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Natural Language Processing for Drug Discovery Knowledge Graphs: Promises and Pitfalls
Building and analyzing knowledge graphs (KGs) to aid drug discovery is a topical area of research. A salient feature of KGs is their ability to...
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Cellular Blood Flow Modeling with HemoCell
Many of the intriguing properties of blood originate from its cellular nature. Bulk effects, such as viscosity, depend on the local shear rates and...
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A Blood Flow Modeling Framework for Stroke Treatments
Circulatory models can significantly help develop new ways to alleviate the burden of stroke on society. However, it is not always easy to know what...
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Teaching Medical Students to Use Supercomputers: A Personal Reflection
At the “Kick Off” meeting for CompBioMed (compbiomed.eu), which was first funded in October 2016, I had no idea that one single sentence (“I wish I...
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Automated Virtual Screening
Computational methods in modern drug discovery have become ubiquitous, with methods that cover most of the discovery stages: from hit finding and...
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Alzheimer’s Disease Prevention and Treatment Based on Population-Based Approaches
The development of effective prevention and treatment strategies for Alzheimer’s disease (AD) and dementia is hindered by limited knowledge of the...
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CSF N-Glycomics Using MALDI MS Techniques
In this chapter, we will present the methodology currently applied in our laboratory for the structural elucidation of the cerebrospinal fluid (CSF)...
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CSF N-Glycomics Using High-Throughput UPLC-ESI Techniques in Alzheimer’s Disease
In this chapter, we will present a high-throughput method applied in our laboratory for the structural elucidation of the cerebrospinal fluid (CSF)...
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In Silico Models to Validate Novel Blood-Based Biomarkers
Biological validation of preliminary findings is a key prerequisite in biomarker discovery. In recent years, the development of advanced large-scale...
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Mass Spectrometry-Based Metabolomics Multi-platform for Alzheimer’s Disease Research
The integration of complementary analytical platforms is nowadays the most common strategy for comprehensive metabolomics analysis of complex...
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High-Throughput Lipidomic and Metabolomic Profiling for Brain Tissue and Biofluid Samples in Neurodegenerative Disorders
Recent research has revealed the potential of lipidomics and metabolomics in identifying new biomarkers and mechanistic insights for...
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Magnetic Resonance Spectroscopy (MRS) in Alzheimer’s Disease
MRS is a noninvasive technique to measure different metabolites in the brain. Changes in the levels of certain metabolites can be used as surrogate...
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Analysis of Resting-State Functional Magnetic Resonance Imaging in Alzheimer’s Disease
Alzheimer’s disease (AD) has been characterized by widespread network disconnection among brain regions, widely overlap** with the hallmarks of the...
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Measuring Size and Number Concentration of Metallic Nanoparticles Using spICP-MS
This protocol describes how to measure the size and concentration of individual metallic nanoparticles using inductively coupled plasma-mass...
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Methods for Analysis of Nanoparticle Immunosuppressive Properties
Adverse drug effects on immune system function represent a significant concern in the pharmaceutical industry, because 10–20% of drug withdrawal from...
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Evaluation of the Acute Anaphylactoid Reactogenicity of Nanoparticle-Containing Medicines and Vaccines Using the Porcine CARPA Model
A small fraction, up to 10%, of people treated intravenously with state-of-the-art nanoparticulate drugs or diagnostic agents develop an acute...
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Immunophenoty**, Part I: Instrument Calibration and Reagent Qualification for Immunophenoty** Analysis of Human Peripheral Blood Mononuclear Cell Cultures
Nanoparticles are increasingly used in biomedical applications to influence the way the immune system reacts to tumors and infectious disease-causing...
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Ion Quantitation in Liposomal Products Using RP-HPLC with Charged Aerosol Detection
Ion concentration in liposomal drugs is important for drug stability and drug release profile. However, quantifying ion concentration in liposomal...
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Detection of Antigen Presentation by Murine Bone Marrow–Derived Dendritic Cells After Treatment with Nanoparticles
Nanoparticles are frequently considered in vaccine applications due to their ability to co-deliver multiple antigens and adjuvants to...
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Detection of Pre-Existing Antibodies to Polyethylene Glycol and PEGylated Liposomes in Human Serum
Polyethylene glycol, or PEG, is common in consumer products, over-the-counter medications, food, and pharmaceutical products. Concerns about PEG...