1
|
Seyedmirzaei H, Salmannezhad A, Ashayeri H, Shushtari A, Farazinia B, Heidari MM, Momayezi A, Shaki Baher S. Growth-Associated Protein 43 and Tensor-Based Morphometry Indices in Mild Cognitive Impairment. Neuroinformatics 2024; 22:239-250. [PMID: 38630411 DOI: 10.1007/s12021-024-09663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2024] [Indexed: 08/17/2024]
Abstract
Growth-associated protein 43 (GAP-43) is found in the axonal terminal of neurons in the limbic system, which is affected in people with Alzheimer's disease (AD). We assumed GAP-43 may contribute to AD progression and serve as a biomarker. So, in a two-year follow-up study, we assessed GAP-43 changes and whether they are correlated with tensor-based morphometry (TBM) findings in patients with mild cognitive impairment (MCI). We included MCI and cognitively normal (CN) people with available baseline and follow-up cerebrospinal fluid (CSF) GAP-43 and TBM findings from the ADNI database. We assessed the difference between the two groups and correlations in each group at each time point. CSF GAP-43 and TBM measures were similar in the two study groups in all time points, except for the accelerated anatomical region of interest (ROI) of CN subjects that were significantly greater than those of MCI. The only significant correlations with GAP-43 observed were those inverse correlations with accelerated and non-accelerated anatomical ROI in MCI subjects at baseline. Plus, all TBM metrics decreased significantly in all study groups during the follow-up in contrast to CSF GAP-43 levels. Our study revealed significant associations between CSF GAP-43 levels and TBM indices among people of the AD spectrum.
Collapse
Affiliation(s)
- Homa Seyedmirzaei
- Sports Medicine Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hamidreza Ashayeri
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Shushtari
- Faculty of Medicine , Mazandaran University of Medical Sciences, Sari, Iran.
| | - Bita Farazinia
- Faculty of Economics and Management, Shiraz Branch, Islamic Azad University, Shiraz, Iran
| | - Mohammad Mahdi Heidari
- Student Research Committee, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Amirali Momayezi
- School of Chemical engineering, Iran University of Science and Technology, Tehran, Iran
| | - Sara Shaki Baher
- Faculty of Medicine, Tehran Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
2
|
de Mélo Silva Júnior ML, Diniz PRB, de Souza Vilanova MV, Basto GPT, Valença MM. Brain ventricles, CSF and cognition: a narrative review. Psychogeriatrics 2022; 22:544-552. [PMID: 35488797 DOI: 10.1111/psyg.12839] [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: 01/19/2022] [Revised: 03/07/2022] [Accepted: 04/12/2022] [Indexed: 11/29/2022]
Abstract
The brain ventricles are structures that have been related to cognition since antiquity. They are essential components in the development and maintenance of brain functions. The aging process runs with the enlargement of ventricles and is related to a less selective blood-cerebrospinal fluid barrier and then a more toxic cerebrospinal fluid environment. The study of brain ventricles as a biological marker of aging is promissing because they are structures easily identified in neuroimaging studies, present good inter-rater reliability, and measures of them can identify brain atrophy earlier than cortical structures. The ventricular system also plays roles in the development of dementia, since dysfunction in the clearance of beta-amyloid protein is a key mechanism in sporadic Alzheimer's disease. The morphometric and volumetric studies of the brain ventricles can help to distinguish between healthy elderly and persons with mild cognitive impairment (MCI) and dementia. Brain ventricle data may contribute to the appropriate allocation of individuals in groups at higher risk for MCI-dementia progression in clinical trials and to measuring therapeutic responses in these studies, as well as providing differential diagnosis, such as normal pressure hydrocephalus. Here, we reviewed the pathophysiology of healthy aging and cognitive decline, focusing on the role of the choroid plexus and brain ventricles in this process.
Collapse
Affiliation(s)
- Mário Luciano de Mélo Silva Júnior
- Medical School, Universidade Federal de Pernambuco, Recife, Brazil.,Medical School, Centro Universitário Maurício de Nassau, Recife, Brazil.,Neurology Unit, Hospital da Restauração, Recife, Brazil
| | | | | | | | | |
Collapse
|
3
|
Tu Y, Mi L, Zhang W, Zhang H, Zhang J, Fan Y, Goradia D, Chen K, Caselli RJ, Reiman EM, Gu X, Wang Y. Computing Univariate Neurodegenerative Biomarkers with Volumetric Optimal Transportation: A Pilot Study. Neuroinformatics 2020; 18:531-548. [PMID: 32253701 PMCID: PMC7502473 DOI: 10.1007/s12021-020-09459-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Changes in cognitive performance due to neurodegenerative diseases such as Alzheimer's disease (AD) are closely correlated to the brain structure alteration. A univariate and personalized neurodegenerative biomarker with strong statistical power based on magnetic resonance imaging (MRI) will benefit clinical diagnosis and prognosis of neurodegenerative diseases. However, few biomarkers of this type have been developed, especially those that are robust to image noise and applicable to clinical analyses. In this paper, we introduce a variational framework to compute optimal transportation (OT) on brain structural MRI volumes and develop a univariate neuroimaging index based on OT to quantify neurodegenerative alterations. Specifically, we compute the OT from each image to a template and measure the Wasserstein distance between them. The obtained Wasserstein distance, Wasserstein Index (WI) for short to specify the distance to a template, is concise, informative and robust to random noise. Comparing to the popular linear programming-based OT computation method, our framework makes use of Newton's method, which makes it possible to compute WI in large-scale datasets. Experimental results, on 314 subjects (140 Aβ + AD and 174 Aβ- normal controls) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) baseline dataset, provide preliminary evidence that the proposed WI is correlated with a clinical cognitive measure (the Mini-Mental State Examination (MMSE) score), and it is able to identify group difference and achieve a good classification accuracy, outperforming two other popular univariate indices including hippocampal volume and entorhinal cortex thickness. The current pilot work suggests the application of WI as a potential univariate neurodegenerative biomarker.
Collapse
Affiliation(s)
- Yanshuai Tu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA
| | - Liang Mi
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA
| | - Wen Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA
| | - Haomeng Zhang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA
| | - Junwei Zhang
- Department of Computer Science, Stony Brook University, Stony Brook, NY, USA
| | - Yonghui Fan
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA
| | | | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ, USA
| | | | | | - Xianfeng Gu
- Department of Computer Science, Stony Brook University, Stony Brook, NY, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University, P.O. Box 878809, Tempe, AZ, 85287, USA.
| |
Collapse
|
4
|
Group Guided Fused Laplacian Sparse Group Lasso for Modeling Alzheimer's Disease Progression. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:4036560. [PMID: 32104201 PMCID: PMC7033952 DOI: 10.1155/2020/4036560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/27/2019] [Accepted: 06/18/2019] [Indexed: 11/18/2022]
Abstract
As the largest cause of dementia, Alzheimer's disease (AD) has brought serious burdens to patients and their families, mostly in the financial, psychological, and emotional aspects. In order to assess the progression of AD and develop new treatment methods for the disease, it is essential to infer the trajectories of patients' cognitive performance over time to identify biomarkers that connect the patterns of brain atrophy and AD progression. In this article, a structured regularized regression approach termed group guided fused Laplacian sparse group Lasso (GFL-SGL) is proposed to infer disease progression by considering multiple prediction of the same cognitive scores at different time points (longitudinal analysis). The proposed GFL-SGL simultaneously exploits the interrelated structures within the MRI features and among the tasks with sparse group Lasso (SGL) norm and presents a novel group guided fused Laplacian (GFL) regularization. This combination effectively incorporates both the relatedness among multiple longitudinal time points with a general weighted (undirected) dependency graphs and useful inherent group structure in features. Furthermore, an alternating direction method of multipliers- (ADMM-) based algorithm is also derived to optimize the nonsmooth objective function of the proposed approach. Experiments on the dataset from Alzheimer's Disease Neuroimaging Initiative (ADNI) show that the proposed GFL-SGL outperformed some other state-of-the-art algorithms and effectively fused the multimodality data. The compact sets of cognition-relevant imaging biomarkers identified by our approach are consistent with the results of clinical studies.
Collapse
|
5
|
La Joie R, Visani AV, Baker SL, Brown JA, Bourakova V, Cha J, Chaudhary K, Edwards L, Iaccarino L, Janabi M, Lesman-Segev OH, Miller ZA, Perry DC, O'Neil JP, Pham J, Rojas JC, Rosen HJ, Seeley WW, Tsai RM, Miller BL, Jagust WJ, Rabinovici GD. Prospective longitudinal atrophy in Alzheimer's disease correlates with the intensity and topography of baseline tau-PET. Sci Transl Med 2020; 12:eaau5732. [PMID: 31894103 PMCID: PMC7035952 DOI: 10.1126/scitranslmed.aau5732] [Citation(s) in RCA: 314] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/13/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022]
Abstract
β-Amyloid plaques and tau-containing neurofibrillary tangles are the two neuropathological hallmarks of Alzheimer's disease (AD) and are thought to play crucial roles in a neurodegenerative cascade leading to dementia. Both lesions can now be visualized in vivo using positron emission tomography (PET) radiotracers, opening new opportunities to study disease mechanisms and improve patients' diagnostic and prognostic evaluation. In a group of 32 patients at early symptomatic AD stages, we tested whether β-amyloid and tau-PET could predict subsequent brain atrophy measured using longitudinal magnetic resonance imaging acquired at the time of PET and 15 months later. Quantitative analyses showed that the global intensity of tau-PET, but not β-amyloid-PET, signal predicted the rate of subsequent atrophy, independent of baseline cortical thickness. Additional investigations demonstrated that the specific distribution of tau-PET signal was a strong indicator of the topography of future atrophy at the single patient level and that the relationship between baseline tau-PET and subsequent atrophy was particularly strong in younger patients. These data support disease models in which tau pathology is a major driver of local neurodegeneration and highlight the relevance of tau-PET as a precision medicine tool to help predict individual patient's progression and design future clinical trials.
Collapse
Affiliation(s)
- Renaud La Joie
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
| | - Adrienne V Visani
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Suzanne L Baker
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jesse A Brown
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Viktoriya Bourakova
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jungho Cha
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kiran Chaudhary
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren Edwards
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Leonardo Iaccarino
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mustafa Janabi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Orit H Lesman-Segev
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary A Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - David C Perry
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - James P O'Neil
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Julie Pham
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Julio C Rojas
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Howard J Rosen
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - William W Seeley
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Richard M Tsai
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce L Miller
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - William J Jagust
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gil D Rabinovici
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
6
|
Cole JH, Jolly A, de Simoni S, Bourke N, Patel MC, Scott G, Sharp DJ. Spatial patterns of progressive brain volume loss after moderate-severe traumatic brain injury. Brain 2019; 141:822-836. [PMID: 29309542 PMCID: PMC5837530 DOI: 10.1093/brain/awx354] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury leads to significant loss of brain volume, which continues into the chronic stage. This can be sensitively measured using volumetric analysis of MRI. Here we: (i) investigated longitudinal patterns of brain atrophy; (ii) tested whether atrophy is greatest in sulcal cortical regions; and (iii) showed how atrophy could be used to power intervention trials aimed at slowing neurodegeneration. In 61 patients with moderate-severe traumatic brain injury (mean age = 41.55 years ± 12.77) and 32 healthy controls (mean age = 34.22 years ± 10.29), cross-sectional and longitudinal (1-year follow-up) brain structure was assessed using voxel-based morphometry on T1-weighted scans. Longitudinal brain volume changes were characterized using a novel neuroimaging analysis pipeline that generates a Jacobian determinant metric, reflecting spatial warping between baseline and follow-up scans. Jacobian determinant values were summarized regionally and compared with clinical and neuropsychological measures. Patients with traumatic brain injury showed lower grey and white matter volume in multiple brain regions compared to controls at baseline. Atrophy over 1 year was pronounced following traumatic brain injury. Patients with traumatic brain injury lost a mean (± standard deviation) of 1.55% ± 2.19 of grey matter volume per year, 1.49% ± 2.20 of white matter volume or 1.51% ± 1.60 of whole brain volume. Healthy controls lost 0.55% ± 1.13 of grey matter volume and gained 0.26% ± 1.11 of white matter volume; equating to a 0.22% ± 0.83 reduction in whole brain volume. Atrophy was greatest in white matter, where the majority (84%) of regions were affected. This effect was independent of and substantially greater than that of ageing. Increased atrophy was also seen in cortical sulci compared to gyri. There was no relationship between atrophy and time since injury or age at baseline. Atrophy rates were related to memory performance at the end of the follow-up period, as well as to changes in memory performance, prior to multiple comparison correction. In conclusion, traumatic brain injury results in progressive loss of brain tissue volume, which continues for many years post-injury. Atrophy is most prominent in the white matter, but is also more pronounced in cortical sulci compared to gyri. These findings suggest the Jacobian determinant provides a method of quantifying brain atrophy following a traumatic brain injury and is informative in determining the long-term neurodegenerative effects after injury. Power calculations indicate that Jacobian determinant images are an efficient surrogate marker in clinical trials of neuroprotective therapeutics.
Collapse
Affiliation(s)
- James H Cole
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Imperial College London, Division of Brain Sciences, Hammersmith Hospital, London, UK
| | - Amy Jolly
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Imperial College London, Division of Brain Sciences, Hammersmith Hospital, London, UK
| | - Sara de Simoni
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Imperial College London, Division of Brain Sciences, Hammersmith Hospital, London, UK
| | - Niall Bourke
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Imperial College London, Division of Brain Sciences, Hammersmith Hospital, London, UK
| | - Maneesh C Patel
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Imperial College London, Division of Brain Sciences, Hammersmith Hospital, London, UK
| | - Gregory Scott
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Imperial College London, Division of Brain Sciences, Hammersmith Hospital, London, UK
| | - David J Sharp
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Imperial College London, Division of Brain Sciences, Hammersmith Hospital, London, UK
| |
Collapse
|
7
|
Cao P, Liu X, Liu H, Yang J, Zhao D, Huang M, Zaiane O. Generalized fused group lasso regularized multi-task feature learning for predicting cognitive outcomes in Alzheimers disease. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2018; 162:19-45. [PMID: 29903486 DOI: 10.1016/j.cmpb.2018.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/19/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE Alzheimers disease (AD) is characterized by gradual neurodegeneration and loss of brain function, especially for memory during early stages. Regression analysis has been widely applied to AD research to relate clinical and biomarker data such as predicting cognitive outcomes from Magnetic Resonance Imaging (MRI) measures. Recently, the multi-task feature learning (MTFL) methods have been widely studied to predict cognitive outcomes and select the discriminative feature subset from MRI features by incorporating inherent correlations among multiple clinical cognitive measures. However, the existing MTFL assumes the correlation among all the tasks is uniform, and the task relatedness is modeled by encouraging a common subset of features with neglecting the inherent structure of tasks and MRI features. METHODS In this paper, we proposed a generalized fused group lasso (GFGL) regularization to model the underlying structures, involving (1) a graph structure within tasks and (2) a group structure among the image features. Then, we present a multi-task learning framework (called GFGL-MTFL), combining the ℓ2, 1-norm with the GFGL regularization, to model the flexible structures. RESULTS Through empirical evaluation and comparison with different baseline methods and the state-of-the-art MTL methods on data from Alzheimer's Disease Neuroimaging Initiative (ADNI) database, we illustrate that the proposed GFGL-MTFL method outperforms other methods in terms of both Mean Squared Error (nMSE) and weighted correlation coefficient (wR). Improvements are statistically significant for most scores (tasks). CONCLUSIONS The experimental results with real and synthetic data demonstrate that incorporating the two prior structures by the generalized fused group lasso norm into the multi task feature learning can improve the prediction performance over several state-of-the-art competing methods, and the estimated correlation of the cognitive functions and the identification of cognition relevant imaging markers are clinically and biologically meaningful.
Collapse
Affiliation(s)
- Peng Cao
- Computer Science and Engineering, Northeastern University, Shenyang, China.
| | - Xiaoli Liu
- Computer Science and Engineering, Northeastern University, Shenyang, China
| | - Hezi Liu
- The Third People's Hospital of Fushun, Fushun, China
| | - Jinzhu Yang
- Computer Science and Engineering, Northeastern University, Shenyang, China
| | - Dazhe Zhao
- Computer Science and Engineering, Northeastern University, Shenyang, China
| | - Min Huang
- College of Information Science and Engineering, Northeastern University, Shenyang, China
| | - Osmar Zaiane
- Computing Science, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
8
|
Liu X, Goncalves AR, Cao P, Zhao D, Banerjee A. Modeling Alzheimer's disease cognitive scores using multi-task sparse group lasso. Comput Med Imaging Graph 2017; 66:100-114. [PMID: 29602022 DOI: 10.1016/j.compmedimag.2017.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 06/10/2017] [Accepted: 11/14/2017] [Indexed: 01/12/2023]
Abstract
Alzheimer's disease (AD) is a severe neurodegenerative disorder characterized by loss of memory and reduction in cognitive functions due to progressive degeneration of neurons and their connections, eventually leading to death. In this paper, we consider the problem of simultaneously predicting several different cognitive scores associated with categorizing subjects as normal, mild cognitive impairment (MCI), or Alzheimer's disease (AD) in a multi-task learning framework using features extracted from brain images obtained from ADNI (Alzheimer's Disease Neuroimaging Initiative). To solve the problem, we present a multi-task sparse group lasso (MT-SGL) framework, which estimates sparse features coupled across tasks, and can work with loss functions associated with any Generalized Linear Models. Through comparisons with a variety of baseline models using multiple evaluation metrics, we illustrate the promising predictive performance of MT-SGL on ADNI along with its ability to identify brain regions more likely to help the characterization Alzheimer's disease progression.
Collapse
Affiliation(s)
- Xiaoli Liu
- College of Computer Science and Engineering, Northeastern University, Shenyang, China; Key Laboratory of Medical Image Computing of Ministry of Education, Northeastern University, Shenyang, China; Computing Science & Engineering, University of Minnesota, Twin Cities, USA
| | - André R Goncalves
- Center for Research and Development in Telecommunications (CPqD), Brazil
| | - Peng Cao
- College of Computer Science and Engineering, Northeastern University, Shenyang, China.
| | - Dazhe Zhao
- College of Computer Science and Engineering, Northeastern University, Shenyang, China; Key Laboratory of Medical Image Computing of Ministry of Education, Northeastern University, Shenyang, China
| | - Arindam Banerjee
- Computing Science & Engineering, University of Minnesota, Twin Cities, USA
| | | |
Collapse
|
9
|
Cao P, Liu X, Yang J, Zhao D, Huang M, Zhang J, Zaiane O. Nonlinearity-aware based dimensionality reduction and over-sampling for AD/MCI classification from MRI measures. Comput Biol Med 2017; 91:21-37. [DOI: 10.1016/j.compbiomed.2017.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 12/26/2022]
|
10
|
Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Green RC, Harvey D, Jack CR, Jagust W, Morris JC, Petersen RC, Saykin AJ, Shaw LM, Toga AW, Trojanowski JQ. Recent publications from the Alzheimer's Disease Neuroimaging Initiative: Reviewing progress toward improved AD clinical trials. Alzheimers Dement 2017; 13:e1-e85. [PMID: 28342697 DOI: 10.1016/j.jalz.2016.11.007] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/21/2016] [Accepted: 11/28/2016] [Indexed: 01/31/2023]
Abstract
INTRODUCTION The Alzheimer's Disease Neuroimaging Initiative (ADNI) has continued development and standardization of methodologies for biomarkers and has provided an increased depth and breadth of data available to qualified researchers. This review summarizes the over 400 publications using ADNI data during 2014 and 2015. METHODS We used standard searches to find publications using ADNI data. RESULTS (1) Structural and functional changes, including subtle changes to hippocampal shape and texture, atrophy in areas outside of hippocampus, and disruption to functional networks, are detectable in presymptomatic subjects before hippocampal atrophy; (2) In subjects with abnormal β-amyloid deposition (Aβ+), biomarkers become abnormal in the order predicted by the amyloid cascade hypothesis; (3) Cognitive decline is more closely linked to tau than Aβ deposition; (4) Cerebrovascular risk factors may interact with Aβ to increase white-matter (WM) abnormalities which may accelerate Alzheimer's disease (AD) progression in conjunction with tau abnormalities; (5) Different patterns of atrophy are associated with impairment of memory and executive function and may underlie psychiatric symptoms; (6) Structural, functional, and metabolic network connectivities are disrupted as AD progresses. Models of prion-like spreading of Aβ pathology along WM tracts predict known patterns of cortical Aβ deposition and declines in glucose metabolism; (7) New AD risk and protective gene loci have been identified using biologically informed approaches; (8) Cognitively normal and mild cognitive impairment (MCI) subjects are heterogeneous and include groups typified not only by "classic" AD pathology but also by normal biomarkers, accelerated decline, and suspected non-Alzheimer's pathology; (9) Selection of subjects at risk of imminent decline on the basis of one or more pathologies improves the power of clinical trials; (10) Sensitivity of cognitive outcome measures to early changes in cognition has been improved and surrogate outcome measures using longitudinal structural magnetic resonance imaging may further reduce clinical trial cost and duration; (11) Advances in machine learning techniques such as neural networks have improved diagnostic and prognostic accuracy especially in challenges involving MCI subjects; and (12) Network connectivity measures and genetic variants show promise in multimodal classification and some classifiers using single modalities are rivaling multimodal classifiers. DISCUSSION Taken together, these studies fundamentally deepen our understanding of AD progression and its underlying genetic basis, which in turn informs and improves clinical trial design.
Collapse
Affiliation(s)
- Michael W Weiner
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA; Department of Radiology, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, CA, USA.
| | - Dallas P Veitch
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA
| | - Paul S Aisen
- Alzheimer's Therapeutic Research Institute, University of Southern California, San Diego, CA, USA
| | - Laurel A Beckett
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Nigel J Cairns
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, Saint Louis, MO, USA; Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Danielle Harvey
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | | | - William Jagust
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - John C Morris
- Alzheimer's Therapeutic Research Institute, University of Southern California, San Diego, CA, USA
| | | | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, Institute of Neuroimaging and Informatics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Alzheimer's Disease Core Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Udall Parkinson's Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | |
Collapse
|
11
|
Fang L, Chen Q, Shi K, Li X, Shi Q, He F, Zhou J, Yu Y, Hua X. Step-Wise Increase in Tigecycline Resistance in Klebsiella pneumoniae Associated with Mutations in ramR, lon and rpsJ. PLoS One 2016; 11:e0165019. [PMID: 27764207 PMCID: PMC5072711 DOI: 10.1371/journal.pone.0165019] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022] Open
Abstract
Klebsiella pneumoniae is a gram-negative bacterium that causes numerous diseases, including pneumonia and urinary tract infections. An increase in multidrug resistance has complicated the treatment of these bacterial infections, and although tigecycline shows activity against a broad spectrum of bacteria, resistant strains have emerged. In this study, the whole genomes of two clinical and six laboratory-evolved strains were sequenced to identify putative mutations related to tigecycline resistance. Of seven tigecycline-resistant strains, seven (100%) had ramR mutations, five (71.4%) had lon mutations, one (14.2%) had a ramA mutation, and one (14.2%) had an rpsJ mutation. A higher fitness cost was observed in the laboratory-evolved strains but not in the clinical strains. A transcriptome analysis demonstrated high expression of the ramR operon and acrA in all tigecycline-resistant strains. Genes involved in nitrogen metabolism were induced in the laboratory-evolved strains compared with the wild-type and clinical strains, and this difference in nitrogen metabolism reflected the variation between the laboratory-evolved and the clinical strains. Complementation experiments showed that both the wild-type ramR and the lon genes could partially restore the tigecycline sensitivity of K. pneumoniae. We believe that this manuscript describes the first construct of a lon mutant in K. pneumoniae, which allowed confirmation of its association with tigecycline resistance. Our findings illustrate the importance of the ramR operon and the lon and rpsJ genes in K. pneumoniae resistance to tigecycline.
Collapse
Affiliation(s)
- Li Fang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Qiong Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Keren Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xi Li
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Qiucheng Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Fang He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiancang Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- * E-mail: (XH); (YY)
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- * E-mail: (XH); (YY)
| |
Collapse
|
12
|
Edland SD, Ard MC, Sridhar J, Cobia D, Martersteck A, Mesulam MM, Rogalski EJ. Proof of concept demonstration of optimal composite MRI endpoints for clinical trials. ALZHEIMERS & DEMENTIA-TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS 2016; 2:177-181. [PMID: 28345017 PMCID: PMC5363955 DOI: 10.1016/j.trci.2016.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Introduction Atrophy measures derived from structural MRI are promising outcome measures for early phase clinical trials, especially for rare diseases such as primary progressive aphasia (PPA), where the small available subject pool limits our ability to perform meaningfully powered trials with traditional cognitive and functional outcome measures. Methods We investigated a composite atrophy index in 26 PPA participants with longitudinal MRIs separated by 2 years. Rogalski et al.[5] previously demonstrated that atrophy of the left perisylvian temporal cortex (PSTC) is a highly sensitive measure of disease progression in this population and a promising endpoint for clinical trials. Using methods described by Ard et al.[1], we constructed a composite atrophy index composed of a weighted sum of volumetric measures of 10 regions of interest within the left perisylvian cortex using weights that maximize signal-to-noise and minimize sample size required of trials using the resulting score. Sample size required to detect a fixed percentage slowing in atrophy in a 2-year clinical trial with equal allocation of subjects across arms and 90% power was calculated for the PSTC and optimal composite surrogate biomarker endpoints. Results The optimal composite endpoint required 38% fewer subjects to detect the same percent slowing in atrophy than required by the left PSTC endpoint. Conclusions Optimal composites can increase the power of clinical trials and increase the probability that smaller trials are informative, an observation especially relevant for PPA but also for related neurodegenerative disorders including Alzheimer's disease.
Collapse
Affiliation(s)
- Steven D Edland
- Division of Biostatistics, Department of Family Medicine & Public Health, University of California San Diego, La Jolla, CA, USA; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - M Colin Ard
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Jaiashre Sridhar
- Northwestern University Feinberg School of Medicine, Cognitive Neurology and Alzheimer's Disease Center, Chicago, IL, USA
| | - Derin Cobia
- Northwestern University Feinberg School of Medicine, Department of Psychiatry and Behavioral Sciences, Chicago, IL, USA
| | - Adam Martersteck
- Northwestern University Feinberg School of Medicine, Cognitive Neurology and Alzheimer's Disease Center, Chicago, IL, USA; Northwestern University Feinberg School of Medicine, Department of Radiology, Chicago, IL, USA
| | - M Marsel Mesulam
- Northwestern University Feinberg School of Medicine, Cognitive Neurology and Alzheimer's Disease Center, Chicago, IL, USA; Northwestern University Feinberg School of Medicine, Department of Neurology, Chicago, IL, USA
| | - Emily J Rogalski
- Northwestern University Feinberg School of Medicine, Cognitive Neurology and Alzheimer's Disease Center, Chicago, IL, USA
| |
Collapse
|
13
|
Jack CR, Barnes J, Bernstein MA, Borowski BJ, Brewer J, Clegg S, Dale AM, Carmichael O, Ching C, DeCarli C, Desikan RS, Fennema-Notestine C, Fjell AM, Fletcher E, Fox NC, Gunter J, Gutman BA, Holland D, Hua X, Insel P, Kantarci K, Killiany RJ, Krueger G, Leung KK, Mackin S, Maillard P, Malone IB, Mattsson N, McEvoy L, Modat M, Mueller S, Nosheny R, Ourselin S, Schuff N, Senjem ML, Simonson A, Thompson PM, Rettmann D, Vemuri P, Walhovd K, Zhao Y, Zuk S, Weiner M. Magnetic resonance imaging in Alzheimer's Disease Neuroimaging Initiative 2. Alzheimers Dement 2016; 11:740-56. [PMID: 26194310 DOI: 10.1016/j.jalz.2015.05.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/28/2015] [Accepted: 05/05/2015] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Alzheimer's Disease Neuroimaging Initiative (ADNI) is now in its 10th year. The primary objective of the magnetic resonance imaging (MRI) core of ADNI has been to improve methods for clinical trials in Alzheimer's disease (AD) and related disorders. METHODS We review the contributions of the MRI core from present and past cycles of ADNI (ADNI-1, -Grand Opportunity and -2). We also review plans for the future-ADNI-3. RESULTS Contributions of the MRI core include creating standardized acquisition protocols and quality control methods; examining the effect of technical features of image acquisition and analysis on outcome metrics; deriving sample size estimates for future trials based on those outcomes; and piloting the potential utility of MR perfusion, diffusion, and functional connectivity measures in multicenter clinical trials. DISCUSSION Over the past decade the MRI core of ADNI has fulfilled its mandate of improving methods for clinical trials in AD and will continue to do so in the future.
Collapse
Affiliation(s)
| | - Josephine Barnes
- Department of Neurodegenerative Disease, Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | | | | | - James Brewer
- Department of Neuroscience, University of California at San Diego, La Jolla, CA, USA
| | - Shona Clegg
- Department of Neurodegenerative Disease, Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | - Anders M Dale
- Department of Neuroscience, University of California at San Diego, La Jolla, CA, USA
| | - Owen Carmichael
- Department of Neurology, University of California at Davis, Davis, CA, USA
| | - Christopher Ching
- Department of Neurology, Imaging Genetics Center, Institute for Neuroimaging & Informatics, University of Southern California, Marina del Rey, CA, USA
| | - Charles DeCarli
- Department of Neurology, University of California at Davis, Davis, CA, USA; Center for Neuroscience, University of California at Davis, Davis, CA, USA
| | - Rahul S Desikan
- Department of Radiology, University of California at San Diego, La Jolla, CA, USA
| | - Christine Fennema-Notestine
- Department of Radiology, University of California at San Diego, La Jolla, CA, USA; Department of Psychiatry, University of California at San Diego, La Jolla, CA, USA
| | - Anders M Fjell
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Evan Fletcher
- Department of Neurology, University of California at Davis, Davis, CA, USA; Center for Neuroscience, University of California at Davis, Davis, CA, USA
| | - Nick C Fox
- Department of Neurodegenerative Disease, Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | - Jeff Gunter
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - Boris A Gutman
- Department of Neurology, Imaging Genetics Center, Institute for Neuroimaging & Informatics, University of Southern California, Marina del Rey, CA, USA
| | - Dominic Holland
- Department of Neuroscience, University of California at San Diego, La Jolla, CA, USA
| | - Xue Hua
- Department of Neurology, Imaging Genetics Center, Institute for Neuroimaging & Informatics, University of Southern California, Marina del Rey, CA, USA
| | - Philip Insel
- Department of Radiology and Biomedical Imaging, Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Kejal Kantarci
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - Ron J Killiany
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | | | - Kelvin K Leung
- Translational Imaging Group, Centre for Medical Image Computing, University College London, London, United Kingdom
| | - Scott Mackin
- Department of Radiology and Biomedical Imaging, Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA; Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA
| | - Pauline Maillard
- Department of Neurology, University of California at Davis, Davis, CA, USA; Center for Neuroscience, University of California at Davis, Davis, CA, USA
| | - Ian B Malone
- Department of Neurodegenerative Disease, Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | - Niklas Mattsson
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
| | - Linda McEvoy
- Department of Radiology, University of California at San Diego, La Jolla, CA, USA
| | - Marc Modat
- Department of Neurodegenerative Disease, Dementia Research Centre, Institute of Neurology, University College London, London, UK; Translational Imaging Group, Centre for Medical Image Computing, University College London, London, United Kingdom
| | - Susanne Mueller
- Department of Radiology and Biomedical Imaging, Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA; Department of Radiology, University of California at San Francisco, San Francisco, CA, USA
| | - Rachel Nosheny
- Department of Radiology and Biomedical Imaging, Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA; Department of Radiology, University of California at San Francisco, San Francisco, CA, USA
| | - Sebastien Ourselin
- Department of Neurodegenerative Disease, Dementia Research Centre, Institute of Neurology, University College London, London, UK; Translational Imaging Group, Centre for Medical Image Computing, University College London, London, United Kingdom
| | - Norbert Schuff
- Department of Radiology and Biomedical Imaging, Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA; Department of Radiology, University of California at San Francisco, San Francisco, CA, USA
| | | | - Alix Simonson
- Department of Radiology and Biomedical Imaging, Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Paul M Thompson
- Department of Neurology, Imaging Genetics Center, Institute for Neuroimaging & Informatics, University of Southern California, Marina del Rey, CA, USA
| | - Dan Rettmann
- MR Applications and Workflow, GE Healthcare, Rochester, MN, USA
| | | | | | | | - Samantha Zuk
- Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - Michael Weiner
- Department of Radiology and Biomedical Imaging, Center for Imaging of Neurodegenerative Diseases, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA; Department of Psychiatry, University of California at San Francisco, San Francisco, CA, USA; Department of Radiology, University of California at San Francisco, San Francisco, CA, USA; Department of Medicine, University of California at San Francisco, San Francisco, CA, USA; Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| |
Collapse
|
14
|
Population imaging in neuroepidemiology. Neuroepidemiology 2016. [DOI: 10.1016/b978-0-12-802973-2.00005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
|
15
|
Hua X, Ching CRK, Mezher A, Gutman BA, Hibar DP, Bhatt P, Leow AD, Jack CR, Bernstein MA, Weiner MW, Thompson PM. MRI-based brain atrophy rates in ADNI phase 2: acceleration and enrichment considerations for clinical trials. Neurobiol Aging 2015; 37:26-37. [PMID: 26545631 PMCID: PMC4827255 DOI: 10.1016/j.neurobiolaging.2015.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 08/30/2015] [Accepted: 09/22/2015] [Indexed: 01/31/2023]
Abstract
The goal of this work was to assess statistical power to detect treatment effects in Alzheimer’s disease (AD) clinical trials using magnetic resonance imaging (MRI)–derived brain biomarkers. We used unbiased tensor-based morphometry (TBM) to analyze n = 5,738 scans, from Alzheimer’s Disease Neuroimaging Initiative 2 participants scanned with both accelerated and nonaccelerated T1-weighted MRI at 3T. The study cohort included 198 healthy controls, 111 participants with significant memory complaint, 182 with early mild cognitive impairment (EMCI) and 177 late mild cognitive impairment (LMCI), and 155 AD patients, scanned at screening and 3, 6, 12, and 24 months. The statistical power to track brain change in TBM-based imaging biomarkers depends on the interscan interval, disease stage, and methods used to extract numerical summaries. To achieve reasonable sample size estimates for potential clinical trials, the minimal scan interval was 6 months for LMCI and AD and 12 months for EMCI. TBM-based imaging biomarkers were not sensitive to MRI scan acceleration, which gave results comparable with nonaccelerated sequences. ApoE status and baseline amyloid-beta positron emission tomography data improved statistical power. Among healthy, EMCI, and LMCI participants, sample size requirements were significantly lower in the amyloid+/ApoE4+ group than for the amyloid−/ApoE4− group. ApoE4 strongly predicted atrophy rates across brain regions most affected by AD, but the remaining 9 of the top 10 AD risk genes offered no added predictive value in this cohort.
Collapse
Affiliation(s)
- Xue Hua
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher R K Ching
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA; Interdepartmental Neuroscience Graduate Program, University of California, Los Angeles, School of Medicine, Los Angeles, CA, USA
| | - Adam Mezher
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA
| | - Boris A Gutman
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA
| | - Derrek P Hibar
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Priya Bhatt
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA
| | - Alex D Leow
- Department of Psychiatry, University of Illinois at Chicago, College of Medicine, Chicago, IL, USA; Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | | | | | - Michael W Weiner
- Department of Radiology, University of California, San Francisco, San Francisco, CA, USA; Department of Medicine and Psychiatry, University of California, San Francisco, San Francisco, CA, USA; Department Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA, USA; Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Engineering, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | | |
Collapse
|
16
|
Zhan L, Liu Y, Wang Y, Zhou J, Jahanshad N, Ye J, Thompson PM. Boosting brain connectome classification accuracy in Alzheimer's disease using higher-order singular value decomposition. Front Neurosci 2015; 9:257. [PMID: 26257601 PMCID: PMC4513242 DOI: 10.3389/fnins.2015.00257] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/10/2015] [Indexed: 11/14/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive brain disease. Accurate detection of AD and its prodromal stage, mild cognitive impairment (MCI), are crucial. There is also a growing interest in identifying brain imaging biomarkers that help to automatically differentiate stages of Alzheimer's disease. Here, we focused on brain structural networks computed from diffusion MRI and proposed a new feature extraction and classification framework based on higher order singular value decomposition and sparse logistic regression. In tests on publicly available data from the Alzheimer's Disease Neuroimaging Initiative, our proposed framework showed promise in detecting brain network differences that help in classifying different stages of Alzheimer's disease.
Collapse
Affiliation(s)
- Liang Zhan
- Imaging Genetics Center, Keck School of Medicine, University of Southern California Marina del Rey, CA, USA
| | - Yashu Liu
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University Tempe, AZ, USA
| | - Yalin Wang
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University Tempe, AZ, USA
| | - Jiayu Zhou
- School of Computing, Informatics, and Decision Systems Engineering, Arizona State University Tempe, AZ, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Keck School of Medicine, University of Southern California Marina del Rey, CA, USA
| | - Jieping Ye
- Department of Computational Medicine and Bioinformatics, University of Michigan Ann Arbor, MI, USA ; Department of Electrical Engineering and Computer Science, University of Michigan Ann Arbor, MI, USA
| | - Paul M Thompson
- Imaging Genetics Center, Keck School of Medicine, University of Southern California Marina del Rey, CA, USA
| | | |
Collapse
|