Biology subjects

ter Horst, R.

Publications and source records attributed to ter Horst, R..

4 recordsLinked to original sources

bioRxiv2023

Validation of the sleep EEG headband ZMax

Polysomnography (PSG) is the gold standard for recording sleep. However, the standard PSG systems are bulky, expensive, and often confined to lab environments. These systems are also time-consuming in electrode placement and sleep scoring. Such limitations render standard PSG systems less suitable for large-scale or longitudinal studies of sleep. Recent advances in electronics and artificial intelligence enabled wearable PSG systems. Here, we present a study aimed at validating the performance of ZMax, a widely-used wearable PSG that includes frontal electroencephalography (EEG) and actigraphy but no submental electromyography (EMG). We analyzed 135 nights with simultaneous ZMax and standard PSG recordings amounting to over 900 hours from four different datasets, and evaluated the performance of the headbands proprietary automatic sleep scoring (ZLab) alongside our open-source algorithm (DreamentoScorer) in comparison with human sleep scoring. ZLab and DreamentoScorer compared to human scorers with moderate and substantial agreement and Cohens kappa scores of 59.61% and 72.18%, respectively. We further analyzed the competence of these algorithms in determining sleep assessment metrics, as well as shedding more lights on the bandpower computation, and morphological analysis of sleep microstructural features between ZMax and standard PSG. Relative bandpower computed by ZMax implied an error of 5.5% (delta), 4.5% (theta), 1.6% (alpha), 0.5% (sigma), 0.8% (beta), and 0.2% (gamma), compared to standard PSG. In addition, the microstructural features detected in ZMax did not represent exactly the same characteristics as in standard PSG. Besides similarities and discrepancies between ZMax and standard PSG, we measured and discussed the technology acceptance rate, feasibility of data collection with ZMax, and highlighted essential factors for utilizing ZMax as a reliable tool for both monitoring and modulating sleep.

neuroscience↗

bioRxiv2023

Large language models are universal biomedical simulators

Computational simulation of biological processes can be a valuable tool in accelerating biomedical research, but usually requires extensive domain knowledge and manual adaptation. Recently, large language models (LLMs) such as GPT-4 have proven surprisingly successful for a wide range of tasks by generating human language at a very large scale. Here we explore the potential of leveraging LLMs as simulators of biological systems. We establish proof-of-concept of a text-based simulator, SimulateGPT, that uses LLM reasoning. We demonstrate good prediction performance for various biomedical applications, without requiring explicit domain knowledge or manual tuning. LLMs thus enable a new class of versatile and broadly applicable biological simulators. This text-based simulation paradigm is well-suited for modeling and understanding complex living systems that are difficult to describe with physics-based first-principles simulation, but for which extensive knowledge and context is available as written text.

bioinformatics↗

bioRxiv2021

The Immunological Factors Predisposing To Severe COVID-19 Are Already Present In Healthy Elderly And Men

BackgroundMale sex and old age are risk factors for COVID-19 severity, but the underlying causes are unknown. A possible explanation for this might be the differences in immunological profiles in males and the elderly before the infection. Given the seasonal profile of COVID-19, the seasonal response against SARS-CoV-2 could also be different in these groups. MethodsThe abundance of circulating proteins and immune populations associated with severe COVID-19 was analyzed in 2 healthy cohorts. PBMCs of female, male, young, and old subjects in different seasons of the year were stimulated with heat-inactivated SARS-CoV-2. ResultSeveral T cell subsets, which are known to be depleted in severe COVID-19 patients, were intrinsically less abundant in men and older individuals. Plasma proteins increasing with disease severity, including HGF, IL-8, and MCP-1, were more abundant in the elderly and males. The elderly produced significantly more IL-1RA and had a dysregulated IFN{gamma} response with lower production in the summer compared with young individuals. ConclusionsThe immune characteristics of severe COVID-19, described by a differential abundance of immune cells and circulating inflammatory proteins, are intrinsically present in healthy men and the elderly. This might explain the susceptibility of men and the elderly to SARS-CoV-2 infection. SummaryImmunological profile of severe COVID-19, characterized by altered immune cell populations and inflammatory plasma proteins is intrinsically present in healthy men and the elderly. Different age and sex groups show distinct seasonal responses to SARS-CoV-2.

immunology↗

bioRxiv2017

Induction of differentiation and metabolic reprogramming in human hepatoma cells by adult human serum

Tissue culture medium routinely contains fetal bovine serum (FBS). Here we show that culturing human hepatoma cells in their native, adult serum (human serum, HS) results in the restoration of key morphological and metabolic features of normal liver cells. When moved to HS, these cells show differential transcription of 22-32% of the genes, stop proliferating, and assume a hepatocyte-like morphology. Metabolic analysis shows that the Warburg-like metabolic profile, typical for FBS-cultured cells, is replaced by a diverse metabolic profile consistent with in vivo hepatocytes. We demonstrate the formation of large lipid and glycogen stores, increased glycogenesis, increased {beta}-oxidation, increased ketogenesis, and decreased glycolysis. Finally, organ-specific functions are restored, including xenobiotics degradation and secretion of bile, very low density lipoprotein, and albumin. Thus, organ-specific functions are not necessarily lost in cell cultures, but might be merely suppressed in FBS. Together, we showed that cells that are representative of normal physiology can be produced from cancer cells simply by replacing FBS by HS in culture media. The effect of serum is often overseen in cell culture and we provide a detailed study in the changes that occur, provide insight in some of the serum components that may play a role in the establishment of the different phenotypes, and discuss how these finding might be beneficial to a variety of research fields.

cell biology↗