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Articles 1 - 12 of 12
Full-Text Articles in Life Sciences
Rare And Low Frequency Genomic Variants Impacting Neuronal Functions Modify The Dup7q11.23 Phenotype, Farah Qaiser, Yue Yin, Carolyn B. Mervis, Colleen A. Morris, Bonita P. Klein-Tasman, Elaine Tam, Lucy R. Osborne, Ryan K.C. Yuen
Rare And Low Frequency Genomic Variants Impacting Neuronal Functions Modify The Dup7q11.23 Phenotype, Farah Qaiser, Yue Yin, Carolyn B. Mervis, Colleen A. Morris, Bonita P. Klein-Tasman, Elaine Tam, Lucy R. Osborne, Ryan K.C. Yuen
School of Medicine Faculty Publications
© 2021, The Author(s). Background: 7q11.23 duplication (Dup7) is one of the most frequent recurrent copy number variants (CNVs) in individuals with autism spectrum disorder (ASD), but based on gold-standard assessments, only 19% of Dup7 carriers have ASD, suggesting that additional genetic factors are necessary to manifest the ASD phenotype. To assess the contribution of additional genetic variants to the Dup7 phenotype, we conducted whole-genome sequencing analysis of 20 Dup7 carriers: nine with ASD (Dup7-ASD) and 11 without ASD (Dup7-non-ASD). Results: We identified three rare variants of potential clinical relevance for ASD: a 1q21.1 microdeletion (Dup7-non-ASD) and two deletions which …
The Costs Of Developing Treatments For Alzheimer’S Disease: A Retrospective Exploration, Jeffrey L. Cummings, Dana P. Goldman, Nicholas R. Simmons-Stern, Eric Ponton
The Costs Of Developing Treatments For Alzheimer’S Disease: A Retrospective Exploration, Jeffrey L. Cummings, Dana P. Goldman, Nicholas R. Simmons-Stern, Eric Ponton
School of Medicine Faculty Publications
Introduction: With the exception of the recent accelerated approval of aducanumab, in over 26 years of research and development (R&D) investment in Alzheimer's disease (AD), only five novel drugs—all for symptomatic treatment only—have reached FDA approval. Here, we estimate the costs of AD drug development during this period in the private sector. Methods: To estimate private R&D funding, we collected information on AD clinical trials (n = 1099; phases 1–4) conducted between January 1, 1995 and June 21, 2021 from various databases. Costs were derived using previously published methodologies and adjusted for inflation. Results: Since 1995, cumulative private expenditures on …
Estimating Progression Rates Across The Spectrum Of Alzheimer’S Disease For Amyloid-Positive Individuals Using National Alzheimer’S Coordinating Center Data, Michele Potashman, Marric Buessing, Mihaela Levitchi Benea, Jeffrey Cummings, Soo Borson, Peter Pemberton-Ross, Andrew J. Epstein
Estimating Progression Rates Across The Spectrum Of Alzheimer’S Disease For Amyloid-Positive Individuals Using National Alzheimer’S Coordinating Center Data, Michele Potashman, Marric Buessing, Mihaela Levitchi Benea, Jeffrey Cummings, Soo Borson, Peter Pemberton-Ross, Andrew J. Epstein
School of Medicine Faculty Publications
Introduction: Published estimates of Alzheimer’s disease (AD) progression do not capture the full disease continuum. This study provides transition probabilities of individuals with amyloid-β (Aβ+) pathology across the disease continuum. Methods: Patient-level longitudinal data from the National Alzheimer’s Coordinating Center were used to estimate progression rates. Progression rates through five clinically defined AD stages—asymptomatic, mild cognitive impairment due to AD (MCI-AD), mild AD dementia, moderate AD dementia, severe AD dementia—and death were measured as transition probabilities. Rates were assessed in “incident” patients who recently entered the stage, controlling for covariates. Transition probabilities were generated from multinomial logit regression models that …
Artificial Image Objects For Classification Of Schizophrenia With Gwas-Selected Snvs And Convolutional Neural Network, Xiangning Chen, Daniel G. Chen, Zhongming Zhao, Justin Zhan, Changrong Ji, Jingchun Chen
Artificial Image Objects For Classification Of Schizophrenia With Gwas-Selected Snvs And Convolutional Neural Network, Xiangning Chen, Daniel G. Chen, Zhongming Zhao, Justin Zhan, Changrong Ji, Jingchun Chen
School of Medicine Faculty Publications
In this article, we propose a new approach to analyze large genomics data. We considered individual genetic variants as pixels in an image and transformed a collection of variants into an artificial image object (AIO), which could be classified as a regular image by CNN algorithms. Using schizophrenia as a case study, we demonstrate the principles and their applications with 3 datasets. With 4,096 SNVs, the CNN models achieved an accuracy of 0.678 ± 0.007 and an AUC of 0.738 ± 0.008 for the diagnosis phenotype. With 44,100 SNVs, the models achieved class-specific accuracies of 0.806 ± 0.032 and 0.820 …
Developing Methods To Detect And Diagnose Chronic Traumatic Encephalopathy During Life: Rationale, Design, And Methodology For The Diagnose Cte Research Project, Jeffrey Cummings, Numerous Authors, See Full List Below
Developing Methods To Detect And Diagnose Chronic Traumatic Encephalopathy During Life: Rationale, Design, And Methodology For The Diagnose Cte Research Project, Jeffrey Cummings, Numerous Authors, See Full List Below
School of Medicine Faculty Publications
Background: Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease that has been neuropathologically diagnosed in brain donors exposed to repetitive head impacts, including boxers and American football, soccer, ice hockey, and rugby players. CTE cannot yet be diagnosed during life. In December 2015, the National Institute of Neurological Disorders and Stroke awarded a seven-year grant (U01NS093334) to fund the “Diagnostics, Imaging, and Genetics Network for the Objective Study and Evaluation of Chronic Traumatic Encephalopathy (DIAGNOSE CTE) Research Project.” The objectives of this multicenter project are to: develop in vivo fluid and neuroimaging biomarkers for CTE; characterize its clinical presentation; refine …
Aducanumab Produced A Clinically Meaningful Benefit In Association With Amyloid Lowering, Jeffrey Cummings, Paul Aisen, Cynthia Lemere, Alireza Atri, Marwan Sabbagh, Stephen Salloway
Aducanumab Produced A Clinically Meaningful Benefit In Association With Amyloid Lowering, Jeffrey Cummings, Paul Aisen, Cynthia Lemere, Alireza Atri, Marwan Sabbagh, Stephen Salloway
School of Medicine Faculty Publications
No abstract provided.
Rewired Pathways And Disrupted Pathway Crosstalk In Schizophrenia Transcriptomes By Multiple Differential Coexpression Methods, Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao
Rewired Pathways And Disrupted Pathway Crosstalk In Schizophrenia Transcriptomes By Multiple Differential Coexpression Methods, Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao
School of Medicine Faculty Publications
Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or intercoordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired …
Vitamin D3 Induces Mesenchymal-To-Endothelial Transition And Promotes A Proangiogenic Niche Through Igf-1 Signaling, Lei Chen, Anweshan Samanta, Lin Zhao, Nathaniel R. Dudley, Tanner Buehler, Robert J. Vincent, Jeryl Hauptman, Magdy Girgis, Buddhadeb Dawn
Vitamin D3 Induces Mesenchymal-To-Endothelial Transition And Promotes A Proangiogenic Niche Through Igf-1 Signaling, Lei Chen, Anweshan Samanta, Lin Zhao, Nathaniel R. Dudley, Tanner Buehler, Robert J. Vincent, Jeryl Hauptman, Magdy Girgis, Buddhadeb Dawn
School of Medicine Faculty Publications
Biological Sciences; Physiology; Molecular Biology; Cell Biology
A Randomized, Double-Blind, Phase 2b Proof-Of-Concept Clinical Trial In Early Alzheimer’S Disease With Lecanemab, An Anti-Aβ Protofibril Antibody, Chad J. Swanson, Yong Zhang, Shobha Dhadda, Jinping Wang, June Kaplow, Robert Y.K. Lai, Lars Lannfelt, Heather Bradley, Martin Rabe, Akihiko Koyama, Larisa Reyderman, Donald A. Berry, Scott Berry, Robert Gordon, Lynn D. Kramer, Jeffrey L. Cummings
A Randomized, Double-Blind, Phase 2b Proof-Of-Concept Clinical Trial In Early Alzheimer’S Disease With Lecanemab, An Anti-Aβ Protofibril Antibody, Chad J. Swanson, Yong Zhang, Shobha Dhadda, Jinping Wang, June Kaplow, Robert Y.K. Lai, Lars Lannfelt, Heather Bradley, Martin Rabe, Akihiko Koyama, Larisa Reyderman, Donald A. Berry, Scott Berry, Robert Gordon, Lynn D. Kramer, Jeffrey L. Cummings
School of Medicine Faculty Publications
Background: Lecanemab (BAN2401), an IgG1 monoclonal antibody, preferentially targets soluble aggregated amyloid beta (Aβ), with activity across oligomers, protofibrils, and insoluble fibrils. BAN2401-G000-201, a randomized double-blind clinical trial, utilized a Bayesian design with response-adaptive randomization to assess 3 doses across 2 regimens of lecanemab versus placebo in early Alzheimer’s disease, mild cognitive impairment due to Alzheimer’s disease (AD) and mild AD dementia. Methods: BAN2401-G000-201 aimed to establish the effective dose 90% (ED90), defined as the simplest dose that achieves ≥90% of the maximum treatment effect. The primary endpoint was Bayesian analysis of 12-month clinical change on the Alzheimer’s Disease Composite …
Validation Of Induced Microglia-Like Cells (Img Cells) For Future Studies Of Brain Diseases, Atoshi Banerjee, Yimei Lu, Kenny Do, Travis Mize, Xiaogang Wu, Xiangning Chen, Jingchun Chen
Validation Of Induced Microglia-Like Cells (Img Cells) For Future Studies Of Brain Diseases, Atoshi Banerjee, Yimei Lu, Kenny Do, Travis Mize, Xiaogang Wu, Xiangning Chen, Jingchun Chen
School of Medicine Faculty Publications
Microglia are the primary resident immune cells of the central nervous system that maintain physiological homeostasis in the brain and contribute to the pathogenesis of many psychiatric disorders and neurodegenerative diseases. Due to the lack of appropriate human cellular models, it is difficult to study the basic pathophysiological processes linking microglia to brain diseases. In this study, we adopted a microglia-like cellular model derived from peripheral blood monocytes with granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin-34 (IL-34). We characterized and validated this in vitro cellular model by morphology, immunocytochemistry, gene expression profiles, and functional study. Our results indicated that the iMG …
Machine Learning Approaches For The Prediction Of Bone Mineral Density By Using Genomic And Phenotypic Data Of 5130 Older Men, Qing Wu, Fatma Nasoz, Jongyun Jung, Bibek Bhattarai, Mira V. Han, Robert A. Greenes, Kenneth G. Saag
Machine Learning Approaches For The Prediction Of Bone Mineral Density By Using Genomic And Phenotypic Data Of 5130 Older Men, Qing Wu, Fatma Nasoz, Jongyun Jung, Bibek Bhattarai, Mira V. Han, Robert A. Greenes, Kenneth G. Saag
School of Medicine Faculty Publications
The study aimed to utilize machine learning (ML) approaches and genomic data to develop a prediction model for bone mineral density (BMD) and identify the best modeling approach for BMD prediction. The genomic and phenotypic data of Osteoporotic Fractures in Men Study (n = 5130) was analyzed. Genetic risk score (GRS) was calculated from 1103 associated SNPs for each participant after a comprehensive genotype imputation. Data were normalized and divided into a training set (80%) and a validation set (20%) for analysis. Random forest, gradient boosting, neural network, and linear regression were used to develop BMD prediction models separately. Ten-fold …
Multimodal Single-Cell/Nucleus Rna Sequencing Data Analysis Uncovers Molecular Networks Between Disease-Associated Microglia And Astrocytes With Implications For Drug Repurposing In Alzheimer’S Disease, Jielin Xu, Pengyue Zhang, Yin Huang, Yadi Zhou, Yuan Hou, Lynn M. Bekris, Justin Lathia, Chien-Wei Chiang, Lang Li, Andrew A. Pieper, James B. Leverenz, Jeffrey Cummings, Feixiong Cheng
Multimodal Single-Cell/Nucleus Rna Sequencing Data Analysis Uncovers Molecular Networks Between Disease-Associated Microglia And Astrocytes With Implications For Drug Repurposing In Alzheimer’S Disease, Jielin Xu, Pengyue Zhang, Yin Huang, Yadi Zhou, Yuan Hou, Lynn M. Bekris, Justin Lathia, Chien-Wei Chiang, Lang Li, Andrew A. Pieper, James B. Leverenz, Jeffrey Cummings, Feixiong Cheng
School of Medicine Faculty Publications
Because disease-associated microglia (DAM) and disease-associated astrocytes (DAA) are involved in the pathophysiology of Alzheimer's disease (AD), we systematically identified molecular networks between DAM and DAA to uncover novel therapeutic targets for AD. Specifically, we develop a network-based methodology that leverages single-cell/nucleus RNA sequencing data from both transgenic mouse models and AD patient brains, as well as drug-target network, metaboliteenzyme associations, the human protein-protein interactome, and large-scale longitudinal patient data. Through this approach, we find both common and unique gene network regulators between DAM (i.e., PAK1, MAPK14, and CSF1R) and DAA (i.e., NFKB1, FOS, and JUN) that are significantly enriched …