Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.

Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.

Two heads are better than one: current landscape of integrating QSP and machine learning : An ISoP QSP SIG white paper by the working group on the integration of quantitative systems pharmacology and machine learning.

Quantitative systems pharmacology (QSP) modeling is applied to address essential questions in drug development, such as the mechanism of action of a therapeutic agent and the progression of disease. Meanwhile, machine learning (ML) approaches also contribute to answering these questions via the analysis of multi-layer 'omics' data such as gene expression, proteomics, metabolomics, and high-throughput imaging. Furthermore, ML approaches can also be applied to aspects of QSP modeling. Both approaches are powerful tools and there is considerable interest in integrating QSP modeling and ML. So far, a few successful implementations have been carried out from which we have learned about how each approach can overcome unique limitations of the other. The QSP + ML working group of the International Society of Pharmacometrics QSP Special Interest Group was convened in September, 2019 to identify and begin realizing new opportunities in QSP and ML integration. The working group, which comprises 21 members representing 18 academic and industry organizations, has identified four categories of current research activity which will be described herein together with case studies of applications to drug development decision making. The working group also concluded that the integration of QSP and ML is still in its early stages of moving from evaluating available technical tools to building case studies. This paper reports on this fast-moving field and serves as a foundation for future codification of best practices.

Review of applications and challenges of quantitative systems pharmacology modeling and machine learning for heart failure.

Quantitative systems pharmacology (QSP) is an important approach in pharmaceutical research and development that facilitates in silico generation of quantitative mechanistic hypotheses and enables in silico trials. As demonstrated by applications from numerous industry groups and interest from regulatory authorities, QSP is becoming an increasingly critical component in clinical drug development. With rapidly evolving computational tools and methods, QSP modeling has achieved important progress in pharmaceutical research and development, including for heart failure (HF). However, various challenges exist in the QSP modeling and clinical characterization of HF. Machine/deep learning (ML/DL) methods have had success in a wide variety of fields and disciplines. They provide data-driven approaches in HF diagnosis and modeling, and offer a novel strategy to inform QSP model development and calibration. The combination of ML/DL and QSP modeling becomes an emergent direction in the understanding of HF and clinical development new therapies. In this work, we review the current status and achievement in QSP and ML/DL for HF, and discuss remaining challenges and future perspectives in the field.

Determination the cut-off point for the Bergen social media addiction (BSMAS): Diagnostic contribution of the six criteria of the components model of addiction for social media disorder.

OBJECTIVE: Social media disorder (SMD) is an increasing problem, especially in adolescents. The lack of a consensual classification for SMD hinders the further development of the research field. The six components of Griffiths' biopsychosocial model of addiction have been the most widely used criteria to assess and diagnosis SMD. The Bergen social media addiction scale (BSMAS) based on Griffiths' six criteria is a widely used instrument to assess the symptoms and prevalence of SMD in populations. This study aims to: (1) determine the optimal cut-off point for the BSMAS to identify SMD among Chinese adolescents, and (2) evaluate the contribution of specific criteria to the diagnosis of SMD. METHOD: Structured diagnostic interviews in a clinical sample (n = 252) were performed to determine the optimal clinical cut-off point for the BSMAS. The BSMAS was further used to investigate SMD in a community sample of 21,375 adolescents. RESULTS: The BSMAS score of 24 was determined as the best cut-off score based on the gold standards of clinical diagnosis. The estimated 12-month prevalence of SMD among Chinese adolescents was 3.5%. According to conditional inference trees analysis, the criteria "mood modification", "conflict", "withdrawal", and "relapse" showed the higher predictive power for SMD diagnosis. CONCLUSIONS: Results suggest that a BSMAS score of 24 is the optimal clinical cut-off score for future research that measure SMD and its impact on health among adolescents. Furthermore, criteria of "mood modification", "conflict", "withdrawal", and "relapse" are the most relevant to the diagnosis of SMA in Chinese adolescents.

Clarification of the Cut-off Score for Nine-Item Internet Gaming Disorder Scale-Short Form (IGDS9-SF) in a Chinese Context.

BACKGROUND: The nine-item Internet Gaming Disorder Scale-Short-Form (IGDS9-SF) is a self-reported screening measure based on the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) criteria. It has been used to assesses symptoms and prevalence of Internet Gaming Disorder (IGD) in general population. Despite its widespread use, there is confusion arising from the recommended cutoff score for a positive diagnosis. This study aimed to identify the appropriate cutoff score for IGDS9-SF in a Chinese context. METHODS: The present study included a sample from clinical settings (n = 131) and another from universities (n = 3742). IGDS9-SF measurement and structured clinical interviews based on DSM-5 criteria for IGD were conducted in the sample from clinical settings. The cutoff score was determined using the receiver operating characteristics (ROC) curve. The validity of this cutoff score was further assessed in a sample from universities. RESULTS: Mathematical models suggest that the score of 32 is the optimal cutoff point (Youden's index, 96.2%; diagnostic accuracy, 96.1%; sensitivity, 98.0%; specificity, 91.9%; NPV, 91.9%; and NPY, 100%). The prevalence of IGD is 2.9% in this study. CONCLUSION: This study suggested that the optimal cutoff score of IGDS9-SF is 32 for the positive diagnosis of IGD in a Chinese context.

Review of quantitative systems pharmacological modeling in thrombosis.

Hemostasis and thrombosis are often thought as two sides of the same clotting mechanism whereas hemostasis is a natural protective mechanism to prevent bleeding and thrombosis is a blood clot abnormally formulated inside a blood vessel, blocking the normal blood flow. The evidence to date suggests that at least arterial thrombosis results from the same critical pathways of hemostasis. Analysis of these complex processes and pathways using quantitative systems pharmacological model-based approach can facilitate the delineation of the causal pathways that lead to the emergence of thrombosis. In this paper, we provide an overview of the main molecular and physiological mechanisms associated with hemostasis and thrombosis, and review the models and quantitative system pharmacological modeling approaches that are relevant in characterizing the interplay among the multiple factors and pathways of thrombosis. An emphasis is given to computational models for drug development. Future trends are discussed.

A Robust Inner and Outer Loop Control Method for Trajectory Tracking of a Quadrotor.

In order to achieve the complicated trajectory tracking of quadrotor, a geometric inner and outer loop control scheme is presented. The outer loop generates the desired rotation matrix for the inner loop. To improve the response speed and robustness, a geometric SMC controller is designed for the inner loop. The outer loop is also designed via sliding mode control (SMC). By Lyapunov theory and cascade theory, the closed-loop system stability is guaranteed. Next, the tracking performance is validated by tracking three representative trajectories. Then, the robustness of the proposed control method is illustrated by trajectory tracking in presence of model uncertainty and disturbances. Subsequently, experiments are carried out to verify the method. In the experiment, ultra wideband (UWB) is used for indoor positioning. Extended Kalman Filter (EKF) is used for fusing inertial measurement unit (IMU) and UWB measurements. The experimental results show the feasibility of the designed controller in practice. The comparative experiments with PD and PD loop demonstrate the robustness of the proposed control method.

Indoor Autonomous Control of a Two-Wheeled Inverted Pendulum Vehicle Using Ultra Wide Band Technology.

In this paper, we aimed to achieve the indoor tracking control of a two-wheeled inverted pendulum (TWIP) vehicle. The attitude data are acquired from a low cost micro inertial measurement unit (IMU), and the ultra-wideband (UWB) technology is utilized to obtain an accurate estimation of the TWIP's position. We propose a dual-loop control method to realize the simultaneous balance and trajectory tracking control for the TWIP vehicle. A robust adaptive second-order sliding mode control (2-RASMC) method based on an improved super-twisting (STW) algorithm is investigated to obtain the control laws, followed by several simulations to verify its robustness. The outer loop controller is designed using the idea of backstepping. Moreover, three typical trajectories, including a circle, a trifolium and a hexagon, have been designed to prove the adaptability of the control combinations. Six different combinations of inner and outer loop control algorithms have been compared, and the characteristics of inner and outer loop algorithm combinations have been analyzed. Simulation results demonstrate its tracking performance and thus verify the validity of the proposed control methods. Trajectory tracking experiments in a real indoor environment have been performed using our experimental vehicle to further validate the feasibility of the proposed algorithm in practice.

An integrated mathematical model of the human cardiopulmonary system: model validation under hypercapnia and hypoxia.

A novel integrated physiological model of the interactions between the cardiovascular and respiratory systems has been in development for the past few years. The model has hundreds of parameters and variables representing the physical and physiological properties of the human cardiopulmonary system. It can simulate many dynamic states and scenarios. The description of the model and the results in normal resting conditions were presented in a companion paper (Albanese A, Cheng L, Ursino M, Chbat NW.Am J Physiol Heart Circ Physiol 310: 2016; doi:10.1152/ajpheart.00230.2014), where model predictions were compared against average population data from literature. However, it is also essential to test the model in abnormal or pathological conditions to prove its consistency. Hence, in this paper, we concentrate on testing the cardiopulmonary model under hypercapnic and hypoxic conditions, by comparing model's outputs to population-averaged cardiorespiratory data reported in the literature. The utility of this comprehensive model is demonstrated by testing the internal consistency of the simulated responses of a significant number of cardiovascular variables (heart rate, arterial pressure, and cardiac output) and respiratory variables (tidal volume, respiratory rate, minute ventilation, alveolar O2 and CO2 partial pressures) over a wide range of perturbations and conditions; namely, hypercapnia at 3-7% CO2 levels and hypoxia at 7-9% O2 levels with controlled CO2(isocapnic hypoxia) and without controlled CO2(hypocapnic hypoxia). Finally, a sensitivity analysis is performed to analyze the role of the main cardiorespiratory control mechanisms triggered by hypercapnia and hypoxia.

An integrated mathematical model of the human cardiopulmonary system: model development.

Several cardiovascular and pulmonary models have been proposed in the last few decades. However, very few have addressed the interactions between these two systems. Our group has developed an integrated cardiopulmonary model (CP Model) that mathematically describes the interactions between the cardiovascular and respiratory systems, along with their main short-term control mechanisms. The model has been compared with human and animal data taken from published literature. Due to the volume of the work, the paper is divided in two parts. The present paper is on model development and normophysiology, whereas the second is on the model's validation on hypoxic and hypercapnic conditions. The CP Model incorporates cardiovascular circulation, respiratory mechanics, tissue and alveolar gas exchange, as well as short-term neural control mechanisms acting on both the cardiovascular and the respiratory functions. The model is able to simulate physiological variables typically observed in adult humans under normal and pathological conditions and to explain the underlying mechanisms and dynamics.

Heterozygous carriers of classical homocystinuria tend to have higher fasting serum homocysteine concentrations than non-carriers in the presence of folate deficiency.

BACKGROUND & AIMS: Many studies have reported that serum total homocysteine (tHcy) levels in cystathionine-beta-synthase (CBS) carriers are usually normal and only elevated after a methionine load. However, the amount of methionine required for a loading test is non-physiological and is never reached with regular feeding. Therefore, CBS carriers do not seem to be at an increased risk of cardiovascular diseases. However, the risk of cardiovascular diseases of CBS carriers with folate deficiency has not been studied. We recently found an extraordinarily high carrier rate (1/7.78) of a novel CBS mutation (p.D47E, c.T141A) in an Austronesian Taiwanese Tao tribe who live in a geographic area with folate deficiency. We evaluated if the CBS carriers tend to have higher fasting serum tHcy concentrations than non-carriers in presence of folate deficiency. METHODS: The serum tHcy and folate levels before and after folate replacement were measured in 48 adult Tao carriers, 40 age-matched Tao non-carriers and 40 age-matched Han Taiwanese controls. RESULTS: The serum tHcy level of the Tao CBS carriers (17.9 ± 3.8 µmol/l) was significantly higher than in Tao non-carriers (15.7 ± 3.5 µmol/l; p < 0.008) and Taiwanese controls (11.8 ± 2.9 µmol/l; p < 0.001). Furthermore, a high prevalence of folate deficiency in the Tao compared with the Taiwanese controls (4.9 ± 1.8 ng/ml vs. 10.6 ± 5.5 ng/ml; p < 0.001) was also noted. Of note, the difference in tHcy levels between the carriers and non-carriers was eliminated by folate supplementation. (carriers:13.65 ± 2.13 µmol/l; non-carriers:12.39 ± 3.25 µmol/l, p = 0.321). CONCLUSIONS: CBS carriers tend to have a higher tHcy level in the presence of folate deficiency than non-carriers. Although many reports have indicated that CBS carriers are not associated with cardiovascular disease, the risk for CBS carriers with folate deficiency has not been well studied. Owing to a significantly elevated level of fasting tHcy without methionine loading, it is important to evaluate the risk of cardiovascular disease in CBS carriers with folate deficiency.

Understanding the metabolic syndrome: a modeling perspective.

The prevalence of obesity is growing at an alarming rate, placing many at risk for developing diabetes, hypertension, sleep apnea, or a combination of disorders known as "metabolic syndrome". The evidence to date suggests that metabolic syndrome results from an imbalance in the mechanisms that link diet, physical activity, glucose-insulin control, and autonomic cardiovascular control. There is also growing recognition that sleep-disordered breathing and other forms of sleep disruption can contribute significantly to autonomic dysfunction and insulin resistance. Chronic sleep deprivation resulting from sleep-disordered breathing or behavioral causes can lead to excessive daytime sleepiness and lethargy, which in turn contribute to increasing obesity. Analysis of this complex dynamic system using a model-based approach can facilitate the delineation of the causal pathways that lead to the emergence of the metabolic syndrome. In this paper, we provide an overview of the main physiological mechanisms associated with obesity and sleep-disordered breathing that are believed to result in metabolic and autonomic dysfunction, and review the models and modeling approaches that are relevant in characterizing the interplay among the multiple factors that underlie the development of the metabolic syndrome.

Homocystinuria in Taiwan: an inordinately high prevalence in an Austronesian aboriginal tribe, Tao.

The newborn screening of homocystinuria in Taiwan has never been formally reported before. Since 1984, out of 5 million newborns screened, only 3 newborns (Han Taiwanese) suffering from homocystinuria were detected in this newborn screening program. Four mutations (p.R121L [c.362G>T], p.E176K [c.526G>A], p.V320G [c.959T>G] and p.G259D [c.776G>A]) were identified in these 3 patients. Unexpectedly, we recently found 8 patients presenting with homocystinuria in an Austronesian Taiwanese Tao tribe. Out of them, three patients participated in the newborn screening program but were unidentified by the current newborn homocystinuria (using methionine as a marker) screening. All the Tao patients are homozygous for a new p.D47E (c.141T>A) mutation. Among the 428 adult islanders screened for the D47E mutation, approximately 1 in 7.78 is a carrier of the mutation, and an estimated 1 in 240 islanders suffered from homocystinuria. This is the highest known prevalence of homocystinuria worldwide. The result of expression studies of all the mutations identified in Taiwan revealed that, except for p.D47E mutation, all mutations were severely limited in their ability to form functional tetramers. The clinical manifestations of the Tao patients varied widely, despite sharing the same mutation and very similar genetic and environmental backgrounds. Comparisons of clinical and biochemical phenotypes of these patients were presented in this report.

Modeling the autonomic and metabolic effects of obstructive sleep apnea: a simulation study.

Long-term exposure to intermittent hypoxia and sleep fragmentation introduced by recurring obstructive sleep apnea (OSA) has been linked to subsequent cardiovascular disease and Type 2 diabetes. The underlying mechanisms remain unclear, but impairment of the normal interactions among the systems that regulate autonomic and metabolic function is likely involved. We have extended an existing integrative model of respiratory, cardiovascular, and sleep-wake state control, to incorporate a sub-model of glucose-insulin-fatty acid regulation. This computational model is capable of simulating the complex dynamics of cardiorespiratory control, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, respiratory and circulatory mechanics, as well as the metabolic control of glucose-insulin dynamics and its interactions with the autonomic control. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free-fatty acid in plasma, metabolic coupling among tissues and organs provided by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. These model simulations provide insight into the relative importance of the various mechanisms that determine the acute and chronic physiological effects of sleep-disordered breathing. The model can also be used to investigate the effects of a variety of interventions, such as different glucose clamps, the intravenous glucose tolerance test, and the application of continuous positive airway pressure on OSA subjects. As such, this model provides the foundation on which future efforts to simulate disease progression and the long-term effects of pharmacological intervention can be based.

An integrative model of respiratory and cardiovascular control in sleep-disordered breathing.

While many physiological control models exist in the literature, none thus far has focused on characterizing the interactions among the respiratory, cardiovascular and sleep-wake regulation systems that occur in sleep-disordered breathing. The model introduced in this study integrates the autonomic control of the cardiovascular system, chemoreflex and state-related control of respiration, including respiratory and upper airway mechanics, along with a model of circadian and sleep-wake regulation. The integrative model provides realistic predictions of the physiological responses under a variety of conditions including: the sleep-wake cycle, hypoxia-induced periodic breathing, Cheyne-Stokes respiration in chronic heart failure, and obstructive sleep apnoea (OSA). It can be used to investigate the effects of a variety of interventions, such as isocapnic and hypercapnic and/or hypoxic gas administration, the Valsalva and Mueller maneuvers, and the application of continuous positive airway pressure on OSA subjects. By being able to delineate the influences of the various interacting physiological mechanisms, the model is useful in providing a more lucid understanding of the complex dynamics that characterize state-cardiorespiratory control in the different forms of sleep-disordered breathing.