><3D Print><3D printer><3D printing><AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Age><Animals><Anti-HIV Positivity><Apoplexy><Area><Arterial Disorder><Arteriopathy><Atrophic><Atrophy><Autopsy><Binswanger Disease><Binswanger Encephalopathy><Body Tissues><Brain><Brain Metastasis><Brain Nervous System><Brain Vascular Accident><Brain region><COVID-19 infection><COVID-19 virus infection><COVID19 infection><Categories><Cell Body><Cells><Cerebral Stroke><Cerebrovascular Apoplexy><Cerebrovascular Stroke><Cerebrum><Chronic Progressive Subcortical Encephalopathy><Classification><Clinical><Clinical Trials><Collaborations><Communities><Computer Software Development><Computer Software Engineering><Computer software><Contrast Agent><Contrast Drugs><Contrast Media><Core Facility><DICOM><Data Analyses><Data Analysis><Digital Imaging and Communications in Medicine><Disseminated Sclerosis><Encephalon><Freezing><Goals><HIV><HIV Positive><HIV Positivity><HIV Seroconversion><HIV Seropositivity><HIV antibody positive><HSC transplantation><HTLV-III Seroconversion><HTLV-III Seropositivity><Hematopoietic Stem Cell Transplant><Hematopoietic Stem Cell Transplantation><Histopathology><Human><Human Immunodeficiency Viruses><Human Resources><Image><Imaging Procedures><Imaging Technics><Imaging Techniques><In Situ><Investigators><JC Polyomavirus Encephalitis><JC Polyomavirus Encephalopathy><Keytruda><LAV-HTLV-III><Label><Lesion><Long-Term Effects><Longterm Effects><Lymphadenopathy-Associated Virus><MR Imaging><MR Tomography><MRI><MRI Scans><MRI biomarker><MRI marker><MRIs><MS patient><Machine Learning><Magnetic Resonance><Magnetic Resonance Imaging><Magnetic Resonance Imaging Scan><Manpower><Measures><Medical Imaging, Magnetic Resonance / Nuclear Magnetic Resonance><Medulla Spinalis><Metastatic Neoplasm to the Brain><Metastatic Tumor to the Brain><Metastatic malignant neoplasm to brain><Methods><Mice><Mice Mammals><Microscopy><Mission><Modern Man><Multiple Sclerosis><Murine><Mus><NIH><NIMH><NINDS><NMR Imaging><NMR Tomography><National Institute of Mental Health><National Institute of Neurological Diseases and Stroke><National Institute of Neurological Disorders and Stroke><National Institutes of Health><Nervous System Diseases><Nervous System Disorder><Neurologic><Neurologic Disorders><Neurological><Neurological Disorders><Neurology><Neuropsychologies><Neuropsychology><Non-Polyadenylated RNA><Nuclear Magnetic Resonance Imaging><Oat cell carcinoma><Organ><Outcome Measure><PASC><Participant><Pathologic><Pathologic Processes><Pathological Processes><Persons><Phase><Phenotype><Physiologic pulse><Post Acute Sequelae of COVID19><Post Acute Sequelae of SARS-CoV-2><Post Acute Sequelae of SARS-CoV2><Post Acute Sequelae of severe acute respiratory syndrome coronavirus 2><Post Technic><Post Techniques><Post-Acute Sequelae of SARS-CoV-2 Infection><Post-Operative><Postbaccalaureate><Postdoc><Postdoctoral Fellow><Postoperative><Postoperative Period><Progressive Multifocal Leukoencephalopathy><Pulse><RNA><RNA Gene Products><Radiopaque Media><Research><Research Activity><Research Associate><Research Personnel><Research Resources><Researchers><Resolution><Resources><Ribonucleic Acid><SARS-CoV-2 infection><SARS-CoV2 infection><Sampling><Scanning><Services><Severe acute respiratory syndrome coronavirus 2 infection><Slice><Small Cell Lung Cancer><Software><Software Engineering><Spinal Cord><Stroke><Study Subject><Subcortical Arteriosclerotic Encephalopathy><Subcortical Infarctions><Subcortical Infarcts><Subcortical Leukoencephalopathy><Systematics><Techniques><Testing><Time><Tissue imaging><Tissues><Treatment outcome><United States National Institutes of Health><Universities><Virus-HIV><Visualization><White Matter Hyperintensity><Work><Zeugmatography><adverse sequelae of COVID><adverse sequelae of COVID-19><adverse sequelae of coronavirus disease><adverse sequelae of coronavirus disease 2019><ages><autosome><brain attack><brain based><brain micrometastasis><brain tissue><brain volume><cerebral><cerebral vascular accident><cerebrovascular accident><chronic COVID-19 sequelae><clinical center><contrast enhanced><coronavirus disease 2019 infection><data interpretation><design><designing><drug safety><facilities for imaging><falls><graduate student><gray matter><hematopoietic cell transplantation><hematopoietic cellular transplantation><hematopoietic progenitor cell transplantation><high resolution imaging><image-based method><imaging><imaging center><imaging facilities><imaging in vivo><imaging method><imaging modality><imaging-related facilities><improved><in vivo><in vivo imaging><infected with COVID-19><infected with COVID19><infected with SARS-CoV-2><infected with SARS-CoV2><infected with coronavirus disease 2019><infected with severe acute respiratory syndrome coronavirus 2><insular sclerosis><interest><long haul sequelae of COVID-19><long haul sequelae of coronavirus disease 2019><long-term sequelae of COVID-19><long-term sequelae of SARS-CoV-2><long-term sequelae of coronavirus disease 2019><long-term sequelae of severe acute respiratory syndrome coronavirus 2><lung oat cell carcinoma><lung small cell neuroendocrine carcinoma><machine based learning><magnetic resonance imaging biomarker><magnetic resonance imaging marker><measurable outcome><medication safety><multiple sclerosis patient><necropsy><neural imaging><neuro-imaging><neuroimaging><neurological disease><neurological imaging><neuropsychologic><oat cell cancer><outcome measurement><patients with MS><patients with multiple sclerosis><pembrolizumab><people with Multiple sclerosis><personnel><pharmaceutical safety><post COVID-19 sequelae><post acute sequelae following COVID-19><post-acute sequelae following SARS-CoV-2 infection><post-acute sequelae of COVID-19><post-acute sequelae of acute COVID infection><post-acute sequelae of coronavirus disease 2019><post-doc><post-doctoral><post-doctoral trainee><postbac><postbacc><postmortem><preservation><research associates><resolutions><segmentation algorithm><small cell lung carcinoma><small cell undifferentiated carcinoma><socio-economic><socio-economically><socioeconomically><socioeconomics><spinal cord imaging><stroked><strokes><substantia grisea><super high resolution><superresolution><three dimensional printing><tool><transfer learning><ultra high resolution><user-friendly>