FastSurfer - A fast and accurate deep learning based neuroimaging pipeline

NeuroImage, Год журнала: 2020, Номер 219, С. 117012 - 117012

Опубликована: Июнь 8, 2020

Traditional neuroimage analysis pipelines involve computationally intensive, time-consuming optimization steps, and thus, do not scale well to large cohort studies with thousands or tens of individuals. In this work we propose a fast accurate deep learning based neuroimaging pipeline for the automated processing structural human brain MRI scans, replicating FreeSurfer's anatomical segmentation including surface reconstruction cortical parcellation. To end, introduce an advanced architecture capable whole into 95 classes. The network incorporates local global competition via competitive dense blocks skip pathways, as multi-slice information aggregation that specifically tailor performance towards both sub-cortical structures. Further, perform thickness by introducing spectral spherical embedding directly mapping labels from image surface. This approach provides full FreeSurfer alternative volumetric (in under 1 minute) surface-based (within only around 1h runtime). For sustainability extensive validation: assert high accuracy on several unseen datasets, measure generalizability demonstrate increased test-retest reliability, sensitivity group differences in dementia.

Язык: Английский

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Objectives, design and main findings until 2020 from the Rotterdam Study

European Journal of Epidemiology, Год журнала: 2020, Номер 35(5), С. 483 - 517

Опубликована: Май 1, 2020

The Rotterdam Study is an ongoing prospective cohort study that started in 1990 the city of Rotterdam, Netherlands. aims to unravel etiology, preclinical course, natural history and potential targets for intervention chronic diseases mid-life late-life. focuses on cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, respiratory diseases. As 2008, 14,926 subjects aged 45 years or over comprise cohort. Since 2016, being expanded by persons 40 over. findings have been presented 1700 research articles reports. This article provides update rationale design study. It also presents a summary major from preceding 3 outlines developments coming period.

Язык: Английский

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Plasma tau, neurofilament light chain and amyloid-β levels and risk of dementia; a population-based cohort study

Brain, Год журнала: 2020, Номер 143(4), С. 1220 - 1232

Опубликована: Фев. 5, 2020

CSF biomarkers, including total-tau, neurofilament light chain (NfL) and amyloid-β, are increasingly being used to define stage Alzheimer's disease. These biomarkers can be measured more quickly less invasively in plasma may provide important information for early diagnosis of We stored samples clinical data obtained from 4444 non-demented participants the Rotterdam study at baseline (between 2002 2005) during follow-up until January 2016. Plasma concentrations NfL, amyloid-β40 amyloid-β42 were using Simoa NF-light® N3PA assays. Associations between biomarker levels incident all-cause disease dementia assessed Cox proportional-hazard regression models adjusted age, sex, education, cardiovascular risk factors APOE ε4 status. Moreover, rates change over time who developed compared with age sex-matched dementia-free control subjects. During up 14 years follow-up, 549 dementia, 374 cases dementia. A log2 higher level was associated a lower developing or hazard ratio (HR) 0.61 [95% confidence interval (CI), 0.47-0.78; P < 0.0001] 0.59 (95% CI, 0.43-0.79; = 0.0006), respectively. Conversely, NfL [adjusted HR 1.59 1.38-1.83); 1.50 1.26-1.78); 0.0001]. Combining lowest quartile group highest resulted stronger association 9.5 2.3-40.4); 0.002] 15.7 2.1-117.4); 0.0001], NfL. Total-tau not risk. Trajectory analyses revealed that mean increased 3.4 times faster those remained (P 0.0001), values diverged controls 9.6 before diagnosis. Amyloid-β42 began decrease few diagnosis, although decline did reach significance participants. In conclusion, our shows low high each independently combination strongly indicate assess population. levels, specific, also useful monitoring progression

Язык: Английский

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Gut microbiome-wide association study of depressive symptoms

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Дек. 6, 2022

Depression is one of the most poorly understood diseases due to its elusive pathogenesis. There an urgency identify molecular and biological mechanisms underlying depression gut microbiome a novel area interest. Here we investigate relation fecal diversity composition with depressive symptoms in 1,054 participants from Rotterdam Study cohort validate these findings Amsterdam HELIUS 1,539 subjects. We association thirteen microbial taxa, including genera Eggerthella, Subdoligranulum, Coprococcus, Sellimonas, Lachnoclostridium, Hungatella, Ruminococcaceae (UCG002, UCG003 UCG005), LachnospiraceaeUCG001, Eubacterium ventriosum Ruminococcusgauvreauiigroup, family symptoms. These bacteria are known be involved synthesis glutamate, butyrate, serotonin gamma amino butyric acid (GABA), which key neurotransmitters for depression. Our study suggests that may play role

Язык: Английский

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The effect of APOE and other common genetic variants on the onset of Alzheimer's disease and dementia: a community-based cohort study

The Lancet Neurology, Год журнала: 2018, Номер 17(5), С. 434 - 444

Опубликована: Март 16, 2018

Язык: Английский

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Intestinal microbiome composition and its relation to joint pain and inflammation

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Окт. 25, 2019

Abstract Macrophage-mediated inflammation is thought to have a causal role in osteoarthritis-related pain and severity, has been suggested be triggered by endotoxins produced the gastrointestinal microbiome. Here we investigate relationship between joint microbiome composition, knee Rotterdam Study; large population based cohort study. We show that abundance of Streptococcus species associated with increased pain, which validate absolute quantification species. In addition, replicate these results 867 Caucasian adults Lifelines-DEEP Finally evidence this association driven local joint. Our indicate possible therapeutic target for pain.

Язык: Английский

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Antihypertensive medications and risk for incident dementia and Alzheimer's disease: a meta-analysis of individual participant data from prospective cohort studies

The Lancet Neurology, Год журнала: 2019, Номер 19(1), С. 61 - 70

Опубликована: Ноя. 6, 2019

Язык: Английский

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Metabolomic profiles predict individual multidisease outcomes

Nature Medicine, Год журнала: 2022, Номер 28(11), С. 2309 - 2320

Опубликована: Сен. 22, 2022

Abstract Risk stratification is critical for the early identification of high-risk individuals and disease prevention. Here we explored potential nuclear magnetic resonance (NMR) spectroscopy-derived metabolomic profiles to inform on multidisease risk beyond conventional clinical predictors onset 24 common conditions, including metabolic, vascular, respiratory, musculoskeletal neurological diseases cancers. Specifically, trained a neural network learn disease-specific states from 168 circulating metabolic markers measured in 117,981 participants with ~1.4 million person-years follow-up UK Biobank validated model four independent cohorts. We found be associated incident event rates all investigated except breast cancer. For 10-year outcome prediction 15 endpoints, without established contribution, combination age sex state equaled or outperformed predictors. Moreover, added predictive information over comprehensive variables eight diseases, type 2 diabetes, dementia heart failure. Decision curve analyses showed that improvements translated into utility wide range decision thresholds. Taken together, our study demonstrates both limitations NMR-derived as assay many simultaneously.

Язык: Английский

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Relationship between gut microbiota and circulating metabolites in population-based cohorts

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Дек. 20, 2019

Abstract Gut microbiota has been implicated in major diseases affecting the human population and also linked to triglycerides high-density lipoprotein levels circulation. Recent development metabolomics allows classifying particles into more details. Here, we examine impact of gut on circulating metabolites measured by Nuclear Magnetic Resonance technology 2309 individuals from Rotterdam Study LifeLines-DEEP cohort. We assess relationship between linear regression analysis while adjusting for age, sex, body-mass index, technical covariates, medication use, multiple testing. report an association 32 microbial families genera with very-low-density subfractions, serum lipid measures, glycolysis-related metabolites, ketone bodies, amino acids, acute-phase reaction markers. These observations provide insights role host metabolism support potential as a target therapeutic preventive interventions.

Язык: Английский

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Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2

Communications Biology, Год журнала: 2021, Номер 4(1)

Опубликована: Апрель 12, 2021

Abstract COVID-19 is a respiratory illness caused by novel coronavirus called SARS-CoV-2. The viral spike (S) protein engages the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells with ~10–15-fold higher affinity compared SARS-CoV S-protein, making it highly infectious. Here, we assessed if ACE2 polymorphisms can alter susceptibility SARS-CoV-2 affecting this interaction. We analyzed over 290,000 samples representing >400 population groups from public genomic datasets and identified multiple protein-altering variants. Using reported structural data, natural variants that could potentially affect virus–host interaction thereby susceptibility. These include S19P, I21V, E23K, K26R, T27A, N64K, T92I, Q102P H378R were predicted increase susceptibility, while K31R, N33I, H34R, E35K, E37K, D38V, Y50F, N51S, M62V, K68E, F72V, Y83H, G326E, G352V, D355N, Q388L D509Y be protective show decreased binding S-protein. biochemical assays, confirmed K31R E37K had affinity, K26R T92I showed increased for S-protein when wildtype ACE2. Consistent this, soluble more effective in blocking entry of pseudotyped virus suggesting modulate

Язык: Английский

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