MSTPublications: January 2021
Generalizing deep whole-brain segmentation for post-contrast MRI with transfer learning.
Bermudez C, Remedios SW, Ramadass K, McHugo M, Heckers S, Huo Y, Landman BA.
J Med Imaging (Bellingham). 2020 Nov;7(6):064004. doi: 10.1117/1.JMI.7.6.064004. Epub 2020 Dec 23. PMID: 33381612
Purpose: Generalizability is an important problem in deep neural networks, especially with variability of data acquisition in clinical magnetic resonance imaging (MRI). Recently, the spatially localized atlas network tiles (SLANT) can effectively segment whole brain, non-contrast T1w MRI with 132 volumetric labels. Transfer learning (TL) is a commonly used domain adaptation tool to update the neural network weights for local factors, yet risks degradation of performance on the original validation/test cohorts. Approach: We explore TL using unlabeled clinical data to address these concerns in the context of adapting SLANT to scanning protocol variations. We optimize whole-brain segmentation on heterogeneous clinical data by leveraging 480 unlabeled pairs of clinically acquired T1w MRI with and without intravenous contrast. We use labels generated on the pre-contrast image to train on the post-contrast image in a five-fold cross-validation framework. We further validated on a withheld test set of 29 paired scans over a different acquisition domain. Results: Using TL, we improve reproducibility across imaging pairs measured by the reproducibility Dice coefficient (rDSC) between the pre- and post-contrast image. We showed an increase over the original SLANT algorithm (rDSC 0.82 versus 0.72) and the FreeSurfer v6.0.1 segmentation pipeline (rDSC = 0.53). We demonstrate the impact of this work decreasing the root-mean-squared error of volumetric estimates of the hippocampus between paired images of the same subject by 67%. Conclusion: This work demonstrates a pipeline for unlabeled clinical data to translate algorithms optimized for research data to generalize toward heterogeneous clinical acquisitions.
Incomplete hippocampal inversion in schizophrenia: prevalence, severity, and impact on hippocampal structure.
Roeske MJ, McHugo M, Vandekar S, Blackford JU, Woodward ND, Heckers S.
Mol Psychiatry. 2021 Jan 12. doi: 10.1038/s41380-020-01010-z. Online ahead of print. PMID: 33437006
Incomplete hippocampal inversion (IHI) is an anatomical variant of the human brain resulting from an arrest in brain development, especially prevalent in the left hemisphere. We hypothesized that IHI is more common in schizophrenia and contributes to the well-known hippocampal structural differences. We studied 199 schizophrenia patients and 161 healthy control participants with 3 T MRI to establish IHI prevalence and the relationship of IHI with hippocampal volume and asymmetry. IHI was more prevalent (left hemisphere: 15% of healthy control participants, 27% of schizophrenia patients; right hemisphere: 4% of healthy control participants, 10% of schizophrenia patients) and more severe in schizophrenia patients compared to healthy control participants. Severe IHI cases were associated with a higher rate of automated segmentation failure. IHI contributed to smaller hippocampal volume and increased R > L volume asymmetry in schizophrenia. The increased prevalence and severity of IHI supports the neurodevelopmental model of schizophrenia. The impact of this developmental variant deserves further exploration in studies of the hippocampus in schizophrenia.
Hiding in plain sight: Gene panel and genetic markers reveal 26-year undiagnosed tumor-induced osteomalacia of the rib concurrently misdiagnosed as X-linked hypophosphatemia.
Colazo JM, DeCorte JA, Gillaspie EA, Folpe AL, Dahir KM.
Bone Rep. 2020 Dec 24;14:100744. doi: 10.1016/j.bonr.2020.100744. eCollection 2021 Jun.
The influence of evolutionary history on human health and disease.
Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA.
Nat Rev Genet. 2021 Jan 6. doi: 10.1038/s41576-020-00305-9. Online ahead of print. PMID: 33408383 Review.
High-resolution 3D abdominal segmentation with random patch network fusion.
Tang Y, Gao R, Lee HH, Han S, Chen Y, Gao D, Nath V, Bermudez C, Savona MR, Abramson RG, Bao S, Lyu I, Huo Y, Landman BA.
Med Image Anal. 2020 Dec 16;69:101894. doi: 10.1016/j.media.2020.101894. Online ahead of print. PMID: 33421919
Phase Identification for Dynamic CT enhancements with Generative Adversarial Network.
Tang Y, Gao R, Lee HH, Chen Y, Gao D, Bermudez C, Bao S, Huo Y, Savoie BV, Landman BA.
Med Phys. 2021 Jan 7. doi: 10.1002/mp.14706. Online ahead of print.
BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database.
Mendenhall J, Brown BP, Kothiwale S, Meiler J.
J Chem Inf Model. 2020 Dec 22. doi: 10.1021/acs.jcim.0c01140. Online ahead of print. PMID: 33351632
Rare and de novo coding variants in chromodomain genes in Chiari I malformation.
Sadler B, Wilborn J, Antunes L, Kuensting T, Hale AT, Gannon SR, McCall K, Cruchaga C, Harms M, Voisin N, Reymond A, Cappuccio G, Burnetti-Pierri N, Tartaglia M, Niceta M, Leoni C, Zampino G, Ashley-Koch A, Urbizu A, Garrett ME, Soldano K, Macaya A, Conrad D, Strahle J, Dobbs MB, Turner TN, Shannon CN, Brockmeyer D, Limbrick DD, Gurnett CA, Haller G.
Am J Hum Genet. 2020 Dec 14:S0002-9297(20)30437-7. doi: 10.1016/j.ajhg.2020.12.001. Online ahead of print. PMID: 33352116
Health Management in the Home: A Qualitative Study of Pregnant Women and Their Caregivers.
Huth HB, Skeens R, Anders S, Herzberg S, Simpson C, Novak L, Jackson GP.
J Patient Exp. 2020 Dec;7(6):1227-1233. doi: 10.1177/2374373520948442. Epub 2020 Aug 14. PMID: 33457569
Role of the Nucleus Basalis as a Key Network Node in Temporal Lobe Epilepsy.
González HFJ, Narasimhan S, Johnson GW, Wills KE, Haas KF, Konrad PE, Chang C, Morgan VL, Rubinov M, Englot DJ.
Neurology. 2021 Jan 13:10.1212/WNL.0000000000011523. doi: 10.1212/WNL.0000000000011523. Online ahead of print. PMID: 33441453
People with mesial temporal lobe epilepsy have altered thalamo-occipital brain networks.
Wills KE, González HFJ, Johnson GW, Haas KF, Morgan VL, Narasimhan S, Englot DJ.
Epilepsy Behav. 2020 Dec 14:107645. doi: 10.1016/j.yebeh.2020.107645. Online ahead of print. PMID: 33334720
Bidirectional and State-Dependent Modulation of Brain Activity by Transcranial Focused Ultrasound in Non-human Primates.
Yang PF, Phipps MA, Jonathan S, Newton AT, Byun N, Gore JC, Grissom WA, Caskey CF, Chen LM.
Brain Stimul. 2021 Jan 15:S1935-861X(21)00007-3. doi: 10.1016/j.brs.2021.01.006. Online ahead of print.
IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues.
Radtke AJ, Kandov E, Lowekamp B, Speranza E, Chu CJ, Gola A, Thakur N, Shih R, Yao L, Yaniv ZR, Beuschel RT, Kabat J, Croteau J, Davis J, Hernandez JM, Germain RN.
Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33455-33465. doi: 10.1073/pnas.2018488117. Epub 2020 Dec 21. PMID: 33376221
Epidemiology of Functional Seizures Among Adults Treated at a University Hospital.
Goleva SB, Lake AM, Torstenson ES, Haas KF, Davis LK.
JAMA Netw Open. 2020 Dec 1;3(12):e2027920. doi: 10.1001/jamanetworkopen.2020.27920. PMID: 33372972
Cannabinoid type 1 receptors in A2a neurons contribute to cocaine-environment association.
Turner BD, Smith NK, Manz KM, Chang BT, Delpire E, Grueter CA, Grueter BA.
Psychopharmacology (Berl). 2021 Jan 16. doi: 10.1007/s00213-021-05759-1. Online ahead of print. PMID: 33454843
Perspectives in immunotherapy: meeting report from the “Immunotherapy Bridge” (December 4th-5th, 2019, Naples, Italy).
Ascierto PA, Butterfield LH, Campbell K, Daniele B, Dougan M, Emens LA, Formenti S, Janku F, Khleif SN, Kirchhoff T, Morabito A, Najjar Y, Nathan P, Odunsi K, Patnaik A, Paulos CM, Reinfeld BI, Skinner HD, Timmerman J, Puzanov I.
J Transl Med. 2021 Jan 6;19(1):13. doi: 10.1186/s12967-020-02627-y.
Dapagliflozin Does Not Directly Affect Human α or β Cells.
Dai C, Walker JT, Shostak A, Bouchi Y, Poffenberger G, Hart NJ, Jacobson DA, Calcutt MW, Bottino R, Greiner DL, Shultz LD, McGuinness OP, Dean ED, Powers AC.
Endocrinology. 2020 Aug 1;161(8):bqaa080. doi: 10.1210/endocr/bqaa080.