ModVizPop: A shiny interface for empowering teams to perform interactive pharmacokinetic/pharmacodynamic simulations.
Ontology highlight
ABSTRACT:
SUBMITTER: Vaddady P
PROVIDER: S-EPMC8592511 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Even though R is one of the most commonly used statistical computing environments, it lacks a graphical user interface (GUI) that appeals to students, researchers, lecturers, and practitioners in medicine and pharmacy for conducting standard data analytics. Current GUIs built on top of R, such as EZR and R-Commander, aim to facilitate R coding and visualization, but most of the functionalities are still accessed through a command-line interface (CLI). To assist practitioners of medicine and pharmacy and researchers to run most routines in fundamental statistical analysis, we developed an interactive GUI; i.e., MEPHAS, to support various web-based systems that are accessible from laptops, workstations, or tablets, under Windows, macOS (and IOS), or Linux. In addition to fundamental statistical analysis, advanced statistics such as the extended Cox regression and dimensional analyses including partial least squares regression (PLS-R) and sparse partial least squares regression (SPLS-R), are also available in MEPHAS. RESULTS:MEPHAS is a web-based GUI (https://alain003.phs.osaka-u.ac.jp/mephas/) that is based on a shiny framework. We also created the corresponding R package mephas (https://mephas.github.io/). Thus far, MEPHAS has supported four categories of statistics, including probability, hypothesis testing, regression models, and dimensional analyses. Instructions and help menus were accessible during the entire analytical process via the web-based GUI, particularly advanced dimensional data analysis that required much explanation. The GUI was designed to be intuitive for non-technical users to perform various statistical functions, e.g., managing data, customizing plots, setting parameters, and monitoring real-time results, without any R coding from users. All generated graphs can be saved to local machines, and tables can be downloaded as CSV files. CONCLUSION:MEPHAS is a free and open-source web-interactive GUI that was designed to support statistical data analyses and prediction for medical and pharmaceutical practitioners and researchers. It enables various medical and pharmaceutical statistical analyses through interactive parameter settings and dynamic visualization of the results.
| S-EPMC7216538 | biostudies-literature
Project description:ObjectivebPeaks is a peak calling program to detect protein DNA-binding sites from ChIPseq data in small eukaryotic genomes. The simplicity of the bPeaks method is well appreciated by users, but its use via an R package is challenging and time-consuming for people without programming skills. In addition, user feedback has highlighted the lack of a convenient way to carefully explore bPeaks result files. In this context, the development of a web user interface represents an important added value for expanding the bPeaks user community.ResultsWe developed a new bPeaks application (bPeaks App). The application allows the user to perform all the peak-calling analysis steps with bPeaks in a few mouse clicks via a web browser. We added new features relative to the original R package, particularly the possibility to import personal annotation files to compare the location of the detected peaks with specific genomic elements of interest of the user, in any organism, and a new organization of the result files which are directly manageable via a user-interactive genome browser. This significantly improves the ability of the user to explore all detected basic peaks in detail.
| S-EPMC6172709 | biostudies-literature
Project description:Avibactam is a novel non-β-lactam β-lactamase inhibitor that has been approved in the United States and Europe for use in combination with ceftazidime. Combinations of avibactam with aztreonam or ceftaroline fosamil have also been clinically evaluated. Until recently, there has been very little precedence of which pharmacokinetic/pharmacodynamic (PK/PD) indices and magnitudes are appropriate to use for β-lactamase inhibitors in population PK modeling for analyzing potential doses and susceptibility breakpoints. For avibactam, several preclinical studies using different in vitro and in vivo models have been conducted to identify the PK/PD index of avibactam and the magnitude of exposure necessary for effect in combination with ceftazidime, aztreonam, or ceftaroline fosamil. The PD driver of avibactam critical for restoring the activity of all three partner β-lactams was found to be time dependent rather than concentration dependent and was defined as the time that the concentration of avibactam exceeded a critical concentration threshold (%fT>CT). The magnitude of the CT and the time that this threshold needed to be exceeded to elicit particular PD endpoints varied depending on the model and the partner β-lactam. This review describes the preclinical studies used to determine the avibactam PK/PD target in combination with its β-lactam partners.
| S-EPMC5971577 | biostudies-literature
Project description:Interactive applications, developed using Shiny for the R programming language, have the potential to revolutionize the sharing and communication of pharmacometric model simulations. Shiny allows customization of the application's user-interface to provide an elegant environment for displaying user-input controls and simulation output-where the latter simultaneously updates with changing input. The flexible nature of the R language makes simulations of population variability possible thus promoting the combination of Shiny with R in model visualization.
| S-EPMC4394611 | biostudies-literature
Project description:MotivationFirst-line data quality assessment and exploratory data analysis are integral parts of any data analysis workflow. In high-throughput quantitative omics experiments (e.g. transcriptomics, proteomics and metabolomics), after initial processing, the data are typically presented as a matrix of numbers (feature IDs × samples). Efficient and standardized data quality metrics calculation and visualization are key to track the within-experiment quality of these rectangular data types and to guarantee for high-quality datasets and subsequent biological question-driven inference.ResultsWe present MatrixQCvis, which provides interactive visualization of data quality metrics at the per-sample and per-feature level using R's shiny framework. It provides efficient and standardized ways to analyze data quality of quantitative omics data types that come in a matrix-like format (features IDs × samples). MatrixQCvis builds upon the Bioconductor SummarizedExperiment S4 class and thus facilitates the integration into existing workflows.Availability and implementationMatrixQCVis is implemented in R. It is available via Bioconductor and released under the GPL v3.0 license.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC8796383 | biostudies-literature
Project description:BackgroundThis study aims to explore relationships between baseline demographic covariates, plasma antibiotic exposure, sputum bacillary load, and clinical outcome data to help improve future tuberculosis (TB) treatment response predictions.MethodsData were available from a longitudinal cohort study in Malawian drug-sensitive TB patients on standard therapy, including steady-state plasma antibiotic exposure (154 patients), sputum bacillary load (102 patients), final outcome (95 patients), and clinical details. Population pharmacokinetic and pharmacokinetic-pharmacodynamic models were developed in the software package NONMEM. Outcome data were analyzed using univariate logistic regression and Cox proportional hazard models in R, a free software for statistical computing.ResultsHigher isoniazid exposure correlated with increased bacillary killing in sputum (P < .01). Bacillary killing in sputum remained fast, with later progression to biphasic decline, in patients with higher rifampicin area under the curve (AUC)0-24 (P < .01). Serial sputum colony counting negativity at month 2 (P < .05), isoniazid C MAX (P < .05), isoniazid C MAX/minimum inhibitory concentration ([MIC] P < .01), and isoniazid AUC0-24/MIC (P < .01) correlated with treatment success but not with remaining free of TB. Slower bacillary killing (P < .05) and earlier progression to biphasic bacillary decline (P < .01) both correlate with treatment failure. Posttreatment recurrence only correlated with slower bacillary killing (P < .05).ConclusionsPatterns of early bacillary clearance matter. Static measurements such as month 2 sputum conversion and pharmacokinetic parameters such as C MAX/MIC and AUC0-24/MIC were predictive of treatment failure, but modeling of quantitative longitudinal data was required to assess the risk of recurrence. Pooled individual patient data analyses from larger datasets are needed to confirm these findings.
| S-EPMC7378673 | biostudies-literature
Project description:Immune check-point inhibitors are drugs that are markedly different from other anticancer drugs because of their indirect mechanisms of antitumoral action and their apparently random effect in terms of efficacy and toxicity. This marked pharmacodynamics variability in patients calls for reconsidering to what extent approved dosing used in clinical practice are optimal or whether they should require efforts for customization in outlier patients. To better understand whether or not dosing could be an actionable item in oncology, in this review, preclinical and clinical development of immune checkpoint inhibitors are described, particularly from the angle of dose finding studies. Other issues in connection with dosing issues are developed, such as the flat dosing alternative, the putative role therapeutic drug monitoring could play, the rise of combinatorial strategies, and pharmaco-economic aspects.
| S-EPMC7712135 | biostudies-literature
Project description:Oral riociguat is a soluble guanylate cyclase (sGC) stimulator that targets the nitric oxide (NO)-sGC-cyclic guanosine monophosphate pathway with a dual mode of action: directly by stimulating sGC, and indirectly by increasing the sensitivity of sGC to NO. It is rapidly absorbed, displays almost complete bioavailability (94.3%), and can be taken with or without food and as crushed or whole tablets. Riociguat exposure shows pronounced interindividual (60%) and low intraindividual (30%) variability in patients with pulmonary arterial hypertension (PAH) or chronic thromboembolic pulmonary hypertension (CTEPH), and is therefore administered using an individual dose-adjustment scheme at treatment initiation. The half-life of riociguat is approximately 12 h in patients and approximately 7 h in healthy individuals. Riociguat and its metabolites are excreted via both renal (33-45%) and biliary routes (48-59%), and dose adjustment should be performed with particular care in patients with moderate hepatic impairment or mild to severe renal impairment (no data exist for patients with severe hepatic impairment). The pharmacodynamic effects of riociguat reflect the action of a vasodilatory agent, and the hemodynamic response to riociguat correlated with riociguat exposure in patients with PAH or CTEPH in phase III population pharmacokinetic/pharmacodynamic analyses. Riociguat has a low risk of clinically relevant drug interactions due to its clearance by multiple cytochrome P450 (CYP) enzymes and its lack of effect on major CYP isoforms and transporter proteins at therapeutic levels. Riociguat has been approved for the treatment of PAH and CTEPH that is inoperable or persistent/recurrent after surgical treatment.
| S-EPMC5974002 | biostudies-literature
Project description:AIM: To quantitatively evaluate the blood glucose-lowering effect of exenatide in diabetic rats. METHODS: Male Harlan-Sprague-Dawley rats were treated with high-fat diet/streptozotocin to induce type 2 diabetes. After subcutaneous administration of a single dose of exenatide (4.2, 42, or 210 μg/kg), serum exenatide, insulin concentration and blood glucose were measured. The pharmacokinetics of exenatide was characterized by a two-compartment model with first-order absorption. Insulin turnover was characterized by an effect compartment and indirect response combined model. Glucose turnover was described using an indirect response model with insulin (in effect compartment) stimulating glucose disposition and insulin (in insulin compartment) inhibiting glucose production simultaneously. The model parameters were estimated using nonlinear mixed-effects model program. Visual predictive check and model evaluation were used to make assessments. RESULTS: Exenatide exhibited rapid absorption with k(a)=4.45 h(-1), and the two-compartment model well described its pharmacokinetic profile. For the pharmacodynamic model, exenatide increased insulin release with the estimated S(m1) of 0.822 and SC(50) of 4.02 μg/L. It was demonstrated that insulin stimulated glucose dissipation (S(m2)=0.0513) and inhibited the production of glucose (I(m)=0.0381). Visual predictive check and model evaluation study indicated that a credible model was developed. CONCLUSION: The glucose-lowering effect of exenatide in diabetic rats is reliably described and predicted by the combined effect compartment/indirect response model.
| S-EPMC4011360 | biostudies-other
Project description:In the PREPA observational study, we investigated the factors influencing pharmacokinetic and pharmacodynamic variability in the responses to fluindione, an oral anticoagulant drug, in a general population of octogenarian inpatients.Measurements of fluindione concentrations and international normalized ratio (INR ) were obtained for 131 inpatients in whom fluindione treatment was initiated. Treatment was adjusted according to routine clinical practice. The data were analyzed using nonlinear mixed-effects modeling, and the parameters were estimated using MONOLI X 3.2. The pharmacokinetics (PK) of fluindione was monocompartmental, whereas the evolution of INR was modeled in accordance with a turnover model (inhibition of vitamin K recycling). Interindividual variability (II V) was very large. Clearance decreased with age and with prior administration of cordarone. Patients who had undergone surgery before the study had lower IC50 values, leading to an increased sensitivity to fluindione. Pharmacokinetic exposure is substantially increased in elderly patients, warranting a lower dose of fluindione.
| S-EPMC3789273 | biostudies-literature