LIVIVO - Search results -

Search results

Result 1 - 10 of total 213

Search options

Article ; Online: Uncovering the complexities of biological structures with network-based learning: An application in SARS-CoV-2.

Faghri, Faraz / Nalls, Mike A

Patterns (New York, N.Y.)

2021 Volume 2, Issue 5, Page(s) 100259

Abstract: Network-based learning enables the identification of possible undiscovered interactions in biological systems. In this issue ... ...

Abstract	Network-based learning enables the identification of possible undiscovered interactions in biological systems. In this issue of
Language	English
Publishing date	2021-04-15
Publishing country	United States
Document type	News
ISSN	2666-3899
ISSN (online)	2666-3899
DOI	10.1016/j.patter.2021.100259
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Federated Learning for multi-omics: a performance evaluation in Parkinson's disease.

Danek, Benjamin / Makarious, Mary B / Dadu, Anant / Vitale, Dan / Lee, Paul Suhwan / Nalls, Mike A / Sun, Jimeng / Faghri, Faraz

bioRxiv : the preprint server for biology

2024

Abstract: While machine learning (ML) research has recently grown more in popularity, its application in the omics domain is constrained by access to sufficiently large, high-quality datasets needed to train ML models. Federated Learning (FL) represents an ... ...

Abstract	While machine learning (ML) research has recently grown more in popularity, its application in the omics domain is constrained by access to sufficiently large, high-quality datasets needed to train ML models. Federated Learning (FL) represents an opportunity to enable collaborative curation of such datasets among participating institutions. We compare the simulated performance of several models trained using FL against classically trained ML models on the task of multi-omics Parkinson's Disease prediction. We find that FL model performance tracks centrally trained ML models, where the most performant FL model achieves an AUC-PR of 0.876 ± 0.009, 0.014 ± 0.003 less than its centrally trained variation. We also determine that the dispersion of samples within a federation plays a meaningful role in model performance. Our study implements several open source FL frameworks and aims to highlight some of the challenges and opportunities when applying these collaborative methods in multi-omics studies.
Language	English
Publishing date	2024-02-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.04.560604
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article: Genetics of NLRP3 suggests lack of involvement and inefficient druggability in Parkinson's disease.

Senkevich, Konstantin / Liu, Lang / Alvarado, Chelsea X / Leonard, Hampton L / Nalls, Mike A / Gan-Or, Ziv

medRxiv : the preprint server for health sciences

2023

Abstract: Activation of the NLRP3-inflammasome has been proposed to play a role in Parkinson's disease pathogenesis based ... ...

Abstract	Activation of the NLRP3-inflammasome has been proposed to play a role in Parkinson's disease pathogenesis based on
Language	English
Publishing date	2023-09-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.20.23295790
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article: Human brain single nucleus cell type enrichments in neurodegenerative diseases.

Alvarado, Chelsea X / Weller, Cory A / Johnson, Nicholas / Leonard, Hampton L / Singleton, Andrew B / Reed, Xylena / Blauewendraat, Cornelis / Nalls, Mike A

Research square

2023

Abstract: Background: Single-cell RNA sequencing has opened a window into clarifying the complex underpinnings of disease, particularly in quantifying the relevance of tissue- and cell-type-specific gene expression.: Methods: To identify the cell types and ... ...

Abstract	Background: Single-cell RNA sequencing has opened a window into clarifying the complex underpinnings of disease, particularly in quantifying the relevance of tissue- and cell-type-specific gene expression. Methods: To identify the cell types and genes important to therapeutic target development across the neurodegenerative disease spectrum, we leveraged genome-wide association studies, recent single-cell sequencing data, and bulk expression studies in a diverse series of brain region tissues. Results: We were able to identify significant immune-related cell types in the brain across three major neurodegenerative diseases: Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. Subsequently, putative roles of 30 fine-mapped loci implicating seven genes in multiple neurodegenerative diseases and their pathogenesis were identified. Conclusions: We have helped refine the genetic regions and cell types effected across multiple neurodegenerative diseases, helping focus future translational research efforts.
Language	English
Publishing date	2023-11-15
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3390225/v1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article: Genome-wide meta-analysis of CSF biomarkers in Alzheimer's disease and Parkinson's disease cohorts.

Ta, Michael / Blauwendraat, Cornelis / Antar, Tarek / Leonard, Hampton L / Singleton, Andrew B / Nalls, Mike A / Iwaki, Hirotaka

medRxiv : the preprint server for health sciences

2023

Abstract: Background: Amyloid beta (Aβ), phosphorylated tau (p-tau), and total tau (t-tau) in cerebrospinal fluid are established biomarkers for Alzheimer's disease (AD). In other neurodegenerative diseases, such as Parkinson's disease (PD), these biomarkers have ...

Abstract	Background: Amyloid beta (Aβ), phosphorylated tau (p-tau), and total tau (t-tau) in cerebrospinal fluid are established biomarkers for Alzheimer's disease (AD). In other neurodegenerative diseases, such as Parkinson's disease (PD), these biomarkers have also been found to be altered, and the molecular mechanisms responsible for these alterations are still under investigation. Moreover, the interplay between these mechanisms and the diverse underlying disease states remains to be elucidated. Objectives: To investigate genetic contributions to the AD biomarkers and assess the commonality and heterogeneity of the associations per underlying disease status. Methods: We conducted GWAS for the AD biomarkers on subjects from the Parkinson's Progression Markers Initiative (PPMI), the Fox Investigation for New Discovery of Biomarkers (BioFIND), and the Alzheimer's Disease Neuroimaging Initiative (ADNI) and meta-analyzed with the largest AD GWAS.[7] We tested heterogeneity of associations of interest between different disease statuses (AD, PD, and control). Results: We observed three GWAS signals: the Conclusions: Our study identified a novel association at the intronic region of
Language	English
Publishing date	2023-06-19
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.13.23291354
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article ; Online: Genome-Wide Meta-Analysis of Cerebrospinal Fluid Biomarkers in Alzheimer's Disease and Parkinson's Disease Cohorts.

Ta, Michael / Blauwendraat, Cornelis / Antar, Tarek / Leonard, Hampton L / Singleton, Andrew B / Nalls, Mike A / Iwaki, Hirotaka

Movement disorders : official journal of the Movement Disorder Society

2023 Volume 38, Issue 9, Page(s) 1697–1705

Abstract: Background: Amyloid-β, phosphorylated tau (p-tau), and total tau (t-tau) in cerebrospinal fluid are established biomarkers for Alzheimer's disease (AD). In other neurodegenerative diseases, such as Parkinson's disease (PD), these biomarkers have also ... ...

Abstract	Background: Amyloid-β, phosphorylated tau (p-tau), and total tau (t-tau) in cerebrospinal fluid are established biomarkers for Alzheimer's disease (AD). In other neurodegenerative diseases, such as Parkinson's disease (PD), these biomarkers have also been found to be altered, and the molecular mechanisms responsible for these alterations are still under investigation. Moreover, the interplay between these mechanisms and the diverse underlying disease states remains to be elucidated. Objective: To investigate genetic contributions to the AD biomarkers and assess the commonality and heterogeneity of the associations per underlying disease status. Methods: We conducted genome-wide association studies (GWASs) for the AD biomarkers on subjects from the Parkinson's Progression Markers Initiative, the Fox Investigation for New Discovery of Biomarkers, and the Alzheimer's Disease Neuroimaging Initiative, and meta-analyzed with the largest AD GWAS. We tested heterogeneity of associations of interest between different disease statuses (AD, PD, and control). Results: We observed three GWAS signals: the APOE locus for amyloid-β, the 3q28 locus between GEMC1 and OSTN for p-tau and t-tau, and the 7p22 locus (top hit: rs60871478, an intronic variant for DNAAF5, also known as HEATR2) for p-tau. The 7p22 locus is novel and colocalized with the brain DNAAF5 expression. Although no heterogeneity from underlying disease status was observed for the earlier GWAS signals, some disease risk loci suggested disease-specific associations with these biomarkers. Conclusions: Our study identified a novel association at the intronic region of DNAAF5 associated with increased levels of p-tau across all diseases. We also observed some disease-specific genetic associations with these biomarkers. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
MeSH term(s)	Humans ; Alzheimer Disease/genetics ; Alzheimer Disease/cerebrospinal fluid ; Parkinson Disease/genetics ; Parkinson Disease/cerebrospinal fluid ; Genome-Wide Association Study ; tau Proteins/genetics ; tau Proteins/cerebrospinal fluid ; Amyloid beta-Peptides/cerebrospinal fluid ; Biomarkers/cerebrospinal fluid ; Peptide Fragments/cerebrospinal fluid ; Muscle Proteins/genetics ; Transcription Factors/genetics
Chemical Substances	tau Proteins ; Amyloid beta-Peptides ; Biomarkers ; Peptide Fragments ; OSTN protein, human ; Muscle Proteins ; Transcription Factors
Language	English
Publishing date	2023-08-04
Publishing country	United States
Document type	Meta-Analysis ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	607633-6
ISSN	1531-8257 ; 0885-3185
ISSN (online)	1531-8257
ISSN	0885-3185
DOI	10.1002/mds.29511
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 2555: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 238: Show issues

Order via subito

Details ▾

Article ; Online: Federated learning for multi-omics: A performance evaluation in Parkinson's disease.

Danek, Benjamin P / Makarious, Mary B / Dadu, Anant / Vitale, Dan / Lee, Paul Suhwan / Singleton, Andrew B / Nalls, Mike A / Sun, Jimeng / Faghri, Faraz

Patterns (New York, N.Y.)

2024 Volume 5, Issue 3, Page(s) 100945

Abstract	While machine learning (ML) research has recently grown more in popularity, its application in the omics domain is constrained by access to sufficiently large, high-quality datasets needed to train ML models. Federated learning (FL) represents an opportunity to enable collaborative curation of such datasets among participating institutions. We compare the simulated performance of several models trained using FL against classically trained ML models on the task of multi-omics Parkinson's disease prediction. We find that FL model performance tracks centrally trained ML models, where the most performant FL model achieves an AUC-PR of 0.876 ± 0.009, 0.014 ± 0.003 less than its centrally trained variation. We also determine that the dispersion of samples within a federation plays a meaningful role in model performance. Our study implements several open-source FL frameworks and aims to highlight some of the challenges and opportunities when applying these collaborative methods in multi-omics studies.
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2666-3899
ISSN (online)	2666-3899
DOI	10.1016/j.patter.2024.100945
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Open science in precision medicine for neurodegenerative diseases.

Leonard, Hampton L / Nalls, Mike A / Day-Williams, Aaron / Esmaeeli, Sahar / Jarreau, Paige / Bandres-Ciga, Sara / Heutink, Peter / Sardi, S Pablo / Singleton, Andrew B

Nature reviews. Drug discovery

2024 Volume 23, Issue 4, Page(s) 233–234

MeSH term(s)	Humans ; Precision Medicine ; Neurodegenerative Diseases/drug therapy ; Neurodegenerative Diseases/genetics
Language	English
Publishing date	2024-01-29
Publishing country	England
Document type	News
ZDB-ID	2062954-0
ISSN	1474-1784 ; 1474-1776
ISSN (online)	1474-1784
ISSN	1474-1776
DOI	10.1038/d41573-024-00017-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 5564: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 334: Show issues
Zs.MG 63: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: The genetic architecture of Parkinson's disease.

Blauwendraat, Cornelis / Nalls, Mike A / Singleton, Andrew B

The Lancet. Neurology

2019 Volume 19, Issue 2, Page(s) 170–178

Abstract: Parkinson's disease is a complex neurodegenerative disorder for which both rare and common genetic variants contribute to disease risk, onset, and progression. Mutations in more than 20 genes have been associated with the disease, most of which are ... ...

Abstract	Parkinson's disease is a complex neurodegenerative disorder for which both rare and common genetic variants contribute to disease risk, onset, and progression. Mutations in more than 20 genes have been associated with the disease, most of which are highly penetrant and often cause early onset or atypical symptoms. Although our understanding of the genetic basis of Parkinson's disease has advanced considerably, much remains to be done. Further disease-related common genetic variability remains to be identified and the work in identifying rare risk alleles has only just begun. To date, genome-wide association studies have identified 90 independent risk-associated variants. However, most of them have been identified in patients of European ancestry and we know relatively little of the genetics of Parkinson's disease in other populations. We have a limited understanding of the biological functions of the risk alleles that have been identified, although Parkinson's disease risk variants appear to be in close proximity to known Parkinson's disease genes and lysosomal-related genes. In the past decade, multiple efforts have been made to investigate the genetic architecture of Parkinson's disease, and emerging technologies, such as machine learning, single-cell RNA sequencing, and high-throughput screens, will improve our understanding of genetic risk.
MeSH term(s)	Dementia/genetics ; Disease Progression ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Humans ; Mutation/genetics ; Neurodegenerative Diseases/diagnosis ; Neurodegenerative Diseases/genetics ; Parkinson Disease/diagnosis ; Parkinson Disease/genetics ; Risk Factors
Language	English
Publishing date	2019-09-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2081241-3
ISSN	1474-4465 ; 1474-4422
ISSN (online)	1474-4465
ISSN	1474-4422
DOI	10.1016/S1474-4422(19)30287-X
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 5955: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: GBA1 rs3115534 Is Associated with REM Sleep Behavior Disorder in Parkinson's Disease in Nigerians.

Ojo, Oluwadamilola Omolara / Bandres-Ciga, Sara / Makarious, Mary B / Crea, Peter Wild / Hernandez, Dena G / Houlden, Henry / Rizig, Mie / Singleton, Andrew B / Noyce, Alastair J / Nalls, Mike A / Blauwendraat, Cornelis / Okubadejo, Njideka Ulunma

Movement disorders : official journal of the Movement Disorder Society

2024 Volume 39, Issue 4, Page(s) 728–733

Abstract: Background: Rapid eye movement (REM) sleep behavior disorder (RBD) is an early feature of Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Damaging coding variants in Glucocerebrosidase (GBA1) are a genetic risk factor for RBD. Recently, a ... ...

Abstract	Background: Rapid eye movement (REM) sleep behavior disorder (RBD) is an early feature of Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Damaging coding variants in Glucocerebrosidase (GBA1) are a genetic risk factor for RBD. Recently, a population-specific non-coding risk variant (rs3115534) was found to be associated with PD risk and earlier onset in individuals of African ancestry. Objectives: We aimed to investigate whether the GBA1 rs3115534 PD risk variant is associated with RBD in persons with PD. Methods: We studied 709 persons with PD and 776 neurologically healthy controls from Nigeria. All DNA samples were genotyped and imputed, and the GBA1 rs3115534 risk variant was extracted. The RBD screening questionnaire (RBDSQ) was used to assess symptoms of possible RBD. Results: RBD was present in 200 PD (28.2%) and 51 (6.6%) controls. We identified that the non-coding GBA1 rs3115534 risk variant is associated with possible RBD in individuals of Nigerian origin (β, 0.3640; standard error [SE], 0.103, P = 4.093e-04), as well as in all samples after adjusting for PD status (β, 0.2542; SE, 0.108; P = 0.019) suggesting that although non-coding, this variant may have the same downstream consequences as GBA1 coding variants. Conclusions: Our results indicate that the non-coding GBA1 rs3115534 risk variant is associated with an increasing number of RBD symptoms in persons with PD of Nigerian origin. Further research is needed to assess if this variant is also associated with polysomnography-defined RBD and with RBD symptoms in DLB. © 2024 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
MeSH term(s)	Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Genetic Predisposition to Disease ; Genotype ; Glucosylceramidase/genetics ; Nigeria ; Parkinson Disease/genetics ; Parkinson Disease/complications ; Polymorphism, Single Nucleotide ; REM Sleep Behavior Disorder/genetics ; West African People ; Young Adult ; Adult
Chemical Substances	GBA protein, human (EC 3.2.1.45) ; Glucosylceramidase (EC 3.2.1.45)
Language	English
Publishing date	2024-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	607633-6
ISSN	1531-8257 ; 0885-3185
ISSN (online)	1531-8257
ISSN	0885-3185
DOI	10.1002/mds.29753
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 2555: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 238: Show issues

Order via subito

Details ▾

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito