M.J.T. Reinders
451 records found
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Predicting benefit from adjuvant therapy with corticosteroids in community-acquired pneumonia
A data-driven analysis of randomised trials
Background: Despite several randomised controlled trials (RCTs) on the use of adjuvant treatment with corticosteroids in patients with community-acquired pneumonia (CAP), the effect of this intervention on mortality remains controversial. We aimed to evaluate heterogeneity of tre
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Two-Step Transfer Learning Improves Deep Learning–Based Drug Response Prediction in Small Datasets
A Case Study of Glioblastoma
While deep learning (DL) is used in patients’ outcome predictions, the insufficiency of patient samples limits the accuracy. In this study, we investigated how transfer learning (TL) alleviates the small sample size problem. A 2-step TL framework was constructed for a difficult t
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Background and ObjectivesIdentifying genetic causes of dementia in patients visiting memory clinics is important for patient care and family planning. Traditional clinical selection criteria for genetic testing may miss carriers of pathogenic variants in dementia-related genes. T
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Federated learning is a technique that enables the use of distributed datasets for machine learning purposes without requiring data to be pooled, thereby better preserving privacy and ownership of the data. While supervised FL research has grown substantially over the last years,
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Introduction
The field of forensic DNA analysis has undergone rapid advancements in recent decades. The integration of massively parallel sequencing (MPS) has notably expanded the forensic toolkit, moving beyond identity matching to predicting phenotypic traits and biogeograp ...
The field of forensic DNA analysis has undergone rapid advancements in recent decades. The integration of massively parallel sequencing (MPS) has notably expanded the forensic toolkit, moving beyond identity matching to predicting phenotypic traits and biogeograp ...
Multi-omic analyses are necessary to understand the complex biological processes taking place at the tissue and cell level, but also to make reliable predictions about, for example, disease outcome. Several linear methods exist that create a joint embedding using paired informati
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The diagnostic spectrum for AML patients is increasingly based on genetic abnormalities due to their prognostic and predictive value. However, information on the AML blast phenotype regarding their maturational arrest has started to regain importance due to its predictive power f
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Molecular effects of lifestyle interventions are typically studied in a single tissue. Here, we perform a secondary analysis on the sex-specific effects of the Growing Old TOgether trial (GOTO, trial registration number GOT NL3301 (https://onderzoekmetmensen.nl/nl/trial/27183), N
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Anomaly detection in time series data is crucial across various domains. The scarcity of labeled data for such tasks has increased the attention towards unsupervised learning methods. These approaches, often relying solely on reconstruction error, typically fail to detect subtle
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BACKGROUND: Alzheimer's disease (AD) prevalence increases with age, yet a small fraction of the population reaches ages > 100 years without cognitive decline. We studied the genetic factors associated with such resilience against AD. METHODS: Genome-wide association studies id
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Photoplethysmography (PPG) signals, typically acquired from wearable devices, hold significant potential for continuous fitness-health monitoring. In particular, heart conditions that manifest in rare and subtle deviating heart patterns may be interesting. However, robust and rel
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Inflammatory bowel disease (IBD) chronicity results from memory T helper cell (Tmem) reactivation. Identifying patient-specific immunotypes is crucial for tailored treatment. We conducted a comprehensive study integrating circulating immune proteins and circulating Tmem, with int
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Most regulatory elements, especially enhancer sequences, are cell population-specific. One could even argue that a distinct set of regulatory elements is what defines a cell population. However, discovering which non-coding regions of the DNA are essential in which context, and a
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Background
1H-NMR metabolomics and DNA methylation in blood are widely known biomarkers predicting age-related physiological decline and mortality yet exert mutually independent mortality and frailty signals.
Methods
Leveraging multi-omics data in four Dutch popu ...
1H-NMR metabolomics and DNA methylation in blood are widely known biomarkers predicting age-related physiological decline and mortality yet exert mutually independent mortality and frailty signals.
Methods
Leveraging multi-omics data in four Dutch popu ...
Background
Genome-Wide Association Studies (GWAS) have identified 86 SNPs associated with Alzheimer’s disease (AD). GWAS-SNPs are markers of genetic variation in linkage disequilibrium (LD), which may drive the association with AD. One major class of genetic variation are Str ...
Genome-Wide Association Studies (GWAS) have identified 86 SNPs associated with Alzheimer’s disease (AD). GWAS-SNPs are markers of genetic variation in linkage disequilibrium (LD), which may drive the association with AD. One major class of genetic variation are Str ...
Lifestyle factors and metabolomic aging biomarkers
Meta-analysis of cross-sectional and longitudinal associations in three prospective cohorts
Biological age uses biophysiological information to capture a person’s age-related risk of adverse outcomes. MetaboAge and MetaboHealth are metabolomics-based biomarkers of biological age trained on chronological age and mortality risk, respectively. Lifestyle factors contribute
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SIRV
Spatial inference of RNA velocity at the single-cell resolution
RNA Velocity allows the inference of cellular differentiation trajectories from single-cell RNA sequencing (scRNA-seq) data. It would be highly interesting to study these differentiation dynamics in the spatial context of tissues. Estimating spatial RNA velocities is, however, li
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Tandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization of TRs; however, the underlying bioinformatics perspectives remain challenging. We present otter and TREAT: otter is a fast tar
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Introduction
Unraveling how Alzheimer's disease (AD) genetic risk is related to neuropathological heterogeneity, and whether this occurs through specific biological pathways, is a key step toward precision medicine.
Methods
We computed pathway-specific genetic ri ...
Unraveling how Alzheimer's disease (AD) genetic risk is related to neuropathological heterogeneity, and whether this occurs through specific biological pathways, is a key step toward precision medicine.
Methods
We computed pathway-specific genetic ri ...
Subtyping of acute myeloid leukaemia (AML) is predominantly based on recurrent genetic abnormalities, but recent literature indicates that transcriptomic phenotyping holds immense potential to further refine AML classification. Here we integrated five AML transcriptomic datasets
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