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1.
J Clin Monit Comput ; 38(1): 147-156, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37864755

ABSTRACT

PURPOSE: This study aimed to describe the 24-hour cycle of wearable sensor-obtained heart rate in patients with deterioration-free recovery and to compare it with patients experiencing postoperative deterioration. METHODS: A prospective observational trial was performed in patients following bariatric or major abdominal cancer surgery. A wireless accelerometer patch (Healthdot) continuously measured postoperative heart rate, both in the hospital and after discharge, for a period of 14 days. The circadian pattern, or diurnal rhythm, in the wearable sensor-obtained heart rate was described using peak, nadir and peak-nadir excursions. RESULTS: The study population consisted of 137 bariatric and 100 major abdominal cancer surgery patients. In the latter group, 39 experienced postoperative deterioration. Both surgery types showed disrupted diurnal rhythm on the first postoperative days. Thereafter, the bariatric group had significantly lower peak heart rates (days 4, 7-12, 14), lower nadir heart rates (days 3-14) and larger peak-nadir excursions (days 2, 4-14). In cancer surgery patients, significantly higher nadir (days 2-5) and peak heart rates (days 2-3) were observed prior to deterioration. CONCLUSIONS: The postoperative diurnal rhythm of heart rate is disturbed by different types of surgery. Both groups showed recovery of diurnal rhythm but in patients following cancer surgery, both peak and nadir heart rates were higher than in the bariatric surgery group. Especially nadir heart rate was identified as a potential prognostic marker for deterioration after cancer surgery.


Subject(s)
Neoplasms , Wearable Electronic Devices , Humans , Heart Rate/physiology , Circadian Rhythm/physiology , Prospective Studies
2.
Metab Eng ; 77: 128-142, 2023 05.
Article in English | MEDLINE | ID: mdl-36963461

ABSTRACT

Microbial cell factories face changing environments during industrial fermentations. Kinetic metabolic models enable the simulation of the dynamic metabolic response to these perturbations, but their development is challenging due to model complexity and experimental data requirements. An example of this is the well-established microbial cell factory Saccharomyces cerevisiae, for which no consensus kinetic model of central metabolism has been developed and implemented in industry. Here, we aim to bring the academic and industrial communities closer to this consensus model. We developed a physiology informed kinetic model of yeast glycolysis connected to central carbon metabolism by including the effect of anabolic reactions precursors, mitochondria and the trehalose cycle. To parametrize such a large model, a parameter estimation pipeline was developed, consisting of a divide and conquer approach, supplemented with regularization and global optimization. Additionally, we show how this first mechanistic description of a growing yeast cell captures experimental dynamics at different growth rates and under a strong glucose perturbation, is robust to parametric uncertainty and explains the contribution of the different pathways in the network. Such a comprehensive model could not have been developed without using steady state and glucose perturbation data sets. The resulting metabolic reconstruction and parameter estimation pipeline can be applied in the future to study other industrially-relevant scenarios. We show this by generating a hybrid CFD-metabolic model to explore intracellular glycolytic dynamics for the first time. The model suggests that all intracellular metabolites oscillate within a physiological range, except carbon storage metabolism, which is sensitive to the extracellular environment.


Subject(s)
Glucose , Saccharomyces cerevisiae , Saccharomyces cerevisiae/metabolism , Glucose/metabolism , Glycolysis , Fermentation , Carbon/metabolism , Models, Biological
3.
Sensors (Basel) ; 23(9)2023 May 02.
Article in English | MEDLINE | ID: mdl-37177659

ABSTRACT

Assessing post-operative recovery is a significant component of perioperative care, since this assessment might facilitate detecting complications and determining an appropriate discharge date. However, recovery is difficult to assess and challenging to predict, as no universally accepted definition exists. Current solutions often contain a high level of subjectivity, measure recovery only at one moment in time, and only investigate recovery until the discharge moment. For these reasons, this research aims to create a model that predicts continuous recovery scores in perioperative care in the hospital and at home for objective decision making. This regression model utilized vital signs and activity metrics measured using wearable sensors and the XGBoost algorithm for training. The proposed model described continuous recovery profiles, obtained a high predictive performance, and provided outcomes that are interpretable due to the low number of features in the final model. Moreover, activity features, the circadian rhythm of the heart, and heart rate recovery showed the highest feature importance in the recovery model. Patients could be identified with fast and slow recovery trajectories by comparing patient-specific predicted profiles to the average fast- and slow-recovering populations. This identification may facilitate determining appropriate discharge dates, detecting complications, preventing readmission, and planning physical therapy. Hence, the model can provide an automatic and objective decision support tool.


Subject(s)
Neoplasms , Wearable Electronic Devices , Humans , Algorithms , Perioperative Care , Machine Learning
4.
PLoS Comput Biol ; 17(3): e1008852, 2021 03.
Article in English | MEDLINE | ID: mdl-33788828

ABSTRACT

Plasma glucose and insulin responses following an oral glucose challenge are representative of glucose tolerance and insulin resistance, key indicators of type 2 diabetes mellitus pathophysiology. A large heterogeneity in individuals' challenge test responses has been shown to underlie the effectiveness of lifestyle intervention. Currently, this heterogeneity is overlooked due to a lack of methods to quantify the interconnected dynamics in the glucose and insulin time-courses. Here, a physiology-based mathematical model of the human glucose-insulin system is personalized to elucidate the heterogeneity in individuals' responses using a large population of overweight/obese individuals (n = 738) from the DIOGenes study. The personalized models are derived from population level models through a systematic parameter selection pipeline that may be generalized to other biological systems. The resulting personalized models showed a 4-5 fold decrease in discrepancy between measurements and model simulation compared to population level. The estimated model parameters capture relevant features of individuals' metabolic health such as gastric emptying, endogenous insulin secretion and insulin dependent glucose disposal into tissues, with the latter also showing a significant association with the Insulinogenic index and the Matsuda insulin sensitivity index, respectively.


Subject(s)
Diabetes Mellitus, Type 2 , Glucose , Insulin Resistance/physiology , Patient-Specific Modeling , Adult , Blood Glucose/drug effects , Blood Glucose/physiology , Diabetes Mellitus, Type 2/blood , Diabetes Mellitus, Type 2/metabolism , Diabetes Mellitus, Type 2/physiopathology , Female , Glucose/administration & dosage , Glucose/metabolism , Glucose/pharmacology , Glucose Tolerance Test , Humans , Male , Middle Aged , Postprandial Period/drug effects , Postprandial Period/physiology
5.
BMC Cardiovasc Disord ; 22(1): 104, 2022 03 14.
Article in English | MEDLINE | ID: mdl-35287575

ABSTRACT

BACKGROUND: The left atrium (LA) is a key player in the pathophysiology of systolic and diastolic heart failure (HF). Speckle tracking derived LA reservoir strain (LASr) can be used as a prognostic surrogate for elevated left ventricular filling pressure similar to NT-proBNP. The aim of the study is to investigate the correlation between LASr and NT-proBNP and its prognostic value with regards to the composite endpoint of HF hospitalization and all-cause mortality within 1 year. METHODS: Outpatients, sent to the echocardiography core lab because of HF, were enrolled into this study. Patients underwent a transthoracic echocardiographic examination, commercially available software was used to measure LASr. Blood samples were collected directly after the echocardiographic examination to determine NT-proBNP. RESULTS: We included 174 HF patients, 43% with reduced, 36% with mildly reduced, and 21% with preserved ejection fraction. The study population showed a strong inverse correlation between LASr and log-transformed NT-proBNP (r = - 0.75, p < 0.01). Compared to NT-proBNP, LASr predicts the endpoint with a comparable specificity (83% vs. 84%), however with a lower sensitivity (70% vs. 61%). CONCLUSION: LASr is inversely correlated with NT-proBNP and a good echocardiographic predictor for the composite endpoint of hospitalization and all-cause mortality in patients with HF. TRIAL REGISTRATION: https://www.trialregister.nl/trial/7268.


Subject(s)
Heart Failure , Biomarkers , Cohort Studies , Heart Atria/diagnostic imaging , Heart Failure/diagnostic imaging , Heart Failure/epidemiology , Humans , Natriuretic Peptide, Brain , Peptide Fragments , Prognosis , Stroke Volume/physiology , Ventricular Function, Left
6.
Int J Obes (Lond) ; 45(3): 619-630, 2021 03.
Article in English | MEDLINE | ID: mdl-33452416

ABSTRACT

BACKGROUND/OBJECTIVES: Bile acids (BA) act as detergents in intestinal fat absorption and as modulators of metabolic processes via activation of receptors such as FXR and TGR5. Elevated plasma BA as well as increased intestinal BA signalling to promote GLP-1 release have been implicated in beneficial health effects of Roux-en-Y gastric bypass surgery (RYGB). Whether BA also contribute to the postprandial hypoglycaemia that is frequently observed post-RYGB is unknown. METHODS: Plasma BA, fibroblast growth factor 19 (FGF19), 7α-hydroxy-4-cholesten-3-one (C4), GLP-1, insulin and glucose levels were determined during 3.5 h mixed-meal tolerance tests (MMTT) in subjects after RYGB, either with (RYGB, n = 11) or without a functioning gallbladder due to cholecystectomy (RYGB-CC, n = 11). Basal values were compared to those of age, BMI and sex-matched obese controls without RYGB (n = 22). RESULTS: Fasting BA as well as FGF19 levels were elevated in RYGB and RYGB-CC subjects compared to non-bariatric controls, without significant differences between RYGB and RYGB-CC. Postprandial hypoglycaemia was observed in 8/11 RYGB-CC and only in 3/11 RYGB. Subjects who developed hypoglycaemia showed higher postprandial BA levels coinciding with augmented GLP-1 and insulin responses during the MMTT. The nadir of plasma glucose concentrations after meals showed a negative relationship with postprandial BA peaks. Plasma C4 was lower during MMTT in subjects experiencing hypoglycaemia, indicating lower hepatic BA synthesis. Computer simulations revealed that altered intestinal transit underlies the occurrence of exaggerated postprandial BA responses in hypoglycaemic subjects. CONCLUSION: Altered BA kinetics upon ingestion of a meal, as frequently observed in RYGB-CC subjects, appear to contribute to postprandial hypoglycaemia by stimulating intestinal GLP-1 release.


Subject(s)
Bile Acids and Salts/metabolism , Gastric Bypass , Hypoglycemia/metabolism , Postprandial Period/physiology , Adult , Case-Control Studies , Female , Gastric Bypass/adverse effects , Gastric Bypass/statistics & numerical data , Humans , Kinetics , Male , Middle Aged , Obesity/surgery
7.
PLoS Comput Biol ; 15(10): e1007400, 2019 10.
Article in English | MEDLINE | ID: mdl-31581241

ABSTRACT

Given the association of disturbances in non-esterified fatty acid (NEFA) metabolism with the development of Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease, computational models of glucose-insulin dynamics have been extended to account for the interplay with NEFA. In this study, we use arteriovenous measurement across the subcutaneous adipose tissue during a mixed meal challenge test to evaluate the performance and underlying assumptions of three existing models of adipose tissue metabolism and construct a new, refined model of adipose tissue metabolism. Our model introduces new terms, explicitly accounting for the conversion of glucose to glyceraldehye-3-phosphate, the postprandial influx of glycerol into the adipose tissue, and several physiologically relevant delays in insulin signalling in order to better describe the measured adipose tissues fluxes. We then applied our refined model to human adipose tissue flux data collected before and after a diet intervention as part of the Yoyo study, to quantify the effects of caloric restriction on postprandial adipose tissue metabolism. Significant increases were observed in the model parameters describing the rate of uptake and release of both glycerol and NEFA. Additionally, decreases in the model's delay in insulin signalling parameters indicates there is an improvement in adipose tissue insulin sensitivity following caloric restriction.


Subject(s)
Adipose Tissue/metabolism , Computational Biology/methods , Lipid Metabolism/physiology , Arteriovenous Anastomosis/metabolism , Blood Glucose/metabolism , Computer Simulation , Fatty Acids/metabolism , Fatty Acids, Nonesterified/metabolism , Glucose/metabolism , Humans , Insulin/metabolism , Isotopes , Lipids/physiology , Models, Biological , Postprandial Period/physiology
8.
PLoS Comput Biol ; 14(6): e1006145, 2018 06.
Article in English | MEDLINE | ID: mdl-29879115

ABSTRACT

The Metabolic Syndrome (MetS) is a complex, multifactorial disorder that develops slowly over time presenting itself with large differences among MetS patients. We applied a systems biology approach to describe and predict the onset and progressive development of MetS, in a study that combined in vivo and in silico models. A new data-driven, physiological model (MINGLeD: Model INtegrating Glucose and Lipid Dynamics) was developed, describing glucose, lipid and cholesterol metabolism. Since classic kinetic models cannot describe slowly progressing disorders, a simulation method (ADAPT) was used to describe longitudinal dynamics and to predict metabolic concentrations and fluxes. This approach yielded a novel model that can describe long-term MetS development and progression. This model was integrated with longitudinal in vivo data that was obtained from male APOE*3-Leiden.CETP mice fed a high-fat, high-cholesterol diet for three months and that developed MetS as reflected by classical symptoms including obesity and glucose intolerance. Two distinct subgroups were identified: those who developed dyslipidemia, and those who did not. The combination of MINGLeD with ADAPT could correctly predict both phenotypes, without making any prior assumptions about changes in kinetic rates or metabolic regulation. Modeling and flux trajectory analysis revealed that differences in liver fluxes and dietary cholesterol absorption could explain this occurrence of the two different phenotypes. In individual mice with dyslipidemia dietary cholesterol absorption and hepatic turnover of metabolites, including lipid fluxes, were higher compared to those without dyslipidemia. Predicted differences were also observed in gene expression data, and consistent with the emergence of insulin resistance and hepatic steatosis, two well-known MetS co-morbidities. Whereas MINGLeD specifically models the metabolic derangements underlying MetS, the simulation method ADAPT is generic and can be applied to other diseases where dynamic modeling and longitudinal data are available.


Subject(s)
Computational Biology/methods , Computer Simulation , Metabolic Syndrome/metabolism , Metabolic Syndrome/physiopathology , Models, Biological , Animals , Diet, High-Fat , Disease Models, Animal , Humans , Insulin Resistance , Lipid Metabolism , Mice
9.
Methods ; 149: 69-73, 2018 10 01.
Article in English | MEDLINE | ID: mdl-29981382

ABSTRACT

Mining biological information from rich "-omics" datasets is facilitated by organizing features into groups that are related to a biological phenomenon or clinical outcome. For example, microorganisms can be grouped based on a phylogenetic tree that depicts their similarities regarding genetic or physical characteristics. Here, we describe algorithms that incorporate auxiliary information in terms of groups of predictors and the relationships between them into the metagenome learning task to build intelligible models. In particular, our cost function guides the feature selection process using auxiliary information by requiring related groups of predictors to provide similar contributions to the final response. We apply the developed algorithms to a recently published dataset analyzing the effects of fecal microbiota transplantation (FMT) in order to identify factors that are associated with improved peripheral insulin sensitivity, leading to accurate predictions of the response to the FMT.


Subject(s)
Algorithms , Gastrointestinal Microbiome/physiology , Metagenome/physiology , Models, Biological , Phylogeny , Humans
10.
Plant J ; 85(2): 289-304, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26576489

ABSTRACT

Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome-scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome-scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses.


Subject(s)
Droughts , Photosynthesis/genetics , Solanum lycopersicum/metabolism , Gene Expression Regulation, Plant/physiology , Solanum lycopersicum/physiology , Metabolic Networks and Pathways/genetics , Metabolic Networks and Pathways/physiology , Plant Leaves/metabolism , Plant Leaves/physiology
11.
Am J Physiol Regul Integr Comp Physiol ; 312(5): R689-R701, 2017 05 01.
Article in English | MEDLINE | ID: mdl-28179228

ABSTRACT

Muscle weakness and exercise intolerance negatively affect the quality of life of patients with mitochondrial myopathy. Short-term dietary nitrate supplementation has been shown to improve exercise performance and reduce oxygen cost of exercise in healthy humans and trained athletes. We investigated whether 1 wk of dietary inorganic nitrate supplementation decreases the oxygen cost of exercise and improves mitochondrial function in patients with mitochondrial myopathy. Ten patients with mitochondrial myopathy (40 ± 5 yr, maximal whole body oxygen uptake = 21.2 ± 3.2 ml·min-1·kg body wt-1, maximal work load = 122 ± 26 W) received 8.5 mg·kg body wt-1·day-1 inorganic nitrate (~7 mmol) for 8 days. Whole body oxygen consumption at 50% of the maximal work load, in vivo skeletal muscle oxidative capacity (evaluated from postexercise phosphocreatine recovery using 31P-magnetic resonance spectroscopy), and ex vivo mitochondrial oxidative capacity in permeabilized skinned muscle fibers (measured with high-resolution respirometry) were determined before and after nitrate supplementation. Despite a sixfold increase in plasma nitrate levels, nitrate supplementation did not affect whole body oxygen cost during submaximal exercise. Additionally, no beneficial effects of nitrate were found on in vivo or ex vivo muscle mitochondrial oxidative capacity. This is the first time that the therapeutic potential of dietary nitrate for patients with mitochondrial myopathy was evaluated. We conclude that 1 wk of dietary nitrate supplementation does not reduce oxygen cost of exercise or improve mitochondrial function in the group of patients tested.


Subject(s)
Exercise , Mitochondria, Muscle/metabolism , Mitochondrial Myopathies/drug therapy , Mitochondrial Myopathies/physiopathology , Nitrates/administration & dosage , Oxygen Consumption/drug effects , Administration, Oral , Adult , Aged , Exercise Tolerance/drug effects , Female , Humans , Male , Middle Aged , Mitochondria, Muscle/drug effects , Muscle Strength/drug effects , Psychomotor Performance/drug effects , Treatment Outcome , Young Adult
12.
Diabetes Spectr ; 30(3): 182-187, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28848312

ABSTRACT

The Eindhoven Diabetes Education Simulator project was initiated to develop an educational solution that helps diabetes patients understand and learn more about their diabetes. This article describes the identification of user preferences for the development of such solutions. Young seniors (aged 50-65 years) with type 2 diabetes were chosen as the target group because they are likely to have more affinity with digital devices than older people and because 88% of the Dutch diabetes population is >50 years of age. Data about the target group were gathered through literature research and interviews. The literature research covered data about their device use and education preferences. To gain insight into the daily life of diabetes patients and current diabetes education processes, 20 diabetes patients and 10 medical experts were interviewed. The interviews were analyzed using affinity diagrams. Those diagrams, together with the literature data, formed the basis for two personas and corresponding customer journey maps. Literature showed that diabetes prevalence is inversely correlated to educational level. Computer and device use is relatively low within the target group, but is growing. The interviews showed that young seniors like to play board, card, and computer games, with others or alone. Family and loved ones play an important role in their lives. Medical experts are crucial in the diabetes education of young senior diabetes patients. These findings are translated into a list of design aspects that can be used for creating educational solutions.

13.
FASEB J ; 29(4): 1153-64, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25477282

ABSTRACT

Liver X receptor (LXR) agonists exert potent antiatherosclerotic actions but simultaneously induce excessive triglyceride (TG) accumulation in the liver. To obtain a detailed insight into the underlying mechanism of hepatic TG accumulation, we used a novel computational modeling approach called analysis of dynamic adaptations in parameter trajectories (ADAPT). We revealed that both input and output fluxes to hepatic TG content are considerably induced on LXR activation and that in the early phase of LXR agonism, hepatic steatosis results from only a minor imbalance between the two. It is generally believed that LXR-induced hepatic steatosis results from increased de novo lipogenesis (DNL). In contrast, ADAPT predicted that the hepatic influx of free fatty acids is the major contributor to hepatic TG accumulation in the early phase of LXR activation. Qualitative validation of this prediction showed a 5-fold increase in the contribution of plasma palmitate to hepatic monounsaturated fatty acids on acute LXR activation, whereas DNL was not yet significantly increased. This study illustrates that complex effects of pharmacological intervention can be translated into distinct patterns of metabolic regulation through state-of-the-art mathematical modeling.


Subject(s)
Fatty Liver/etiology , Fatty Liver/metabolism , Orphan Nuclear Receptors/metabolism , Animals , Atherosclerosis/drug therapy , Computer Simulation , Fatty Acids, Nonesterified/metabolism , Hydrocarbons, Fluorinated/pharmacology , Hydrocarbons, Fluorinated/toxicity , Lipogenesis , Lipoproteins, VLDL/metabolism , Liver/drug effects , Liver/metabolism , Liver X Receptors , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Models, Biological , Orphan Nuclear Receptors/agonists , Orphan Nuclear Receptors/deficiency , PPAR gamma/deficiency , PPAR gamma/genetics , PPAR gamma/metabolism , Sulfonamides/pharmacology , Sulfonamides/toxicity , Systems Biology , Triglycerides/metabolism
14.
PLoS Comput Biol ; 10(5): e1003579, 2014 May.
Article in English | MEDLINE | ID: mdl-24784354

ABSTRACT

Disturbances of lipoprotein metabolism are recognized as indicators of cardiometabolic disease risk. Lipoprotein size and composition, measured in a lipoprotein profile, are considered to be disease risk markers. However, the measured profile is a collective result of complex metabolic interactions, which complicates the identification of changes in metabolism. In this study we aim to develop a method which quantitatively relates murine lipoprotein size, composition and concentration to the molecular mechanisms underlying lipoprotein metabolism. We introduce a computational framework which incorporates a novel kinetic model of murine lipoprotein metabolism. The model is applied to compute a distribution of plasma lipoproteins, which is then related to experimental lipoprotein profiles through the generation of an in silico lipoprotein profile. The model was first applied to profiles obtained from wild-type C57Bl/6J mice. The results provided insight into the interplay of lipoprotein production, remodelling and catabolism. Moreover, the concentration and metabolism of unmeasured lipoprotein components could be determined. The model was validated through the prediction of lipoprotein profiles of several transgenic mouse models commonly used in cardiovascular research. Finally, the framework was employed for longitudinal analysis of the profiles of C57Bl/6J mice following a pharmaceutical intervention with a liver X receptor (LXR) agonist. The multifaceted regulatory response to the administration of the compound is incompletely understood. The results explain the characteristic changes of the observed lipoprotein profile in terms of the underlying metabolic perturbation and resultant modifications of lipid fluxes in the body. The Murine Lipoprotein Profiler (MuLiP) presented here is thus a valuable tool to assess the metabolic origin of altered murine lipoprotein profiles and can be applied in preclinical research performed in mice for analysis of lipid fluxes and lipoprotein composition.


Subject(s)
Chromatography, Liquid/methods , Gene Expression Profiling/methods , Lipoproteins/blood , Lipoproteins/chemistry , Models, Biological , Peptide Mapping/methods , Animals , Computer Simulation , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic
15.
PLoS Comput Biol ; 9(8): e1003166, 2013.
Article in English | MEDLINE | ID: mdl-23935478

ABSTRACT

The field of medical systems biology aims to advance understanding of molecular mechanisms that drive disease progression and to translate this knowledge into therapies to effectively treat diseases. A challenging task is the investigation of long-term effects of a (pharmacological) treatment, to establish its applicability and to identify potential side effects. We present a new modeling approach, called Analysis of Dynamic Adaptations in Parameter Trajectories (ADAPT), to analyze the long-term effects of a pharmacological intervention. A concept of time-dependent evolution of model parameters is introduced to study the dynamics of molecular adaptations. The progression of these adaptations is predicted by identifying necessary dynamic changes in the model parameters to describe the transition between experimental data obtained during different stages of the treatment. The trajectories provide insight in the affected underlying biological systems and identify the molecular events that should be studied in more detail to unravel the mechanistic basis of treatment outcome. Modulating effects caused by interactions with the proteome and transcriptome levels, which are often less well understood, can be captured by the time-dependent descriptions of the parameters. ADAPT was employed to identify metabolic adaptations induced upon pharmacological activation of the liver X receptor (LXR), a potential drug target to treat or prevent atherosclerosis. The trajectories were investigated to study the cascade of adaptations. This provided a counter-intuitive insight concerning the function of scavenger receptor class B1 (SR-B1), a receptor that facilitates the hepatic uptake of cholesterol. Although activation of LXR promotes cholesterol efflux and -excretion, our computational analysis showed that the hepatic capacity to clear cholesterol was reduced upon prolonged treatment. This prediction was confirmed experimentally by immunoblotting measurements of SR-B1 in hepatic membranes. Next to the identification of potential unwanted side effects, we demonstrate how ADAPT can be used to design new target interventions to prevent these.


Subject(s)
Computational Biology/methods , Drug Therapy , Models, Biological , Pharmacological Phenomena , Animals , Cholesterol, HDL/analysis , Cholesterol, HDL/metabolism , Hydrocarbons, Fluorinated/pharmacokinetics , Hydrocarbons, Fluorinated/pharmacology , Lipoproteins, VLDL/analysis , Lipoproteins, VLDL/metabolism , Liver/chemistry , Liver/metabolism , Liver X Receptors , Mice , Mice, Inbred C57BL , Monte Carlo Method , Orphan Nuclear Receptors/agonists , Phenotype , Reproducibility of Results , Sulfonamides/pharmacokinetics , Sulfonamides/pharmacology , Triglycerides/analysis , Triglycerides/metabolism
16.
Chem Commun (Camb) ; 60(51): 6466-6475, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38847387

ABSTRACT

Cell-free systems have emerged as a versatile platform in synthetic biology, finding applications in various areas such as prototyping synthetic circuits, biosensor development, and biomanufacturing. To streamline the prototyping process, cell-free systems often incorporate a modeling step that predicts the outcomes of various experimental scenarios, providing a deeper insight into the underlying mechanisms and functions. There are two recognized approaches for modeling these systems: mechanism-based modeling, which models the underlying reaction mechanisms; and data-driven modeling, which makes predictions based on data without preconceived interactions between system components. In this highlight, we focus on the latest advancements in both modeling approaches for cell-free systems, exploring their potential for the design and optimization of synthetic genetic circuits.


Subject(s)
Cell-Free System , Synthetic Biology , Synthetic Biology/methods , Gene Regulatory Networks , Models, Biological
17.
Diabetes Res Clin Pract ; 216: 111833, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39179114

ABSTRACT

The global rise in diabetes prevalence poses a significant challenge to healthcare providers, stimulating interest in digital interventions such as educational games. However, the impact and availability of research-developed diabetes games remain uncertain. This scoping review aimed to provide a comprehensive overview of serious games for diabetes, encompassing their availability, characteristics and health effects. Through an electronic search in multiple databases, a total of 21 articles addressing 23 games were included in the literature review. The majority of these games were inaccessible outside of research settings, despite demonstrating positive effects on various aspects of diabetes management, including knowledge, physical activity, self-management, mental well-being, and HbA1c levels. Most games were designed for mobile phones, targeting both children and adults. A subsequent app store search revealed 13 additional diabetes games, however nearly none (7.7%) of these underwent research scrutiny, leaving their expected effects uncertain. The disparity between evidence-based games and those available in app stores underscores the need for bridging this gap to ensure the availability of effective digital games for diabetes management worldwide.


Subject(s)
Diabetes Mellitus , Health Personnel , Video Games , Humans , Diabetes Mellitus/therapy , Exercise , Mobile Applications , Self-Management/methods , Patient Education as Topic/methods
18.
Comput Methods Programs Biomed ; 257: 108424, 2024 Sep 19.
Article in English | MEDLINE | ID: mdl-39326360

ABSTRACT

BACKGROUND AND OBJECTIVE: Patients who underwent Roux-en-Y Gastric Bypass surgery for treatment of obesity or diabetes can suffer from post-bariatric hypoglycemia (PBH). It has been assumed that PBH is caused by increased levels of the hormone GLP-1. In this research, we elucidate the role of GLP-1 in PBH with a physiology-based mathematical model. METHODS: The Eindhoven Diabetes Simulator (EDES) model, simulating postprandial glucose homeostasis, was adapted to include the effect of GLP-1 on insulin secretion. Parameter sensitivity analysis was used to identify parameters that could cause PBH. Virtual patient models were created by defining sets of models parameters based on 63 participants from the HypoBaria study cohort, before and one year after bariatric surgery. RESULTS: Simulations with the virtual patient models showed that glycemic excursions can be correctly simulated for the study population, despite heterogeneity in the glucose, insulin and GLP-1 data. Sensitivity analysis showed that GLP-1 stimulated insulin secretion alone was not able to cause PBH. Instead, analyses showed the increased transit speed of the ingested food resulted in quick and increased glucose absorption in the gut after surgery, which in turn induced postprandial glycemic dips. Furthermore, according to the model post-bariatric increased rate of glucose absorption in combination with different levels of insulin sensitivity can result in PBH. CONCLUSIONS: Our model findings implicate that if initial rapid improvement in insulin sensitivity after gastric bypass surgery is followed by a more gradual decrease in insulin sensitivity, this may result in the emergence of PBH after prolonged time (months to years after surgery).

19.
Sci Rep ; 14(1): 8037, 2024 04 05.
Article in English | MEDLINE | ID: mdl-38580749

ABSTRACT

Continuous glucose monitoring (CGM) is a promising, minimally invasive alternative to plasma glucose measurements for calibrating physiology-based mathematical models of insulin-regulated glucose metabolism, reducing the reliance on in-clinic measurements. However, the use of CGM glucose, particularly in combination with insulin measurements, to develop personalized models of glucose regulation remains unexplored. Here, we simultaneously measured interstitial glucose concentrations using CGM as well as plasma glucose and insulin concentrations during an oral glucose tolerance test (OGTT) in individuals with overweight or obesity to calibrate personalized models of glucose-insulin dynamics. We compared the use of interstitial glucose with plasma glucose in model calibration, and evaluated the effects on model fit, identifiability, and model parameters' association with clinically relevant metabolic indicators. Models calibrated on both plasma and interstitial glucose resulted in good model fit, and the parameter estimates associated with metabolic indicators such as insulin sensitivity measures in both cases. Moreover, practical identifiability of model parameters was improved in models estimated on CGM glucose compared to plasma glucose. Together these results suggest that CGM glucose may be considered as a minimally invasive alternative to plasma glucose measurements in model calibration to quantify the dynamics of glucose regulation.


Subject(s)
Glucose , Insulin , Humans , Blood Glucose/metabolism , Blood Glucose Self-Monitoring , Continuous Glucose Monitoring
20.
iScience ; 27(4): 109362, 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38500825

ABSTRACT

The manifestation of metabolic deteriorations that accompany overweight and obesity can differ greatly between individuals, giving rise to a highly heterogeneous population. This inter-individual variation can impede both the provision and assessment of nutritional interventions as multiple aspects of metabolic health should be considered at once. Here, we apply the Mixed Meal Model, a physiology-based computational model, to characterize an individual's metabolic health in silico. A population of 342 personalized models were generated using data for individuals with overweight and obesity from three independent intervention studies, demonstrating a strong relationship between the model-derived metric of insulin resistance (ρ = 0.67, p < 0.05) and the gold-standard hyperinsulinemic-euglycemic clamp. The model is also shown to quantify liver fat accumulation and ß-cell functionality. Moreover, we show that personalized Mixed Meal Models can be used to evaluate the impact of a dietary intervention on multiple aspects of metabolic health at the individual level.

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