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Gajawelli N, Paulli A, Deoni S, Paquette N, Darakjian D, Salazar C, Dean D, O'Muircheartaigh J, Nelson MD, Wang Y, Lepore N. Surface-based morphometry of the corpus callosum in young children of ages 1-5. Hum Brain Mapp 2024; 45:e26693. [PMID: 38924235 PMCID: PMC11199824 DOI: 10.1002/hbm.26693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 02/05/2024] [Accepted: 04/05/2024] [Indexed: 06/28/2024] Open
Abstract
The corpus callosum (CC) is a large white matter fiber bundle in the brain and is involved in various cognitive, sensory, and motor processes. While implicated in various developmental and psychiatric disorders, much is yet to be uncovered about the normal development of this structure, especially in young children. Additionally, while sexual dimorphism has been reported in prior literature, observations have not necessarily been consistent. In this study, we use morphometric measures including surface tensor-based morphometry (TBM) to investigate local changes in the shape of the CC in children between the ages of 12 and 60 months, in intervals of 12 months. We also analyze sex differences in each of these age groups. We observed larger significant clusters in the earlier ages between 12 v 24 m and between 48 v 60 m and localized differences in the anterior region of the body of the CC. Sex differences were most pronounced in the 12 m group. This study adds to the growing literature of work aiming to understand the developing brain and emphasizes the utility of surface TBM as a useful tool for analyzing regional differences in neuroanatomical morphometry.
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Affiliation(s)
- Niharika Gajawelli
- CIBORG Lab, Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
| | - Athelia Paulli
- CIBORG Lab, Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
| | - Sean Deoni
- Department of PediatricsWarren Alpert Medical School at Brown UniversityProvidenceRhode IslandUSA
- Bill & Melinda Gates FoundationSeattleWashingtonUSA
| | - Natacha Paquette
- CIBORG Lab, Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
- Department of PsychologyCHU Sainte‐JustineMontrealQuebecCanada
| | - Danielle Darakjian
- CIBORG Lab, Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
- College of MedicineCalifornia Northstate UniversityElk GroveCaliforniaUSA
| | - Carlos Salazar
- CIBORG Lab, Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
- Department of Biomedical EngineeringUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Douglas Dean
- Waisman Laboratory for Brain Imaging and BehaviorUniversity of Wisconsin MadisonMadisonWisconsinUSA
| | | | - Marvin D. Nelson
- Department of PediatricsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
| | - Yalin Wang
- Department of Computer ScienceArizona State UniversityTempeArizonaUSA
| | - Natasha Lepore
- CIBORG Lab, Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
- Department of Biomedical EngineeringUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of PediatricsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of RadiologyChildren's Hospital Los AngelesLos AngelesCaliforniaUSA
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Miralles RM, Boscia AR, Kittur S, Vundela SR, Wengert ER, Patel MK. Parvalbumin Interneuron Impairment Leads to Synaptic Transmission Deficits and Seizures in SCN8A Epileptic Encephalopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579511. [PMID: 38464208 PMCID: PMC10925130 DOI: 10.1101/2024.02.09.579511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
SCN8A epileptic encephalopathy (EE) is a severe epilepsy syndrome resulting from de novo mutations in the voltage-gated sodium channel Na v 1.6, encoded by the gene SCN8A . Na v 1.6 is expressed in both excitatory and inhibitory neurons, yet previous studies have primarily focused on the impact SCN8A mutations have on excitatory neuron function, with limited studies on the importance of inhibitory interneurons to seizure onset and progression. Inhibitory interneurons are critical in balancing network excitability and are known to contribute to the pathophysiology of other epilepsies. Parvalbumin (PV) interneurons are the most prominent inhibitory neuron subtype in the brain, making up about 40% of inhibitory interneurons. Notably, PV interneurons express high levels of Na v 1.6. To assess the role of PV interneurons within SCN8A EE, we used two mouse models harboring patient-derived SCN8A gain-of-function mutations, Scn8a D/+ , where the SCN8A mutation N1768D is expressed globally, and Scn8a W/+ -PV, where the SCN8A mutation R1872W is selectively expressed in PV interneurons. Expression of the R1872W SCN8A mutation selectively in PV interneurons led to the development of spontaneous seizures in Scn8a W/+ -PV mice and seizure-induced death, decreasing survival compared to wild-type. Electrophysiology studies showed that PV interneurons in Scn8a D/+ and Scn8a W/+ -PV mice were susceptible to depolarization block, a state of action potential failure. Scn8a D/+ and Scn8a W/+ -PV interneurons also exhibited increased persistent sodium current, a hallmark of SCN8A gain-of-function mutations that contributes to depolarization block. Evaluation of synaptic connections between PV interneurons and pyramidal cells showed an increase in synaptic transmission failure at high frequencies (80-120Hz) as well as an increase in synaptic latency in Scn8a D/+ and Scn8a W/+ -PV interneurons. These data indicate a distinct impairment of synaptic transmission in SCN8A EE, potentially decreasing overall cortical network inhibition. Together, our novel findings indicate that failure of PV interneuron spiking via depolarization block along with frequency-dependent inhibitory synaptic impairment likely elicits an overall reduction in the inhibitory drive in SCN8A EE, leading to unchecked excitation and ultimately resulting in seizures and seizure-induced death.
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Zhang L, Zhang P, Dong Q, Zhao Z, Zheng W, Zhang J, Hu X, Yao Z, Hu B. Fine-grained features characterize hippocampal and amygdaloid change pattern in Parkinson's disease and discriminate cognitive-deficit subtype. CNS Neurosci Ther 2024; 30:e14480. [PMID: 37849445 PMCID: PMC10805398 DOI: 10.1111/cns.14480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 10/19/2023] Open
Abstract
AIMS To extract vertex-wise features of the hippocampus and amygdala in Parkinson's disease (PD) with mild cognitive impairment (MCI) and normal cognition (NC) and further evaluate their discriminatory efficacy. METHODS High-resolution 3D-T1 data were collected from 68 PD-MCI, 211 PD-NC, and 100 matched healthy controls (HC). Surface geometric features were captured using surface conformal representation, and surfaces were registered to a common template using fluid registration. The statistical tests were performed to detect differences between groups. The disease-discriminatory ability of features was also tested in the ensemble classifiers. RESULTS The amygdala, not the hippocampus, showed significant overall differences among the groups. Compared with PD-NC, the right amygdala in MCI patients showed expansion (anterior cortical, anterior amygdaloid, and accessory basal areas) and atrophy (basolateral ventromedial area) subregions. There was notable atrophy in the right CA1 and hippocampal subiculum of PD-MCI. The accuracy of classifiers with multivariate morphometry statistics as features exceeded 85%. CONCLUSION PD-MCI is associated with multiscale morphological changes in the amygdala, as well as subtle atrophy in the hippocampus. These novel metrics demonstrated the potential to serve as biomarkers for PD-MCI diagnosis. Overall, these findings from this study help understand the role of subcortical structures in the neuropathological mechanisms of PD cognitive impairment.
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Affiliation(s)
- Lingyu Zhang
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and EngineeringLanzhou UniversityLanzhouChina
| | - Pengfei Zhang
- Department of Magnetic ResonanceLanzhou University Second HospitalLanzhouChina
- Gansu Province Clinical Research Center for Functional and Molecular ImagingLanzhouChina
| | - Qunxi Dong
- School of Medical TechnologyBeijing Institute of TechnologyBeijingChina
| | - Ziyang Zhao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and EngineeringLanzhou UniversityLanzhouChina
| | - Weihao Zheng
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and EngineeringLanzhou UniversityLanzhouChina
| | - Jing Zhang
- Department of Magnetic ResonanceLanzhou University Second HospitalLanzhouChina
- Gansu Province Clinical Research Center for Functional and Molecular ImagingLanzhouChina
| | - Xiping Hu
- School of Medical TechnologyBeijing Institute of TechnologyBeijingChina
| | - Zhijun Yao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and EngineeringLanzhou UniversityLanzhouChina
| | - Bin Hu
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and EngineeringLanzhou UniversityLanzhouChina
- School of Medical TechnologyBeijing Institute of TechnologyBeijingChina
- CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
- Joint Research Center for Cognitive Neurosensor Technology of Lanzhou University & Institute of SemiconductorsChinese Academy of SciencesLanzhouChina
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Zheng W, Liu H, Li Z, Li K, Wang Y, Hu B, Dong Q, Wang Z. Classification of Alzheimer's disease based on hippocampal multivariate morphometry statistics. CNS Neurosci Ther 2023; 29:2457-2468. [PMID: 37002795 PMCID: PMC10401169 DOI: 10.1111/cns.14189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurodegenerative disease characterized by progressive cognitive decline, and mild cognitive impairment (MCI) is associated with a high risk of developing AD. Hippocampal morphometry analysis is believed to be the most robust magnetic resonance imaging (MRI) markers for AD and MCI. Multivariate morphometry statistics (MMS), a quantitative method of surface deformations analysis, is confirmed to have strong statistical power for evaluating hippocampus. AIMS We aimed to test whether surface deformation features in hippocampus can be employed for early classification of AD, MCI, and healthy controls (HC). METHODS We first explored the differences in hippocampus surface deformation among these three groups by using MMS analysis. Additionally, the hippocampal MMS features of selective patches and support vector machine (SVM) were used for the binary classification and triple classification. RESULTS By the results, we identified significant hippocampal deformation among the three groups, especially in hippocampal CA1. In addition, the binary classification of AD/HC, MCI/HC, AD/MCI showed good performances, and area under curve (AUC) of triple-classification model achieved 0.85. Finally, positive correlations were found between the hippocampus MMS features and cognitive performances. CONCLUSIONS The study revealed significant hippocampal deformation among AD, MCI, and HC. Additionally, we confirmed that hippocampal MMS can be used as a sensitive imaging biomarker for the early diagnosis of AD at the individual level.
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Affiliation(s)
- Weimin Zheng
- Department of Radiology, Aerospace Center Hospital, Beijing, China
| | - Honghong Liu
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Zhigang Li
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Kuncheng Li
- Department of Radiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, Arizona, USA
| | - Bin Hu
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Qunxi Dong
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Zhiqun Wang
- Department of Radiology, Aerospace Center Hospital, Beijing, China
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Chen Z, Hu B, Liu X, Becker B, Eickhoff SB, Miao K, Gu X, Tang Y, Dai X, Li C, Leonov A, Xiao Z, Feng Z, Chen J, Chuan-Peng H. Sampling inequalities affect generalization of neuroimaging-based diagnostic classifiers in psychiatry. BMC Med 2023; 21:241. [PMID: 37400814 DOI: 10.1186/s12916-023-02941-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/13/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The development of machine learning models for aiding in the diagnosis of mental disorder is recognized as a significant breakthrough in the field of psychiatry. However, clinical practice of such models remains a challenge, with poor generalizability being a major limitation. METHODS Here, we conducted a pre-registered meta-research assessment on neuroimaging-based models in the psychiatric literature, quantitatively examining global and regional sampling issues over recent decades, from a view that has been relatively underexplored. A total of 476 studies (n = 118,137) were included in the current assessment. Based on these findings, we built a comprehensive 5-star rating system to quantitatively evaluate the quality of existing machine learning models for psychiatric diagnoses. RESULTS A global sampling inequality in these models was revealed quantitatively (sampling Gini coefficient (G) = 0.81, p < .01), varying across different countries (regions) (e.g., China, G = 0.47; the USA, G = 0.58; Germany, G = 0.78; the UK, G = 0.87). Furthermore, the severity of this sampling inequality was significantly predicted by national economic levels (β = - 2.75, p < .001, R2adj = 0.40; r = - .84, 95% CI: - .41 to - .97), and was plausibly predictable for model performance, with higher sampling inequality for reporting higher classification accuracy. Further analyses showed that lack of independent testing (84.24% of models, 95% CI: 81.0-87.5%), improper cross-validation (51.68% of models, 95% CI: 47.2-56.2%), and poor technical transparency (87.8% of models, 95% CI: 84.9-90.8%)/availability (80.88% of models, 95% CI: 77.3-84.4%) are prevailing in current diagnostic classifiers despite improvements over time. Relating to these observations, model performances were found decreased in studies with independent cross-country sampling validations (all p < .001, BF10 > 15). In light of this, we proposed a purpose-built quantitative assessment checklist, which demonstrated that the overall ratings of these models increased by publication year but were negatively associated with model performance. CONCLUSIONS Together, improving sampling economic equality and hence the quality of machine learning models may be a crucial facet to plausibly translating neuroimaging-based diagnostic classifiers into clinical practice.
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Affiliation(s)
- Zhiyi Chen
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China.
- Faculty of Psychology, Southwest University, Chongqing, China.
| | - Bowen Hu
- Faculty of Psychology, Southwest University, Chongqing, China
| | - Xuerong Liu
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Benjamin Becker
- The Center of Psychosomatic Medicine, Sichuan Provincial Center for Mental Health, Sichuan Provincial People's Hospital, Chengdu, China
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Laboratory for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Simon B Eickhoff
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kuan Miao
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Xingmei Gu
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Yancheng Tang
- School of Business and Management, Shanghai International Studies University, Shanghai, China
| | - Xin Dai
- Faculty of Psychology, Southwest University, Chongqing, China
| | - Chao Li
- Department of Radiology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangdong, China
| | - Artemiy Leonov
- School of Psychology, Clark University, Worcester, MA, USA
| | - Zhibing Xiao
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Zhengzhi Feng
- Experimental Research Center for Medical and Psychological Science (ERC-MPS), School of Psychology, Third Military Medical University, Chongqing, China
| | - Ji Chen
- Department of Psychology and Behavioral Sciences, Zhejiang University, Hangzhou, China.
- Department of Psychiatry, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.
| | - Hu Chuan-Peng
- School of Psychology, Nanjing Normal University, Nanjing, China
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Chen Z, Liu X, Yang Q, Wang YJ, Miao K, Gong Z, Yu Y, Leonov A, Liu C, Feng Z, Chuan-Peng H. Evaluation of Risk of Bias in Neuroimaging-Based Artificial Intelligence Models for Psychiatric Diagnosis: A Systematic Review. JAMA Netw Open 2023; 6:e231671. [PMID: 36877519 PMCID: PMC9989906 DOI: 10.1001/jamanetworkopen.2023.1671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
IMPORTANCE Neuroimaging-based artificial intelligence (AI) diagnostic models have proliferated in psychiatry. However, their clinical applicability and reporting quality (ie, feasibility) for clinical practice have not been systematically evaluated. OBJECTIVE To systematically assess the risk of bias (ROB) and reporting quality of neuroimaging-based AI models for psychiatric diagnosis. EVIDENCE REVIEW PubMed was searched for peer-reviewed, full-length articles published between January 1, 1990, and March 16, 2022. Studies aimed at developing or validating neuroimaging-based AI models for clinical diagnosis of psychiatric disorders were included. Reference lists were further searched for suitable original studies. Data extraction followed the CHARMS (Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modeling Studies) and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines. A closed-loop cross-sequential design was used for quality control. The PROBAST (Prediction Model Risk of Bias Assessment Tool) and modified CLEAR (Checklist for Evaluation of Image-Based Artificial Intelligence Reports) benchmarks were used to systematically evaluate ROB and reporting quality. FINDINGS A total of 517 studies presenting 555 AI models were included and evaluated. Of these models, 461 (83.1%; 95% CI, 80.0%-86.2%) were rated as having a high overall ROB based on the PROBAST. The ROB was particular high in the analysis domain, including inadequate sample size (398 of 555 models [71.7%; 95% CI, 68.0%-75.6%]), poor model performance examination (with 100% of models lacking calibration examination), and lack of handling data complexity (550 of 555 models [99.1%; 95% CI, 98.3%-99.9%]). None of the AI models was perceived to be applicable to clinical practices. Overall reporting completeness (ie, number of reported items/number of total items) for the AI models was 61.2% (95% CI, 60.6%-61.8%), and the completeness was poorest for the technical assessment domain with 39.9% (95% CI, 38.8%-41.1%). CONCLUSIONS AND RELEVANCE This systematic review found that the clinical applicability and feasibility of neuroimaging-based AI models for psychiatric diagnosis were challenged by a high ROB and poor reporting quality. Particularly in the analysis domain, ROB in AI diagnostic models should be addressed before clinical application.
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Affiliation(s)
- Zhiyi Chen
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Xuerong Liu
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Qingwu Yang
- Department of Neurology, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Yan-Jiang Wang
- Department of Neurology, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Kuan Miao
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Zheng Gong
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Yang Yu
- School of Psychology, Third Military Medical University, Chongqing, China
| | - Artemiy Leonov
- Department of Psychology, Clark University, Worcester, Massachusetts
| | - Chunlei Liu
- School of Psychology, Qufu Normal University, Qufu, China
| | - Zhengzhi Feng
- School of Psychology, Third Military Medical University, Chongqing, China
- Experimental Research Center for Medical and Psychological Science, Third Military Medical University, Chongqing, China
| | - Hu Chuan-Peng
- School of Psychology, Nanjing Normal University, Nanjing, China
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Wu J, Su Y, Zhu W, Mallak NJ, Lepore N, Reiman EM, Caselli RJ, Thompson PM, Chen K, Wang Y. Improved Prediction of Amyloid-β and Tau Burden Using Hippocampal Surface Multivariate Morphometry Statistics and Sparse Coding. J Alzheimers Dis 2023; 91:637-651. [PMID: 36463452 PMCID: PMC9940990 DOI: 10.3233/jad-220812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Amyloid-β (Aβ) plaques and tau protein tangles in the brain are the defining 'A' and 'T' hallmarks of Alzheimer's disease (AD), and together with structural atrophy detectable on brain magnetic resonance imaging (MRI) scans as one of the neurodegenerative ('N') biomarkers comprise the "ATN framework" of AD. Current methods to detect Aβ/tau pathology include cerebrospinal fluid (invasive), positron emission tomography (PET; costly and not widely available), and blood-based biomarkers (promising but mainly still in development). OBJECTIVE To develop a non-invasive and widely available structural MRI-based framework to quantitatively predict the amyloid and tau measurements. METHODS With MRI-based hippocampal multivariate morphometry statistics (MMS) features, we apply our Patch Analysis-based Surface Correntropy-induced Sparse coding and max-pooling (PASCS-MP) method combined with the ridge regression model to individual amyloid/tau measure prediction. RESULTS We evaluate our framework on amyloid PET/MRI and tau PET/MRI datasets from the Alzheimer's Disease Neuroimaging Initiative. Each subject has one pair consisting of a PET image and MRI scan, collected at about the same time. Experimental results suggest that amyloid/tau measurements predicted with our PASCP-MP representations are closer to the real values than the measures derived from other approaches, such as hippocampal surface area, volume, and shape morphometry features based on spherical harmonics. CONCLUSION The MMS-based PASCP-MP is an efficient tool that can bridge hippocampal atrophy with amyloid and tau pathology and thus help assess disease burden, progression, and treatment effects.
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Affiliation(s)
- Jianfeng Wu
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, USA
| | - Yi Su
- Banner Alzheimer’s Institute, Phoenix, AZ, USA
| | - Wenhui Zhu
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, USA
| | - Negar Jalili Mallak
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, USA
| | - Natasha Lepore
- CIBORG Lab, Department of Radiology Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | | | | | - Paul M. Thompson
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA
| | - Kewei Chen
- Banner Alzheimer’s Institute, Phoenix, AZ, USA
| | - Yalin Wang
- School of Computing and Augmented Intelligence, Arizona State University, Tempe, AZ, USA
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Cong Z, Fu Y, Chen N, Zhang L, Yao C, Wang Y, Yao Z, Hu B. Individuals with cannabis use are associated with widespread morphological alterations in the subregions of the amygdala, hippocampus, and pallidum. Drug Alcohol Depend 2022; 239:109595. [PMID: 35961268 DOI: 10.1016/j.drugalcdep.2022.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/02/2022] [Accepted: 07/30/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Cannabis is the most frequently used illicit drug worldwide. Although multiple structural MRI studies of individuals with cannabis use (CB) have been undertaken, the reports of the volume alterations in the amygdala, hippocampus, and pallidum are not consistent. This study aims to detect subregion-level morphological alterations, analyze the correlation areas with cannabis usage characteristics, and gain new insights into the neuro mechanisms of CB. METHODS By leveraging the novel surface-based subcortical morphometry method, 20 CB and 22 age- and sex-matched healthy controls (HC) were included to explore their volumetric and morphological differences in the three subcortical structures. Afterward, the correlation analysis between surface morphological eigenvalues and cannabis usage characteristics was performed. RESULTS Compared with volumetric measures, the surface-based subcortical morphometry method detected more significant global morphological deformations in the left amygdala, right hippocampus, and right pallidum (overall-p < 0.05, corrected). More obvious morphological alterations (atrophy or expansion) were observed in specific subregions (vertex-based p-value<0.05, uncorrected) of the three subcortical structures. Both positive and negative subregional correlation areas were reported by the correlation analysis. CONCLUSIONS The current study illuminated new pathophysiologic mechanisms in the amygdala, hippocampus, and pallidum at the subregion level, which may inform the subsequent smaller-scale CB research.
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Affiliation(s)
- Zhaoyang Cong
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Yu Fu
- College of Information Science & Electronic Engineering, Zhejiang University, Hangzhou, Zhejiang Province 310027, China
| | - Nan Chen
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Lingyu Zhang
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Chaofan Yao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province 730000, China
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Zhijun Yao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province 730000, China.
| | - Bin Hu
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province 730000, China; Joint Research Center for Cognitive Neurosensor Technology of Lanzhou University & Institute of Semiconductors, Chinese Academy of Sciences, Lanzhou, Gansu Province 730000, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; Engineering Research Center of Open Source Software and Real-Time System (Lanzhou University), Ministry of Education, Lanzhou, Gansu Province 730000, China.
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9
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Chai H, Sun J, Zhou P, Zhang L. Multivariate morphometry statistics reveal the morphological change pattern of hippocampus during normal aging. Neuroreport 2022; 33:481-486. [PMID: 35775325 DOI: 10.1097/wnr.0000000000001810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There have been numerous studies focusing on normal aging in previous decades which is accompanied by the structural and functional decline in the hippocampus, while the pattern of hippocampal alteration with age remains unclear. Figuring out the mechanism of hippocampal changes precisely is beneficial for a better understanding of the aging process. In this study, we included a total of 451 T1 MRI scans of subjects of age 50-90 who were labeled as normal in the Alzheimer's Disease Neuroimaging Initiative. Taking 10 years of age as an age band, we divided the subjects into four groups (denoted as HC1, HC2, HC3, and HC4, respectively), with the youngest being 50-60 and the oldest 81-90. Then the Multivariate Morphometry Statistics (MMS) of the hippocampus segmented from the four groups were extracted by surface reconstruction, mesh generation, and surface registration. Finally, the significant differences between the youngest group and the other three were statistically analyzed. Results showed that the earliest deformation region of the left hippocampus located in the frontal subiculum and the dorsal CA1 of the tail part and gradually expanded with aging, while the right hippocampal deformation mainly concentrated in the dorsal CA1 and spread to the posterior CA2-3, which occurred later than that of the left. All the results illustrated that the hippocampus is truly a vulnerable structure in the course of aging, and the MMS are sensitive metrics for detecting the changes in the subcortical convex structure.
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Affiliation(s)
- Hong Chai
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Lanzhou Jiaotong University
| | - Jianhua Sun
- Gansu Keyuan Power Group Tongxing Zhineng Technology Development Corporation
| | - Peng Zhou
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Lanzhou Jiaotong University
| | - Lingyu Zhang
- Department of Computer Science and Technology, Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, China
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10
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Wu J, Dong Q, Gui J, Zhang J, Su Y, Chen K, Thompson PM, Caselli RJ, Reiman EM, Ye J, Wang Y. Predicting Brain Amyloid Using Multivariate Morphometry Statistics, Sparse Coding, and Correntropy: Validation in 1,101 Individuals From the ADNI and OASIS Databases. Front Neurosci 2021; 15:669595. [PMID: 34421510 PMCID: PMC8377280 DOI: 10.3389/fnins.2021.669595] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023] Open
Abstract
Biomarker assisted preclinical/early detection and intervention in Alzheimer’s disease (AD) may be the key to therapeutic breakthroughs. One of the presymptomatic hallmarks of AD is the accumulation of beta-amyloid (Aβ) plaques in the human brain. However, current methods to detect Aβ pathology are either invasive (lumbar puncture) or quite costly and not widely available (amyloid PET). Our prior studies show that magnetic resonance imaging (MRI)-based hippocampal multivariate morphometry statistics (MMS) are an effective neurodegenerative biomarker for preclinical AD. Here we attempt to use MRI-MMS to make inferences regarding brain Aβ burden at the individual subject level. As MMS data has a larger dimension than the sample size, we propose a sparse coding algorithm, Patch Analysis-based Surface Correntropy-induced Sparse-coding and Max-Pooling (PASCS-MP), to generate a low-dimensional representation of hippocampal morphometry for each individual subject. Then we apply these individual representations and a binary random forest classifier to predict brain Aβ positivity for each person. We test our method in two independent cohorts, 841 subjects from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and 260 subjects from the Open Access Series of Imaging Studies (OASIS). Experimental results suggest that our proposed PASCS-MP method and MMS can discriminate Aβ positivity in people with mild cognitive impairment (MCI) [Accuracy (ACC) = 0.89 (ADNI)] and in cognitively unimpaired (CU) individuals [ACC = 0.79 (ADNI) and ACC = 0.81 (OASIS)]. These results compare favorably relative to measures derived from traditional algorithms, including hippocampal volume and surface area, shape measures based on spherical harmonics (SPHARM) and our prior Patch Analysis-based Surface Sparse-coding and Max-Pooling (PASS-MP) methods.
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Affiliation(s)
- Jianfeng Wu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, United States
| | - Qunxi Dong
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, United States.,Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China
| | - Jie Gui
- School of Cyber Science and Engineering, Southeast University, Nanjing, China
| | - Jie Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, United States
| | - Yi Su
- Banner Alzheimer's Institute, Phoenix, AZ, United States
| | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ, United States
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, United States
| | - Richard J Caselli
- Department of Neurology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Eric M Reiman
- Banner Alzheimer's Institute, Phoenix, AZ, United States
| | - Jieping Ye
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, United States
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11
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Zhang J, Dong Q, Shi J, Li Q, Stonnington CM, Gutman BA, Chen K, Reiman EM, Caselli RJ, Thompson PM, Ye J, Wang Y. Predicting future cognitive decline with hyperbolic stochastic coding. Med Image Anal 2021; 70:102009. [PMID: 33711742 PMCID: PMC8049149 DOI: 10.1016/j.media.2021.102009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/10/2020] [Accepted: 02/16/2021] [Indexed: 01/18/2023]
Abstract
Hyperbolic geometry has been successfully applied in modeling brain cortical and subcortical surfaces with general topological structures. However, such approaches, similar to other surface-based brain morphology analysis methods, usually generate high dimensional features. It limits their statistical power in cognitive decline prediction research, especially in datasets with limited subject numbers. To address the above limitation, we propose a novel framework termed as hyperbolic stochastic coding (HSC). We first compute diffeomorphic maps between general topological surfaces by mapping them to a canonical hyperbolic parameter space with consistent boundary conditions and extracts critical shape features. Secondly, in the hyperbolic parameter space, we introduce a farthest point sampling with breadth-first search method to obtain ring-shaped patches. Thirdly, stochastic coordinate coding and max-pooling algorithms are adopted for feature dimension reduction. We further validate the proposed system by comparing its classification accuracy with some other methods on two brain imaging datasets for Alzheimer's disease (AD) progression studies. Our preliminary experimental results show that our algorithm achieves superior results on various classification tasks. Our work may enrich surface-based brain imaging research tools and potentially result in a diagnostic and prognostic indicator to be useful in individualized treatment strategies.
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Affiliation(s)
- Jie Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287 USA
| | - Qunxi Dong
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287 USA
| | - Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287 USA
| | - Qingyang Li
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287 USA
| | | | - Boris A Gutman
- Armour College of Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ, USA
| | | | | | - Paul M Thompson
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
| | - Jieping Ye
- Department of Computational Medicine and Bioinformatics & Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287 USA.
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12
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Zhang Z, Wang X, Kong L, Zhu H. High-Dimensional Spatial Quantile Function-on-Scalar Regression. J Am Stat Assoc 2021; 117:1563-1578. [PMID: 37008532 PMCID: PMC10065478 DOI: 10.1080/01621459.2020.1870984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 08/27/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
This article develops a novel spatial quantile function-on-scalar regression model, which studies the conditional spatial distribution of a high-dimensional functional response given scalar predictors. With the strength of both quantile regression and copula modeling, we are able to explicitly characterize the conditional distribution of the functional or image response on the whole spatial domain. Our method provides a comprehensive understanding of the effect of scalar covariates on functional responses across different quantile levels and also gives a practical way to generate new images for given covariate values. Theoretically, we establish the minimax rates of convergence for estimating coefficient functions under both fixed and random designs. We further develop an efficient primal-dual algorithm to handle high-dimensional image data. Simulations and real data analysis are conducted to examine the finite-sample performance.
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Affiliation(s)
- Zhengwu Zhang
- Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC
| | - Xiao Wang
- Department of Statistics, Purdue University, West Lafayette, IN
| | - Linglong Kong
- Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
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13
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Fu Y, Zhang J, Li Y, Shi J, Zou Y, Guo H, Li Y, Yao Z, Wang Y, Hu B. A novel pipeline leveraging surface-based features of small subcortical structures to classify individuals with autism spectrum disorder. Prog Neuropsychopharmacol Biol Psychiatry 2021; 104:109989. [PMID: 32512131 PMCID: PMC9632410 DOI: 10.1016/j.pnpbp.2020.109989] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/19/2020] [Accepted: 05/30/2020] [Indexed: 10/24/2022]
Abstract
Autism spectrum disorder (ASD) is accompanied with widespread impairment in social-emotional functioning. Classification of ASD using sensitive morphological features derived from structural magnetic resonance imaging (MRI) of the brain may help us to better understand ASD-related mechanisms and improve related automatic diagnosis. Previous studies using T1 MRI scans in large heterogeneous ABIDE dataset with typical development (TD) controls reported poor classification accuracies (around 60%). This may because they only considered surface-based morphometry (SBM) as scalar estimates (such as cortical thickness and surface area) and ignored the neighboring intrinsic geometry information among features. In recent years, the shape-related SBM achieves great success in discovering the disease burden and progression of other brain diseases. However, when focusing on local geometry information, its high dimensionality requires careful treatment in its application to machine learning. To address the above challenges, we propose a novel pipeline for ASD classification, which mainly includes the generation of surface-based features, patch-based surface sparse coding and dictionary learning, Max-pooling and ensemble classifiers based on adaptive optimizers. The proposed pipeline may leverage the sensitivity of brain surface morphometry statistics and the efficiency of sparse coding and Max-pooling. By introducing only the surface features of bilateral hippocampus that derived from 364 male subjects with ASD and 381 age-matched TD males, this pipeline outperformed five recent MRI-based ASD classification studies with >80% accuracy in discriminating individuals with ASD from TD controls. Our results suggest shape-related SBM features may further boost the classification performance of MRI between ASD and TD.
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Affiliation(s)
- Yu Fu
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China
| | - Jie Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Yuan Li
- School of Information Science and Engineering, Shandong Normal University, Jinan, Shandong Province, China
| | - Jie Shi
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China
| | - Ying Zou
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China
| | - Hanning Guo
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China
| | - Yongchao Li
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China
| | - Zhijun Yao
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China.
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA.
| | - Bin Hu
- School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China; Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, Lanzhou, Gansu Province, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China.
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14
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Elzoheiry S, Lewen A, Schneider J, Both M, Hefter D, Boffi JC, Hollnagel JO, Kann O. Mild metabolic stress is sufficient to disturb the formation of pyramidal cell ensembles during gamma oscillations. J Cereb Blood Flow Metab 2020; 40:2401-2415. [PMID: 31842665 PMCID: PMC7820691 DOI: 10.1177/0271678x19892657] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Disturbances of cognitive functions occur rapidly during acute metabolic stress. However, the underlying mechanisms are not fully understood. Cortical gamma oscillations (30-100 Hz) emerging from precise synaptic transmission between excitatory principal neurons and inhibitory interneurons, such as fast-spiking GABAergic basket cells, are associated with higher brain functions, like sensory perception, selective attention and memory formation. We investigated the alterations of cholinergic gamma oscillations at the level of neuronal ensembles in the CA3 region of rat hippocampal slice cultures. We combined electrophysiology, calcium imaging (CamKII.GCaMP6f) and mild metabolic stress that was induced by rotenone, a lipophilic and highly selective inhibitor of complex I in the respiratory chain of mitochondria. The detected pyramidal cell ensembles showing repetitive patterns of activity were highly sensitive to mild metabolic stress. Whereas such synchronised multicellular activity diminished, the overall activity of individual pyramidal cells was unaffected. Additionally, mild metabolic stress had no effect on the rate of action potential generation in fast-spiking neural units. However, the partial disinhibition of slow-spiking neural units suggests that disturbances of ensemble formation likely result from alterations in synaptic inhibition. Our study bridges disturbances on the (multi-)cellular and network level to putative cognitive impairment on the system level.
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Affiliation(s)
- Shehabeldin Elzoheiry
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Andrea Lewen
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Justus Schneider
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Martin Both
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Dimitri Hefter
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany.,RG Animal Models in Psychiatry, Clinic of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannheim, Germany
| | - Juan Carlos Boffi
- Institute for Anatomy and Cell Biology, University of Heidelberg, Heidelberg, Germany
| | - Jan-Oliver Hollnagel
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - Oliver Kann
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany.,Interdisciplinary Centre for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
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15
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Lyu X, Sun WW, Wang Z, Liu H, Yang J, Cheng G. Tensor Graphical Model: Non-Convex Optimization and Statistical Inference. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2020; 42:2024-2037. [PMID: 30932830 DOI: 10.1109/tpami.2019.2907679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We consider the estimation and inference of graphical models that characterize the dependency structure of high-dimensional tensor-valued data. To facilitate the estimation of the precision matrix corresponding to each way of the tensor, we assume the data follow a tensor normal distribution whose covariance has a Kronecker product structure. A critical challenge in the estimation and inference of this model is the fact that its penalized maximum likelihood estimation involves minimizing a non-convex objective function. To address it, this paper makes two contributions: (i) In spite of the non-convexity of this estimation problem, we prove that an alternating minimization algorithm, which iteratively estimates each sparse precision matrix while fixing the others, attains an estimator with an optimal statistical rate of convergence. (ii) We propose a de-biased statistical inference procedure for testing hypotheses on the true support of the sparse precision matrices, and employ it for testing a growing number of hypothesis with false discovery rate (FDR) control. The asymptotic normality of our test statistic and the consistency of FDR control procedure are established. Our theoretical results are backed up by thorough numerical studies and our real applications on neuroimaging studies of Autism spectrum disorder and users' advertising click analysis bring new scientific findings and business insights. The proposed methods are encoded into a publicly available R package Tlasso.
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16
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Ahn H, Ko TS. The Genetic Relationship between Paroxysmal Movement Disorders and Epilepsy. ANNALS OF CHILD NEUROLOGY 2020. [DOI: 10.26815/acn.2020.00073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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17
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Dong Q, Zhang W, Stonnington CM, Wu J, Gutman BA, Chen K, Su Y, Baxter LC, Thompson PM, Reiman EM, Caselli RJ, Wang Y. Applying surface-based morphometry to study ventricular abnormalities of cognitively unimpaired subjects prior to clinically significant memory decline. NEUROIMAGE-CLINICAL 2020; 27:102338. [PMID: 32683323 PMCID: PMC7371915 DOI: 10.1016/j.nicl.2020.102338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 12/31/2022]
Abstract
A completely automated surface-based ventricular morphometry system. Generate a whole connected 3D ventricular shape model. Test-retest the system in two independent CU subject cohorts. Subregional ventricular abnormalities prior to clinically memory decline.
Ventricular volume (VV) is a widely used structural magnetic resonance imaging (MRI) biomarker in Alzheimer’s disease (AD) research. Abnormal enlargements of VV can be detected before clinically significant memory decline. However, VV does not pinpoint the details of subregional ventricular expansions. Here we introduce a ventricular morphometry analysis system (VMAS) that generates a whole connected 3D ventricular shape model and encodes a great deal of ventricular surface deformation information that is inaccessible by VV. VMAS contains an automated segmentation approach and surface-based multivariate morphometry statistics. We applied VMAS to two independent datasets of cognitively unimpaired (CU) groups. To our knowledge, it is the first work to detect ventricular abnormalities that distinguish normal aging subjects from those who imminently progress to clinically significant memory decline. Significant bilateral ventricular morphometric differences were first shown in 38 members of the Arizona APOE cohort, which included 18 CU participants subsequently progressing to the clinically significant memory decline within 2 years after baseline visits (progressors), and 20 matched CU participants with at least 4 years of post-baseline cognitive stability (non-progressors). VMAS also detected significant differences in bilateral ventricular morphometry in 44 Alzheimer’s Disease Neuroimaging Initiative (ADNI) subjects (18 CU progressors vs. 26 CU non-progressors) with the same inclusion criterion. Experimental results demonstrated that the ventricular anterior horn regions were affected bilaterally in CU progressors, and more so on the left. VMAS may track disease progression at subregional levels and measure the effects of pharmacological intervention at a preclinical stage.
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Affiliation(s)
- Qunxi Dong
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Wen Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | | | - Jianfeng Wu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Boris A Gutman
- Armour College of Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Yi Su
- Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Leslie C Baxter
- Human Brain Imaging Laboratory, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Paul M Thompson
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
| | | | | | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA.
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18
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Yao Z, Fu Y, Wu J, Zhang W, Yu Y, Zhang Z, Wu X, Wang Y, Hu B. Morphological changes in subregions of hippocampus and amygdala in major depressive disorder patients. Brain Imaging Behav 2020; 14:653-667. [PMID: 30519998 PMCID: PMC6551316 DOI: 10.1007/s11682-018-0003-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite many neuroimaging studies in the past years, the neuroanatomical substrates of major depressive disorder (MDD) subcortical structures are still not well understood. Since hippocampus and amygdala are the two vital subcortical structures that most susceptible to MDD, finding the evidence of morphological changes in their subregions may bring some new insights for MDD research. Combining structural magnetic resonance imaging (MRI) with novel morphometry analysis methods, we recruited 25 MDD patients and 28 healthy controls (HC), and investigated their volume and morphological differences in hippocampus and amygdala. Relative to volumetric method, our methods detected more significant global morphological atrophies (p<0.05). More precisely, subiculum and cornu ammonis (CA) 1 subregions of bilateral hippocampus, lateral (LA) and basolateral ventromedial (BLVM) of left amygdala and LA, BLVM, central (CE), amygdalostriatal transition area (ASTR), anterior cortical (ACO) and anterior amygdaloid area (AAA) of right amygdala were demonstrated prone to atrophy. Correlation analyses between each subject's surface eigenvalues and Hamilton Depression Scale (HAMD) were then performed. Correlation results showed that atrophy areas in hippocampus and amygdala have slight tendencies of expanding into other subregions with the development of MDD. Finally, we performed group morphometric analysis and drew the atrophy and expansion areas between MDD-Medicated group (only 19 medicated subjects in MDD group were included) and HC group, found some preliminary evidence about subregional morphological resilience of hippocampus and amygdala. These findings revealed new pathophysiologic patterns in the subregions of hippocampus and amygdala, which can help with subsequent smaller-scale MDD research.
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Affiliation(s)
- Zhijun Yao
- School of Information Science and Engineering, Lanzhou University, P.O. Box 730000, Lanzhou, China
| | - Yu Fu
- School of Information Science and Engineering, Lanzhou University, P.O. Box 730000, Lanzhou, China
| | - Jianfeng Wu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA
| | - Wenwen Zhang
- Department of Radiology, Gansu Provincial Hospital, Lanzhou, China
| | - Yue Yu
- School of Information Science and Engineering, Lanzhou University, P.O. Box 730000, Lanzhou, China
| | - Zicheng Zhang
- School of Information Science and Engineering, Lanzhou University, P.O. Box 730000, Lanzhou, China
| | - Xia Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China.
- College of Information Science and Technology, Beijing Normal University, P.O. Box 100000, Beijing, China.
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA.
| | - Bin Hu
- School of Information Science and Engineering, Lanzhou University, P.O. Box 730000, Lanzhou, China.
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19
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Dong Q, Zhang J, Li Q, Wang J, Leporé N, Thompson PM, Caselli RJ, Ye J, Wang Y. Integrating Convolutional Neural Networks and Multi-Task Dictionary Learning for Cognitive Decline Prediction with Longitudinal Images. J Alzheimers Dis 2020; 75:971-992. [PMID: 32390615 PMCID: PMC7427104 DOI: 10.3233/jad-190973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Disease progression prediction based on neuroimaging biomarkers is vital in Alzheimer's disease (AD) research. Convolutional neural networks (CNN) have been proved to be powerful for various computer vision research by refining reliable and high-level feature maps from image patches. OBJECTIVE A key challenge in applying CNN to neuroimaging research is the limited labeled samples with high dimensional features. Another challenge is how to improve the prediction accuracy by joint analysis of multiple data sources (i.e., multiple time points or multiple biomarkers). To address these two challenges, we propose a novel multi-task learning framework based on CNN. METHODS First, we pre-trained CNN on the ImageNet dataset and transferred the knowledge from the pre-trained model to neuroimaging representation. We used this deep model as feature extractor to generate high-level feature maps of different tasks. Then a novel unsupervised learning method, termed Multi-task Stochastic Coordinate Coding (MSCC), was proposed for learning sparse features of multi-task feature maps by using shared and individual dictionaries. Finally, Lasso regression was performed on these multi-task sparse features to predict AD progression measured by the Mini-Mental State Examination (MMSE) and the Alzheimer's Disease Assessment Scale cognitive subscale (ADAS-Cog). RESULTS We applied this novel CNN-MSCC system on the Alzheimer's Disease Neuroimaging Initiative dataset to predict future MMSE/ADAS-Cog scales. We found our method achieved superior performances compared with seven other methods. CONCLUSION Our work may add new insights into data augmentation and multi-task deep model research and facilitate the adoption of deep models in neuroimaging research.
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Affiliation(s)
- Qunxi Dong
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Jie Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Qingyang Li
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Junwen Wang
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Natasha Leporé
- Department of Radiology, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Paul M. Thompson
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
| | | | - Jieping Ye
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
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20
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Aortic root sizing for transcatheter aortic valve implantation using a shape model parameterisation. Med Biol Eng Comput 2019; 57:2081-2092. [PMID: 31353427 DOI: 10.1007/s11517-019-01996-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
During a transcatheter aortic valve implantation, an axisymmetric implant is placed in an irregularly shaped aortic root. Implanting an incorrect size can cause complications such as leakage of blood alongside or through the implant. The aim of this study was to construct a method that determines the optimal size of the implant based on the three-dimensional shape of the aortic root. Based on the pre-interventional computed tomography scan of 89 patients, a statistical shape model of their aortic root was constructed. The weights associated with the principal components and the volume of calcification in the aortic valve were used as parameters in a classification algorithm. The classification algorithm was trained using the patients with no or mild leakage after their intervention. Subsequently, the algorithms were applied to the patients with moderate to severe leakage. Cross validation showed that a random forest classifier assigned the same size in 65 ± 7% of the training cases, while 57 ± 8% of the patients with moderate to severe leakage were assigned a different size. This initial study showed that this semi-automatic method has the potential to correctly assign an implant size. Further research is required to assess whether the different size implants would improve the outcome of those patients.
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21
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Dong Q, Zhang W, Wu J, Li B, Schron EH, McMahon T, Shi J, Gutman BA, Chen K, Baxter LC, Thompson PM, Reiman EM, Caselli RJ, Wang Y. Applying surface-based hippocampal morphometry to study APOE-E4 allele dose effects in cognitively unimpaired subjects. NEUROIMAGE-CLINICAL 2019; 22:101744. [PMID: 30852398 PMCID: PMC6411498 DOI: 10.1016/j.nicl.2019.101744] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/02/2019] [Accepted: 03/02/2019] [Indexed: 11/30/2022]
Abstract
Apolipoprotein E (APOE) e4 is the major genetic risk factor for late-onset Alzheimer's disease (AD). The dose-dependent impact of this allele on hippocampal volumes has been documented, but its influence on general hippocampal morphology in cognitively unimpaired individuals is still elusive. Capitalizing on the study of a large number of cognitively unimpaired late middle aged and older adults with two, one and no APOE-e4 alleles, the current study aims to characterize the ability of our automated surface-based hippocampal morphometry algorithm to distinguish between these three levels of genetic risk for AD and demonstrate its superiority to a commonly used hippocampal volume measurement. We examined the APOE-e4 dose effect on cross-sectional hippocampal morphology analysis in a magnetic resonance imaging (MRI) database of 117 cognitively unimpaired subjects aged between 50 and 85 years (mean = 57.4, SD = 6.3), including 36 heterozygotes (e3/e4), 37 homozygotes (e4/e4) and 44 non-carriers (e3/e3). The proposed automated framework includes hippocampal surface segmentation and reconstruction, higher-order hippocampal surface correspondence computation, and hippocampal surface deformation analysis with multivariate statistics. In our experiments, the surface-based method identified APOE-e4 dose effects on the left hippocampal morphology. Compared to the widely-used hippocampal volume measure, our hippocampal morphometry statistics showed greater statistical power by distinguishing cognitively unimpaired subjects with two, one, and no APOE-e4 alleles. Our findings mirrored previous studies showing that APOE-e4 has a dose effect on the acceleration of brain structure deformities. The results indicated that the proposed surface-based hippocampal morphometry measure is a potential preclinical AD imaging biomarker for cognitively unimpaired individuals. Applied surface-based hippocampal morphometry on cognitively unimpaired subjects. Our study identified APOE-e4 dose effects on cognitively unimpaired subjects. Surface-based hippocampal morphometry outperformed the hippocampal volume measure. Surface-based hippocampal morphometry may be a potential preclinical AD biomarker.
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Affiliation(s)
- Qunxi Dong
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Wen Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Jianfeng Wu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Bolun Li
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | | | - Travis McMahon
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Boris A Gutman
- Armour College of Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Leslie C Baxter
- Human Brain Imaging Laboratory, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Paul M Thompson
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
| | | | | | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA.
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22
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Ekanayake J, Ridgway GR, Winston JS, Feredoes E, Razi A, Koush Y, Scharnowski F, Weiskopf N, Rees G. Volitional modulation of higher-order visual cortex alters human perception. Neuroimage 2018; 188:291-301. [PMID: 30529174 DOI: 10.1016/j.neuroimage.2018.11.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/03/2023] Open
Abstract
Can we change our perception by controlling our brain activation? Awareness during binocular rivalry is shaped by the alternating perception of different stimuli presented separately to each monocular view. We tested the possibility of causally influencing the likelihood of a stimulus entering awareness. To do this, participants were trained with neurofeedback, using realtime functional magnetic resonance imaging (rt-fMRI), to differentially modulate activation in stimulus-selective visual cortex representing each of the monocular images. Neurofeedback training led to altered bistable perception associated with activity changes in the trained regions. The degree to which training influenced perception predicted changes in grey and white matter volumes of these regions. Short-term intensive neurofeedback training therefore sculpted the dynamics of visual awareness, with associated plasticity in the human brain.
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Affiliation(s)
- Jinendra Ekanayake
- Wellcome Trust Centre for Human Neuroimaging, UCL Institute of Neurology, London, UK; UCL Institute of Cognitive Neuroscience, University College London, UK.
| | - Gerard R Ridgway
- Oxford Centre for Functional MRI of the Brain, University of Oxford, Oxford, UK
| | - Joel S Winston
- Wellcome Trust Centre for Human Neuroimaging, UCL Institute of Neurology, London, UK; UCL Institute of Cognitive Neuroscience, University College London, UK
| | - Eva Feredoes
- School of Psychology and Language Sciences, University of Reading, UK
| | - Adeel Razi
- Wellcome Trust Centre for Human Neuroimaging, UCL Institute of Neurology, London, UK; Department of Electronic Engineering, NED University of Engineering and Technology, Karachi, Pakistan
| | - Yury Koush
- Department of Radiology and Biomedical Imaging, Yale University, 300 Cedar Street, New Haven, CT, 06519, USA
| | - Frank Scharnowski
- Psychiatric University Hospital, University of Zürich, Lenggstrasse 31, 8032, Zürich, Switzerland; Neuroscience Center Zürich, University of Zürich and Swiss Federal Institute of Technology, Winterthurerstr. 190, 8057, Zürich, Switzerland; Zürich Center for Integrative Human Physiology (ZIHP), University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland
| | - Nikolaus Weiskopf
- Wellcome Trust Centre for Human Neuroimaging, UCL Institute of Neurology, London, UK; Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Geraint Rees
- Wellcome Trust Centre for Human Neuroimaging, UCL Institute of Neurology, London, UK; UCL Institute of Cognitive Neuroscience, University College London, UK
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23
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Functions and dysfunctions of neocortical inhibitory neuron subtypes. Nat Neurosci 2017; 20:1199-1208. [PMID: 28849791 DOI: 10.1038/nn.4619] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/30/2017] [Indexed: 02/08/2023]
Abstract
Neocortical inhibitory neurons exhibit remarkably diverse morphology, physiological properties and connectivity. Genetic access to molecularly defined subtypes of inhibitory neurons has aided their functional characterization in recent years. These studies have established that, instead of simply balancing excitatory neuron activity, inhibitory neurons actively shape excitatory circuits in a subtype-specific manner. We review the emerging view that inhibitory neuron subtypes perform context-dependent modulation of excitatory activity, as well as regulate experience-dependent plasticity of excitatory circuits. We then review the roles of neuromodulators in regulating the subtype-specific functions of inhibitory neurons. Finally, we discuss the idea that dysfunctions of inhibitory neuron subtypes may be responsible for various aspects of neurological disorders.
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24
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Tsao S, Gajawelli N, Zhou J, Shi J, Ye J, Wang Y, Leporé N. Feature selective temporal prediction of Alzheimer's disease progression using hippocampus surface morphometry. Brain Behav 2017; 7:e00733. [PMID: 28729939 PMCID: PMC5516607 DOI: 10.1002/brb3.733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/10/2017] [Accepted: 04/14/2017] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Prediction of Alzheimer's disease (AD) progression based on baseline measures allows us to understand disease progression and has implications in decisions concerning treatment strategy. To this end, we combine a predictive multi-task machine learning method (cFSGL) with a novel MR-based multivariate morphometric surface map of the hippocampus (mTBM) to predict future cognitive scores of patients. METHODS Previous work has shown that a multi-task learning framework that performs prediction of all future time points simultaneously (cFSGL) can be used to encode both sparsity as well as temporal smoothness. The authors showed that this method is able to predict cognitive outcomes of ADNI subjects using FreeSurfer-based baseline MRI features, MMSE score demographic information and ApoE status. Whilst volumetric information may hold generalized information on brain status, we hypothesized that hippocampus specific information may be more useful in predictive modeling of AD. To this end, we applied a multivariate tensor-based parametric surface analysis method (mTBM) to extract features from the hippocampal surfaces. RESULTS We combined mTBM features with traditional surface features such as middle axis distance, the Jacobian determinant as well as 2 of the Jacobian principal eigenvalues to yield 7 normalized hippocampal surface maps of 300 points each. By combining these 7 × 300 = 2100 features together with the previous ~350 features, we illustrate how this type of sparsifying method can be applied to an entire surface map of the hippocampus that yields a feature space that is 2 orders of magnitude larger than what was previously attempted. CONCLUSIONS By combining the power of the cFSGL multi-task machine learning framework with the addition of AD sensitive mTBM feature maps of the hippocampus surface, we are able to improve the predictive performance of ADAS cognitive scores 6, 12, 24, 36 and 48 months from baseline.
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Affiliation(s)
- Sinchai Tsao
- CIBORG Children's Hospital Los Angeles and University of Southern California Los Angeles CA USA
| | - Niharika Gajawelli
- CIBORG Children's Hospital Los Angeles and University of Southern California Los Angeles CA USA
| | - Jiayu Zhou
- Department of Computer Science and Engineering Michigan State University East Lansing MI USA
| | - Jie Shi
- School of Computing, Informatics and Decision Systems Engineering Arizona State University Phoenix AZ USA
| | - Jieping Ye
- Department of Computational Medicine and Bioinformatics & Department of Electrical Engineering and Computer Science University of Michigan Ann Arbor MI USA
| | - Yalin Wang
- School of Computing, Informatics and Decision Systems Engineering Arizona State University Phoenix AZ USA
| | - Natasha Leporé
- CIBORG Children's Hospital Los Angeles and University of Southern California Los Angeles CA USA
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25
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Zhang W, Shi J, Yu J, Zhan L, Thompson PM, Wang Y. Enhancing Diffusion MRI Measures By Integrating Grey and White Matter Morphometry With Hyperbolic Wasserstein Distance. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2017; 2017:520-524. [PMID: 28936280 DOI: 10.1109/isbi.2017.7950574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In order to improve the preclinical diagnose of Alzheimer's disease (AD), there is a great deal of interest in analyzing the AD related brain structural changes with magnetic resonance image (MRI) analyses. As the major features, variation of the structural connectivity and the cortical surface morphometry provide different views of structural changes to determine whether AD is present on presymptomatic patients. However, the large scale tensor-valued information and relatively low imaging resolution in diffusion MRI (dMRI) have created huge challenges for analysis. In this paper, we propose a novel framework that improves dMRI analysis power by fusing cortical surface morphometry features from structural MRI (sMRI). We first compute the hyperbolic harmonic maps between cortical surfaces with the landmark constraints thus to precisely evaluate surface tensor-based morphometry. Meanwhile, the graph-based analysis of structural connectivity derived from dMRI is conducted. Next, we fuse these two features via the optimal mass transportation (OMT) and eventually the Wasserstein distance (WD) based single image index is computed as a potential clinical multimodality imaging score. We apply our framework to brain images of 20 AD patients and 20 matched healthy controls, randomly chosen from the Alzheimer's Disease Neuroimaging Initiative (AD-NI2) dataset. Our preliminary experimental results of group classification outperformed those of some other single dMRI-based features, such as regional hippocampal volume, mean scores of fractional anisotropy (FA) and mean axial (MD). The novel image fusion pipeline and simple imaging score of structural changes may benefit the preclinical AD and AD prevention research.
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Affiliation(s)
- Wen Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
| | - Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
| | - Jun Yu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
| | - Liang Zhan
- Computer Engineering Program, University of Wisconsin-Stout, Menomonie, WI
| | - Paul M Thompson
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, CA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
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26
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Fan CC, Brown TT, Bartsch H, Kuperman JM, Hagler DJ, Schork A, Searcy Y, Bellugi U, Halgren E, Dale AM. Williams syndrome-specific neuroanatomical profile and its associations with behavioral features. NEUROIMAGE-CLINICAL 2017; 15:343-347. [PMID: 28560159 PMCID: PMC5443907 DOI: 10.1016/j.nicl.2017.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 11/26/2022]
Abstract
Williams Syndrome (WS) is a rare genetic disorder with unique behavioral features. Yet the rareness of WS has limited the number and type of studies that can be conducted in which inferences are made about how neuroanatomical abnormalities mediate behaviors. In this study, we extracted a WS-specific neuroanatomical profile from structural magnetic resonance imaging (MRI) measurements and tested its association with behavioral features of WS. Using a WS adult cohort (22 WS, 16 healthy controls), we modeled a sparse representation of a WS-specific neuroanatomical profile. The predictive performances are robust within the training cohort (10-fold cross-validation, AUC = 1.0) and accurately identify all WS individuals in an independent child WS cohort (seven WS, 59 children with diverse developmental status, AUC = 1.0). The WS-specific neuroanatomical profile includes measurements in the orbitofrontal cortex, superior parietal cortex, Sylvian fissures, and basal ganglia, and variability within these areas related to the underlying size of hemizygous deletion in patients with partial deletions. The profile intensity mediated the overall cognitive impairment as well as personality features related to hypersociability. Our results imply that the unique behaviors in WS were mediated through the constellation of abnormalities in cortical-subcortical circuitry consistent in child WS and adult WS. The robustness of the derived WS-specific neuroanatomical profile also demonstrates the potential utility of our approach in both clinical and research applications.
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Affiliation(s)
- Chun Chieh Fan
- Department of Cognitive Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Multimodal Imaging and Genetics, University of California San Diego, School of Medicine, 9452 Medical Center Drive, La Jolla, CA 92093, USA
| | - Timothy T Brown
- Center for Multimodal Imaging and Genetics, University of California San Diego, School of Medicine, 9452 Medical Center Drive, La Jolla, CA 92093, USA; Department of Neurosciences, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92037, USA; Center for Human Development, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Hauke Bartsch
- Center for Multimodal Imaging and Genetics, University of California San Diego, School of Medicine, 9452 Medical Center Drive, La Jolla, CA 92093, USA
| | - Joshua M Kuperman
- Center for Multimodal Imaging and Genetics, University of California San Diego, School of Medicine, 9452 Medical Center Drive, La Jolla, CA 92093, USA
| | - Donald J Hagler
- Center for Multimodal Imaging and Genetics, University of California San Diego, School of Medicine, 9452 Medical Center Drive, La Jolla, CA 92093, USA; Department of Radiology, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Andrew Schork
- Department of Cognitive Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Multimodal Imaging and Genetics, University of California San Diego, School of Medicine, 9452 Medical Center Drive, La Jolla, CA 92093, USA
| | - Yvonne Searcy
- Laboratory for Cognitive Neuroscience, Salk Institute, La Jolla, CA 92037, USA
| | - Ursula Bellugi
- Laboratory for Cognitive Neuroscience, Salk Institute, La Jolla, CA 92037, USA
| | - Eric Halgren
- Department of Neurosciences, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92037, USA; Department of Radiology, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92037, USA; Center for Human Brain Activity Mapping, University of California San Diego, School of Medicine, 3510 Dunhill Street, San Diego, CA 92121, USA.
| | - Anders M Dale
- Department of Cognitive Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Center for Multimodal Imaging and Genetics, University of California San Diego, School of Medicine, 9452 Medical Center Drive, La Jolla, CA 92093, USA; Department of Neurosciences, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92037, USA; Department of Radiology, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92037, USA.
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27
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Shi R, Zeng W, Su Z, Jiang J, Damasio H, Lu Z, Wang Y, Yau ST, Gu X. Hyperbolic Harmonic Mapping for Surface Registration. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE 2017; 39:965-980. [PMID: 27187948 PMCID: PMC5107180 DOI: 10.1109/tpami.2016.2567398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Automatic computation of surface correspondence via harmonic map is an active research field in computer vision, computer graphics and computational geometry. It may help document and understand physical and biological phenomena and also has broad applications in biometrics, medical imaging and motion capture industries. Although numerous studies have been devoted to harmonic map research, limited progress has been made to compute a diffeomorphic harmonic map on general topology surfaces with landmark constraints. This work conquers this problem by changing the Riemannian metric on the target surface to a hyperbolic metric so that the harmonic mapping is guaranteed to be a diffeomorphism under landmark constraints. The computational algorithms are based on Ricci flow and nonlinear heat diffusion methods. The approach is general and robust. We employ our algorithm to study the constrained surface registration problem which applies to both computer vision and medical imaging applications. Experimental results demonstrate that, by changing the Riemannian metric, the registrations are always diffeomorphic and achieve relatively high performance when evaluated with some popular surface registration evaluation standards.
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28
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Shi J, Zhang W, Tang M, Caselli RJ, Wang Y. Conformal invariants for multiply connected surfaces: Application to landmark curve-based brain morphometry analysis. Med Image Anal 2016; 35:517-529. [PMID: 27639215 DOI: 10.1016/j.media.2016.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 01/01/2023]
Abstract
Landmark curves were widely adopted in neuroimaging research for surface correspondence computation and quantified morphometry analysis. However, most of the landmark based morphometry studies only focused on landmark curve shape difference. Here we propose to compute a set of conformal invariant-based shape indices, which are associated with the landmark curve induced boundary lengths in the hyperbolic parameter domain. Such shape indices may be used to identify which surfaces are conformally equivalent and further quantitatively measure surface deformation. With the surface Ricci flow method, we can conformally map a multiply connected surface to the Poincaré disk. Our algorithm provides a stable method to compute the shape index values in the 2D (Poincaré Disk) parameter domain. The proposed shape indices are succinct, intrinsic and informative. Experimental results with synthetic data and 3D MRI data demonstrate that our method is invariant under isometric transformations and able to detect brain surface abnormalities. We also applied the new shape indices to analyze brain morphometry abnormalities associated with Alzheimer' s disease (AD). We studied the baseline MRI scans of a set of healthy control and AD patients from the Alzheimer' s Disease Neuroimaging Initiative (ADNI: 30 healthy control subjects vs. 30 AD patients). Although the lengths of the landmarks in Euclidean space, cortical surface area, and volume features did not differ between the two groups, our conformal invariant based shape indices revealed significant differences by Hotelling' s T2 test. The novel conformal invariant shape indices may offer a new sensitive biomarker and enrich our brain imaging analysis toolset for studying diagnosis and prognosis of AD.
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Affiliation(s)
- Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287, P.O. Box 878809, USA
| | - Wen Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287, P.O. Box 878809, USA
| | - Miao Tang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287, P.O. Box 878809, USA
| | | | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, 85287, P.O. Box 878809, USA.
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29
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Influence of APOE Genotype on Hippocampal Atrophy over Time - An N=1925 Surface-Based ADNI Study. PLoS One 2016; 11:e0152901. [PMID: 27065111 PMCID: PMC4827849 DOI: 10.1371/journal.pone.0152901] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/21/2016] [Indexed: 11/25/2022] Open
Abstract
The apolipoprotein E (APOE) e4 genotype is a powerful risk factor for late-onset Alzheimer’s disease (AD). In the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort, we previously reported significant baseline structural differences in APOE e4 carriers relative to non-carriers, involving the left hippocampus more than the right—a difference more pronounced in e4 homozygotes than heterozygotes. We now examine the longitudinal effects of APOE genotype on hippocampal morphometry at 6-, 12- and 24-months, in the ADNI cohort. We employed a new automated surface registration system based on conformal geometry and tensor-based morphometry. Among different hippocampal surfaces, we computed high-order correspondences, using a novel inverse-consistent surface-based fluid registration method and multivariate statistics consisting of multivariate tensor-based morphometry (mTBM) and radial distance. At each time point, using Hotelling’s T2 test, we found significant morphological deformation in APOE e4 carriers relative to non-carriers in the full cohort as well as in the non-demented (pooled MCI and control) subjects at each follow-up interval. In the complete ADNI cohort, we found greater atrophy of the left hippocampus than the right, and this asymmetry was more pronounced in e4 homozygotes than heterozygotes. These findings, combined with our earlier investigations, demonstrate an e4 dose effect on accelerated hippocampal atrophy, and support the enrichment of prevention trial cohorts with e4 carriers.
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30
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Zhang J, Stonnington C, Li Q, Shi J, Bauer RJ, Gutman BA, Chen K, Reiman EM, Thompson PM, Ye J, Wang Y. APPLYING SPARSE CODING TO SURFACE MULTIVARIATE TENSOR-BASED MORPHOMETRY TO PREDICT FUTURE COGNITIVE DECLINE. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2016; 2016:646-650. [PMID: 27499829 DOI: 10.1109/isbi.2016.7493350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Alzheimer's disease (AD) is a progressive brain disease. Accurate diagnosis of AD and its prodromal stage, mild cognitive impairment, is crucial for clinical trial design. There is also growing interests in identifying brain imaging biomarkers that help evaluate AD risk presymptomatically. Here, we applied a recently developed multivariate tensor-based morphometry (mTBM) method to extract features from hippocampal surfaces, derived from anatomical brain MRI. For such surface-based features, the feature dimension is usually much larger than the number of subjects. We used dictionary learning and sparse coding to effectively reduce the feature dimensions. With the new features, an Adaboost classifier was employed for binary group classification. In tests on publicly available data from the Alzheimers Disease Neuroimaging Initiative, the new framework outperformed several standard imaging measures in classifying different stages of AD. The new approach combines the efficiency of sparse coding with the sensitivity of surface mTBM, and boosts classification performance.
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Affiliation(s)
- Jie Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
| | | | - Qingyang Li
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
| | - Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
| | | | - Boris A Gutman
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, Univ.of Southern California, Marina del Rey, CA
| | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ
| | | | - Paul M Thompson
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, Univ.of Southern California, Marina del Rey, CA
| | - Jieping Ye
- Dept. of Computational Medicine and Bioinformatics, Univ. of Michigan, Ann Arbor, MI
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ., Tempe, AZ
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31
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Shi J, Collignon O, Xu L, Wang G, Kang Y, Leporé F, Lao Y, Joshi AA, Leporé N, Wang Y. Impact of Early and Late Visual Deprivation on the Structure of the Corpus Callosum: A Study Combining Thickness Profile with Surface Tensor-Based Morphometry. Neuroinformatics 2016; 13:321-336. [PMID: 25649876 DOI: 10.1007/s12021-014-9259-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Blindness represents a unique model to study how visual experience may shape the development of brain organization. Exploring how the structure of the corpus callosum (CC) reorganizes ensuing visual deprivation is of particular interest due to its important functional implication in vision (e.g., via the splenium of the CC). Moreover, comparing early versus late visually deprived individuals has the potential to unravel the existence of a sensitive period for reshaping the CC structure. Here, we develop a novel framework to capture a complete set of shape differences in the CC between congenitally blind (CB), late blind (LB) and sighted control (SC) groups. The CCs were manually segmented from T1-weighted brain MRI and modeled by 3D tetrahedral meshes. We statistically compared the combination of local area and thickness at each point between subject groups. Differences in area are found using surface tensor-based morphometry; thickness is estimated by tracing the streamlines in the volumetric harmonic field. Group differences were assessed on this combined measure using Hotelling's T(2) test. Interestingly, we observed that the total callosal volume did not differ between the groups. However, our fine-grained analysis reveals significant differences mostly localized around the splenium areas between both blind groups and the sighted group (general effects of blindness) and, importantly, specific dissimilarities between the LB and CB groups, illustrating the existence of a sensitive period for reorganization. The new multivariate statistics also gave better effect sizes for detecting morphometric differences, relative to other statistics. They may boost statistical power for CC morphometric analyses.
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Affiliation(s)
- Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | | | - Liang Xu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Gang Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
- School of Information and Electrical Engineering, Ludong University, Yantai, China
| | - Yue Kang
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Franco Leporé
- Department of Psychology, University of Montreal, Montreal, QC, Canada
| | - Yi Lao
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Anand A Joshi
- Signal and Image Processing Institute, Brain and Creativity Institute, University of Southern California, Los Angeles, CA, USA
| | - Natasha Leporé
- Department of Radiology, Children's Hospital Los Angeles, Los Angeles, CA, USA
- Department of Radiology & Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
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32
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Heinzen EL, Neale BM, Traynelis SF, Allen AS, Goldstein DB. The Genetics of Neuropsychiatric Diseases: Looking In and Beyond the Exome. Annu Rev Neurosci 2015; 38:47-68. [DOI: 10.1146/annurev-neuro-071714-034136] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Erin L. Heinzen
- Institute for Genomic Medicine,
- Department of Pathology and Cell Biology,
| | - Benjamin M. Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142
| | - Stephen F. Traynelis
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Andrew S. Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina 27710
| | - David B. Goldstein
- Institute for Genomic Medicine,
- Department of Genetics and Development, Columbia University, New York, NY 10032; ,
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33
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Paz JT, Huguenard JR. Microcircuits and their interactions in epilepsy: is the focus out of focus? Nat Neurosci 2015; 18:351-9. [PMID: 25710837 DOI: 10.1038/nn.3950] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/16/2015] [Indexed: 12/11/2022]
Abstract
Epileptic seizures represent dysfunctional neural networks dominated by excessive and/or hypersynchronous activity. Recent progress in the field has outlined two concepts regarding mechanisms of seizure generation, or ictogenesis. First, all seizures, even those associated with what have historically been thought of as 'primary generalized' epilepsies, appear to originate in local microcircuits and then propagate from that initial ictogenic zone. Second, seizures propagate through cerebral networks and engage microcircuits in distal nodes, a process that can be weakened or even interrupted by suppressing activity in such nodes. We describe various microcircuit motifs, with a special emphasis on one that has been broadly implicated in several epilepsies: feed-forward inhibition. Furthermore, we discuss how, in the dynamic network in which seizures propagate, focusing on circuit 'choke points' remote from the initiation site might be as important as that of the initial dysfunction, the seizure 'focus'.
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Affiliation(s)
- Jeanne T Paz
- Gladstone Institutes and University of California, San Francisco, California, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
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34
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Wade BSC, Valcour VG, Wendelken-Riegelhaupt L, Esmaeili-Firidouni P, Joshi SH, Wang Y, Thompson PM. MAPPING ABNORMAL SUBCORTICAL BRAIN MORPHOMETRY IN AN ELDERLY HIV+ COHORT. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2015; 2015:971-975. [PMID: 26413207 DOI: 10.1109/isbi.2015.7164033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Over 50% of HIV+ individuals exhibit neurocognitive impairment and subcortical atrophy, but the pattern of brain abnormalities associated with HIV is still poorly understood. Using parametric surface-based shape analyses, we mapped the 3D profile of subcortical morphometry in 63 HIV+ participants and 31 uninfected controls. The thalamus, corpus striatum, hippocampus, amygdala, brainstem, callosum and ventricles were segmented from brain MRIs. To investigate subcortical shape, we analyzed the Jacobian determinant (JD) and radial distances (RD) for structure surfaces. We also investigated effects of nadir CD4+ T-cell counts, viral load, and illness duration on subcortical morphology. Our results characterize subcortical morphometry in older HIV+ people, where participants showed significant volumetric enlargements in the thalamus, left pallidum and the ventricles while showing a reduction in the callosum. Further, RD maps revealed atrophy of the left thalamus and expansion of the brainstem in HIV. RD and JD maps of the right pallidum identified tissue expansion associated with illness duration while the left pallidum showed anterior atrophy and posterior expansion associated with viral load.
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Affiliation(s)
- Benjamin S C Wade
- Imaging Genetics Center, University of Southern California, Los Angeles, CA, USA
| | - Victor G Valcour
- Memory and Aging Center, Dept. of Neurology, University of California, San Francisco, CA, USA
| | | | | | - Shantanu H Joshi
- Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, UCLA, CA, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Paul M Thompson
- Imaging Genetics Center, University of Southern California, Los Angeles, CA, USA
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35
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Wade BSC, Valcour V, Busovaca E, Esmaeili-Firidouni P, Joshi SH, Wang Y, Thompson PM. Subcortical shape and volume abnormalities in an elderly HIV+ cohort. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9417. [PMID: 25844123 DOI: 10.1117/12.2082241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Over 50% of HIV+ individuals show significant impairment in psychomotor functioning, processing speed, working memory and attention [1, 2]. Patients receiving combination antiretroviral therapy may still have subcortical atrophy, but the profile of HIV-associated brain changes is poorly understood. With parametric surface-based shape analyses, we mapped the 3D profile of subcortical morphometry in 63 elderly HIV+ subjects (4 female; age=65.35 ± 2.21) and 31 uninfected elderly controls (2 female; age=64.68 ± 4.57) scanned with MRI as part of a San Francisco Bay Area study of elderly people with HIV. We also investigated whether morphometry was associated with nadir CD4+ (T-cell) counts, viral load and illness duration among HIV+ participants. FreeSurfer was used to segment the thalamus, caudate, putamen, pallidum, hippocampus, amygdala, accumbens, brainstem, callosum and ventricles from brain MRI scans. To study subcortical shape, we analyzed: (1) the Jacobian determinant (JD) indexed over structures' surface coordinates and (2) radial distances (RD) of structure surfaces from a medial curve. A JD less than 1 reflects regional tissue atrophy and greater than 1 reflects expansion. The volumes of several subcortical regions were found to be associated with HIV status. No regional volumes showed detectable associations with CD4 counts, viral load or illness duration. The shapes of numerous subcortical regions were significantly linked to HIV status, detectability of viral RNA and illness duration. Our results show subcortical brain differences in HIV+ subjects in both shape and volumetric domains.
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Affiliation(s)
- Benjamin S C Wade
- Imaging Genetics Center, University of Southern California, Marina del Rey, CA, USA
| | - Victor Valcour
- Memory and Aging Center, Department of Neurology University of California, San Francisco, CA, USA
| | - Edgar Busovaca
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Pardis Esmaeili-Firidouni
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Shantanu H Joshi
- Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Paul M Thompson
- Imaging Genetics Center, University of Southern California, Marina del Rey, CA, USA
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36
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CACNA1A haploinsufficiency causes cognitive impairment, autism and epileptic encephalopathy with mild cerebellar symptoms. Eur J Hum Genet 2015; 23:1505-12. [PMID: 25735478 DOI: 10.1038/ejhg.2015.21] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 01/25/2023] Open
Abstract
CACNA1A loss-of-function mutations classically present as episodic ataxia type 2 (EA2), with brief episodes of ataxia and nystagmus, or with progressive spinocerebellar ataxia (SCA6). A minority of patients carrying CACNA1A mutations develops epilepsy. Non-motor symptoms associated with these mutations are often overlooked. In this study, we report 16 affected individuals from four unrelated families presenting with a spectrum of cognitive impairment including intellectual deficiency, executive dysfunction, ADHD and/or autism, as well as childhood-onset epileptic encephalopathy with refractory absence epilepsy, febrile seizures, downbeat nystagmus and episodic ataxia. Sequencing revealed one CACNA1A gene deletion, two deleterious CACNA1A point mutations including one known stop-gain and one new frameshift variant and a new splice-site variant. This report illustrates the phenotypic heterogeneity of CACNA1A loss-of-function mutations and stresses the cognitive and epileptic manifestations caused by the loss of CaV2.1 channels function, presumably affecting cerebellar, cortical and limbic networks.
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37
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Noebels J. Pathway-driven discovery of epilepsy genes. Nat Neurosci 2015; 18:344-50. [PMID: 25710836 DOI: 10.1038/nn.3933] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/22/2014] [Indexed: 12/12/2022]
Abstract
Epilepsy genes deliver critical insights into the molecular control of brain synchronization and are revolutionizing our understanding and treatment of the disease. The epilepsy-associated genome is rapidly expanding, and two powerful complementary approaches, isolation of de novo exome variants in patients and targeted mutagenesis in model systems, account for the steep increase. In sheer number, the tally of genes linked to seizures will likely match that of cancer and exceed it in biological diversity. The proteins act within most intracellular compartments and span the molecular determinants of firing and wiring in the developing brain. Every facet of neurotransmission, from dendritic spine to exocytotic machinery, is in play, and defects of synaptic inhibition are over-represented. The contributions of somatic mutations and noncoding microRNAs are also being explored. The functional spectrum of established epilepsy genes and the arrival of rapid, precise technologies for genome editing now provide a robust scaffold to prioritize hypothesis-driven discovery and further populate this genetic proto-map. Although each gene identified offers translational potential to stratify patient care, the complexity of individual variation and covert actions of genetic modifiers may confound single-gene solutions for the clinical disorder. In vivo genetic deconstruction of epileptic networks, ex vivo validation of variant profiles in patient-derived induced pluripotent stem cells, in silico variant modeling and modifier gene discovery, now in their earliest stages, will help clarify individual patterns. Because seizures stand at the crossroads of all neuronal synchronization disorders in the developing and aging brain, the neurobiological analysis of epilepsy-associated genes provides an extraordinary gateway to new insights into higher cortical function.
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Affiliation(s)
- Jeffrey Noebels
- Developmental Neurogenetics Laboratory, Departments of Neurology, Neuroscience, and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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38
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Gutman BA, Fletcher PT, Cardoso MJ, Fleishman GM, Lorenzi M, Thompson PM, Ourselin S. A Riemannian Framework for Intrinsic Comparison of Closed Genus-Zero Shapes. INFORMATION PROCESSING IN MEDICAL IMAGING : PROCEEDINGS OF THE ... CONFERENCE 2015. [PMID: 26221675 DOI: 10.1007/978-3-319-19992-4_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present a framework for intrinsic comparison of surface metric structures and curvatures. This work parallels the work of Kurtek et al. on parameterization-invariant comparison of genus zero shapes. Here, instead of comparing the embedding of spherically parameterized surfaces in space, we focus on the first fundamental form. To ensure that the distance on spherical metric tensor fields is invariant to parameterization, we apply the conjugation-invariant metric arising from the L2 norm on symmetric positive definite matrices. As a reparameterization changes the metric tensor by a congruent Jacobian transform, this metric perfectly suits our purpose. The result is an intrinsic comparison of shape metric structure that does not depend on the specifics of a spherical mapping. Further, when restricted to tensors of fixed volume form, the manifold of metric tensor fields and its quotient of the group of unitary diffeomorphisms becomes a proper metric manifold that is geodesically complete. Exploiting this fact, and augmenting the metric with analogous metrics on curvatures, we derive a complete Riemannian framework for shape comparison and reconstruction. A by-product of our framework is a near-isometric and curvature-preserving mapping between surfaces. The correspondence is optimized using the fast spherical fluid algorithm. We validate our framework using several subcortical boundary surface models from the ADNI dataset.
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Shi J, Stonnington CM, Thompson PM, Chen K, Gutman B, Reschke C, Baxter LC, Reiman EM, Caselli RJ, Wang Y. Studying ventricular abnormalities in mild cognitive impairment with hyperbolic Ricci flow and tensor-based morphometry. Neuroimage 2015; 104:1-20. [PMID: 25285374 PMCID: PMC4252650 DOI: 10.1016/j.neuroimage.2014.09.062] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/20/2014] [Accepted: 09/29/2014] [Indexed: 11/29/2022] Open
Abstract
Mild Cognitive Impairment (MCI) is a transitional stage between normal aging and dementia and people with MCI are at high risk of progression to dementia. MCI is attracting increasing attention, as it offers an opportunity to target the disease process during an early symptomatic stage. Structural magnetic resonance imaging (MRI) measures have been the mainstay of Alzheimer's disease (AD) imaging research, however, ventricular morphometry analysis remains challenging because of its complicated topological structure. Here we describe a novel ventricular morphometry system based on the hyperbolic Ricci flow method and tensor-based morphometry (TBM) statistics. Unlike prior ventricular surface parameterization methods, hyperbolic conformal parameterization is angle-preserving and does not have any singularities. Our system generates a one-to-one diffeomorphic mapping between ventricular surfaces with consistent boundary matching conditions. The TBM statistics encode a great deal of surface deformation information that could be inaccessible or overlooked by other methods. We applied our system to the baseline MRI scans of a set of MCI subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI: 71 MCI converters vs. 62 MCI stable). Although the combined ventricular area and volume features did not differ between the two groups, our fine-grained surface analysis revealed significant differences in the ventricular regions close to the temporal lobe and posterior cingulate, structures that are affected early in AD. Significant correlations were also detected between ventricular morphometry, neuropsychological measures, and a previously described imaging index based on fluorodeoxyglucose positron emission tomography (FDG-PET) scans. This novel ventricular morphometry method may offer a new and more sensitive approach to study preclinical and early symptomatic stage AD.
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Affiliation(s)
- Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | | | - Paul M Thompson
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
| | - Kewei Chen
- Banner Alzheimer's Institute and Banner Good Samaritan PET Center, Phoenix, AZ, USA
| | - Boris Gutman
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
| | - Cole Reschke
- Banner Alzheimer's Institute and Banner Good Samaritan PET Center, Phoenix, AZ, USA
| | - Leslie C Baxter
- Human Brain Imaging Laboratory, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute and Banner Good Samaritan PET Center, Phoenix, AZ, USA
| | | | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA.
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40
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Shi J, Leporé N, Gutman BA, Thompson PM, Baxter LC, Caselli RJ, Wang Y. Genetic influence of apolipoprotein E4 genotype on hippocampal morphometry: An N = 725 surface-based Alzheimer's disease neuroimaging initiative study. Hum Brain Mapp 2014; 35:3903-18. [PMID: 24453132 PMCID: PMC4269525 DOI: 10.1002/hbm.22447] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/23/2013] [Accepted: 11/26/2013] [Indexed: 01/12/2023] Open
Abstract
The apolipoprotein E (APOE) e4 allele is the most prevalent genetic risk factor for Alzheimer's disease (AD). Hippocampal volumes are generally smaller in AD patients carrying the e4 allele compared to e4 noncarriers. Here we examined the effect of APOE e4 on hippocampal morphometry in a large imaging database-the Alzheimer's Disease Neuroimaging Initiative (ADNI). We automatically segmented and constructed hippocampal surfaces from the baseline MR images of 725 subjects with known APOE genotype information including 167 with AD, 354 with mild cognitive impairment (MCI), and 204 normal controls. High-order correspondences between hippocampal surfaces were enforced across subjects with a novel inverse consistent surface fluid registration method. Multivariate statistics consisting of multivariate tensor-based morphometry (mTBM) and radial distance were computed for surface deformation analysis. Using Hotelling's T(2) test, we found significant morphological deformation in APOE e4 carriers relative to noncarriers in the entire cohort as well as in the nondemented (pooled MCI and control) subjects, affecting the left hippocampus more than the right, and this effect was more pronounced in e4 homozygotes than heterozygotes. Our findings are consistent with previous studies that showed e4 carriers exhibit accelerated hippocampal atrophy; we extend these findings to a novel measure of hippocampal morphometry. Hippocampal morphometry has significant potential as an imaging biomarker of early stage AD.
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Affiliation(s)
- Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State UniversityTempeArizona
| | - Natasha Leporé
- Department of RadiologyChildren's Hospital Los AngelesLos AngelesCalifornia
| | - Boris A. Gutman
- Imaging Genetics CenterInstitute for Neuroimaging and InformaticsUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Paul M. Thompson
- Department of NeurologyImaging Genetics CenterLaboratory of Neuro ImagingUCLA School of MedicineLos AngelesCalifornia
- Department of Psychiatry and Biobehavioral SciencesSemel Institute, UCLA School of MedicineLos AngelesCalifornia
| | - Leslie C. Baxter
- Human Brain Imaging Laboratory, Barrow Neurological InstitutePhoenixArizona
| | | | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State UniversityTempeArizona
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41
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Tsao S, Gajawelli N, Zhou J, Shi J, Ye J, Wang Y, Lepore N. Evaluating the Predictive Power of Multivariate Tensor-based Morphometry in Alzheimers Disease Progression via Convex Fused Sparse Group Lasso. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 9034:90342L. [PMID: 25076826 PMCID: PMC4112760 DOI: 10.1117/12.2042720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Prediction of Alzheimers disease (AD) progression based on baseline measures allows us to understand disease progression and has implications in decisions concerning treatment strategy. To this end we combine a predictive multi-task machine learning method1 with novel MR-based multivariate morphometric surface map of the hippocampus2 to predict future cognitive scores of patients. Previous work by Zhou et al.1 has shown that a multi-task learning framework that performs prediction of all future time points (or tasks) simultaneously can be used to encode both sparsity as well as temporal smoothness. They showed that this can be used in predicting cognitive outcomes of Alzheimers Disease Neuroimaging Initiative (ADNI) subjects based on FreeSurfer-based baseline MRI features, MMSE score demographic information and ApoE status. Whilst volumetric information may hold generalized information on brain status, we hypothesized that hippocampus specific information may be more useful in predictive modeling of AD. To this end, we applied Shi et al.2s recently developed multivariate tensor-based (mTBM) parametric surface analysis method to extract features from the hippocampal surface. We show that by combining the power of the multi-task framework with the sensitivity of mTBM features of the hippocampus surface, we are able to improve significantly improve predictive performance of ADAS cognitive scores 6, 12, 24, 36 and 48 months from baseline.
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Affiliation(s)
- Sinchai Tsao
- University of Washington, Seattle, Washington, USA
| | | | - Jiayu Zhou
- Arizona State University, Phoenix, Arizona, USA
| | - Jie Shi
- Arizona State University, Phoenix, Arizona, USA
| | - Jieping Ye
- Arizona State University, Phoenix, Arizona, USA
| | - Yalin Wang
- Arizona State University, Phoenix, Arizona, USA
| | - Natasha Lepore
- Children's Hospital Los Angeles, Los Angeles, California, USA
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42
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Houser CR. Do structural changes in GABA neurons give rise to the epileptic state? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 813:151-60. [PMID: 25012374 DOI: 10.1007/978-94-017-8914-1_12] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Identifying the role of GABA neurons in the development of an epileptic state has been particularly difficult in acquired epilepsy, in part because of the multiple changes that occur in such conditions. Although once questioned, there is now considerable evidence for loss of GABA neurons in multiple brain regions in models of acquired epilepsy. This loss can affect several cell types, including both somatostatin- and parvalbumin-expressing interneurons, and the cell type that is most severely affected can vary among brain regions and models. Because of the diversity of GABA neurons in the hippocampus and cerebral cortex, resulting functional deficits are unlikely to be compensated fully by remaining GABA neurons of other subtypes. The fundamental importance of GABA neuron loss in epilepsy is supported by findings in genetic mouse models in which GABA neurons appear to be decreased relatively selectively, and increased seizure susceptibility and spontaneous seizures develop. Alterations in remaining GABA neurons also occur in acquired epilepsy. These include alterations in inputs or receptors that could impair function, as well as morphological reorganization of GABAergic axons and their synaptic connections. Such axonal sprouting could be compensatory if normal circuits are reestablished, but the creation of aberrant circuitry could contribute to an epileptic condition. The functional effects of GABA neuron alterations thus may include not only reductions in GABAergic inhibition but also excessive neuronal synchrony and, potentially, depolarizing GABAergic influences. The combination of GABA neuron loss and alterations in remaining GABA neurons provides likely, though still unproven, substrates for the epileptic state.
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Affiliation(s)
- Carolyn R Houser
- Department of Neurobiology and Brain Research Institute, David Geffen School of Medicine at the University of California, Los Angeles, 10833 Le Conte Ave., Los Angeles, CA, 90095, USA,
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43
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Thompson PM, Ge T, Glahn DC, Jahanshad N, Nichols TE. Genetics of the connectome. Neuroimage 2013; 80:475-88. [PMID: 23707675 PMCID: PMC3905600 DOI: 10.1016/j.neuroimage.2013.05.013] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/05/2013] [Accepted: 05/08/2013] [Indexed: 11/24/2022] Open
Abstract
Connectome genetics attempts to discover how genetic factors affect brain connectivity. Here we review a variety of genetic analysis methods--such as genome-wide association studies (GWAS), linkage and candidate gene studies--that have been fruitfully adapted to imaging data to implicate specific variants in the genome for brain-related traits. Studies that emphasized the genetic influences on brain connectivity. Some of these analyses of brain integrity and connectivity using diffusion MRI, and others have mapped genetic effects on functional networks using resting state functional MRI. Connectome-wide genome-wide scans have also been conducted, and we review the multivariate methods required to handle the extremely high dimension of the genomic and network data. We also review some consortium efforts, such as ENIGMA, that offer the power to detect robust common genetic associations using phenotypic harmonization procedures and meta-analysis. Current work on connectome genetics is advancing on many fronts and promises to shed light on how disease risk genes affect the brain. It is already discovering new genetic loci and even entire genetic networks that affect brain organization and connectivity.
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Affiliation(s)
- Paul M Thompson
- Imaging Genetics Center, Laboratory of NeuroImaging, Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA 90095, USA.
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44
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Shi J, Thompson PM, Gutman B, Wang Y. Surface fluid registration of conformal representation: application to detect disease burden and genetic influence on hippocampus. Neuroimage 2013; 78:111-34. [PMID: 23587689 PMCID: PMC3683848 DOI: 10.1016/j.neuroimage.2013.04.018] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 03/06/2013] [Accepted: 04/05/2013] [Indexed: 11/23/2022] Open
Abstract
In this paper, we develop a new automated surface registration system based on surface conformal parameterization by holomorphic 1-forms, inverse consistent surface fluid registration, and multivariate tensor-based morphometry (mTBM). First, we conformally map a surface onto a planar rectangle space with holomorphic 1-forms. Second, we compute surface conformal representation by combining its local conformal factor and mean curvature and linearly scale the dynamic range of the conformal representation to form the feature image of the surface. Third, we align the feature image with a chosen template image via the fluid image registration algorithm, which has been extended into the curvilinear coordinates to adjust for the distortion introduced by surface parameterization. The inverse consistent image registration algorithm is also incorporated in the system to jointly estimate the forward and inverse transformations between the study and template images. This alignment induces a corresponding deformation on the surface. We tested the system on Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline dataset to study AD symptoms on hippocampus. In our system, by modeling a hippocampus as a 3D parametric surface, we nonlinearly registered each surface with a selected template surface. Then we used mTBM to analyze the morphometry difference between diagnostic groups. Experimental results show that the new system has better performance than two publicly available subcortical surface registration tools: FIRST and SPHARM. We also analyzed the genetic influence of the Apolipoprotein E[element of]4 allele (ApoE4), which is considered as the most prevalent risk factor for AD. Our work successfully detected statistically significant difference between ApoE4 carriers and non-carriers in both patients of mild cognitive impairment (MCI) and healthy control subjects. The results show evidence that the ApoE genotype may be associated with accelerated brain atrophy so that our work provides a new MRI analysis tool that may help presymptomatic AD research.
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Affiliation(s)
- Jie Shi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Paul M. Thompson
- Laboratory of Neuro Imaging, UCLA Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Boris Gutman
- Laboratory of Neuro Imaging, UCLA Dept. of Neurology, UCLA School of Medicine, Los Angeles, CA, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, Tempe, AZ, USA
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