Application of ggplot2 to Pharmacometric Graphics.
Ontology highlight
ABSTRACT:
SUBMITTER: Ito K
PROVIDER: S-EPMC3817376 | biostudies-other | 2013
REPOSITORIES: biostudies-other
Similar Datasets
Project description:This article represents the first in a series of tutorials on model evaluation in nonlinear mixed effect models (NLMEMs), from the International Society of Pharmacometrics (ISoP) Model Evaluation Group. Numerous tools are available for evaluation of NLMEM, with a particular emphasis on visual assessment. This first basic tutorial focuses on presenting graphical evaluation tools of NLMEM for continuous data. It illustrates graphs for correct or misspecified models, discusses their pros and cons, and recalls the definition of metrics used.
| S-EPMC5321813 | biostudies-literature
Project description:Summary:The examination of gene neighborhood is an integral part of comparative genomics but no tools to produce publication quality graphics of gene clusters are available. Gene Graphics is a straightforward web application for creating such visuals. Supported inputs include National Center for Biotechnology Information gene and protein identifiers with automatic fetching of neighboring information, GenBank files and data extracted from the SEED database. Gene representations can be customized for many parameters including gene and genome names, colors and sizes. Gene attributes can be copied and pasted for rapid and user-friendly customization of homologous genes between species. In addition to Portable Network Graphics and Scalable Vector Graphics, produced representations can be exported as Tagged Image File Format or Encapsulated PostScript, formats that are standard for publication. Hands-on tutorials with real life examples inspired from publications are available for training. Availability and implementation:Gene Graphics is freely available at https://katlabs.cc/genegraphics/ and source code is hosted at https://github.com/katlabs/genegraphics. Contact:katherinejh@ufl.edu or remizallot@ufl.edu. Supplementary information:Supplementary data are available at Bioinformatics online.
| S-EPMC5905594 | biostudies-literature
Project description:This is the first clinical implementation of the Multistate Tuberculosis Pharmacometric (MTP) model describing fast-, slow-, and nonmultiplying bacterial states of Mycobacterium tuberculosis. Colony forming unit data from 19 patients treated with rifampicin were analyzed. A previously developed rifampicin population pharmacokinetic (PK) model was linked to the MTP model previously developed using in vitro data. Drug effect was implemented as exposure-response relationships tested at several effect sites, both alone and in combination. All MTP model parameters were fixed to in vitro estimates except Bmax . Drug effect was described by an on/off effect inhibiting growth of fast-multiplying bacteria in addition to linear increase of the stimulation of the death rate of slow- and nonmultiplying bacteria with increasing drug exposure. Clinical trial simulations predicted well three retrospective clinical trials using the final model that confirmed the potential utility of the MTP model in antitubercular drug development.
| S-EPMC4873565 | biostudies-literature
Project description:Nonadiabatic molecular dynamics (NAMD) simulations of molecular systems require the efficient evaluation of excited-state properties, such as energies, gradients, and nonadiabatic coupling vectors. Here, we investigate the use of graphics processing units (GPUs) in addition to central processing units (CPUs) to efficiently calculate these properties at the time-dependent density functional theory (TDDFT) level of theory. Our implementation in the FermiONs++ program package uses the J-engine and a preselective screening procedure for the calculation of Coulomb and exchange kernels, respectively. We observe good speed-ups for small and large molecular systems (comparable to those observed in ground-state calculations) and reduced (down to sublinear) scaling behavior with respect to the system size (depending on the spatial locality of the investigated excitation). As a first illustrative application, we present efficient NAMD simulations of a series of newly designed light-driven rotary molecular motors and compare their S1 lifetimes. Although all four rotors show different S1 excitation energies, their ability to rotate upon excitation is conserved, making the series an interesting starting point for rotary molecular motors with tunable excitation energies.
| S-EPMC6909237 | biostudies-literature
Project description:AimsThe aims of the study were to characterize the pharmacokinetics (PK) of alogliptin in healthy and type 2 diabetes mellitus (T2DM) subjects using a population PK approach and to assess the influence of various covariates on alogliptin exposure.MethodsPlasma concentration data collected from two phase 1 studies and one phase 3 study following administration of alogliptin (12.5-400 mg) were used for the PK model development. One- and two-compartment models were evaluated as base structural PK models. The impact of selected covariates was assessed using stepwise forward selection and backward elimination procedures. The predictability and robustness of the final model was evaluated using visual predictive check and bootstrap analyses. The final model was used to perform simulations and guide appropriate dose adjustments.ResultsA two-compartment model with first-order absorption and elimination best described the alogliptin concentration vs. time profiles. Creatinine clearance and weight had a statistically significant effect on the oral clearance (CL/F) of alogliptin. The model predicted a lower CL/F (17%, 35%, 80%) and a higher systemic exposure (56%, 89%, 339%) for subjects with mild, moderate and severe renal impairment, respectively, compared with healthy subjects. Effect of weight on CL/F was not considered clinically relevant. Simulations at different doses of alogliptin support the approved doses of 12.5 mg and 6.25 mg for patients with moderate and severe renal impairment, respectively.ConclusionsThe PK of alogliptin was well characterized by the model. The analysis suggested an alogliptin dose adjustment for subjects with moderate-to-severe renal impairment and no dose adjustments based on weight.
| S-EPMC4799927 | biostudies-literature
Project description:Background and objectivesLoxapine for inhalation is a drug-device combination product approved in adults for the acute treatment of agitation associated with schizophrenia or bipolar I disorder. The primary objective of this study was to develop a clinical trial protocol to support a phase I pharmacokinetic study in children aged 10 years and older. In addition, this report details the results of the clinical study in relation to the predicted likelihood of achieving the target exposure associated with therapeutic effect in adults.MethodsA nonlinear mixed-effects population pharmacokinetic model was developed using adult data and was adjusted for the targeted pediatric age groups by applying allometric scaling to account for body size effects. Based on this pediatric model, age-appropriate regimens to achieve loxapine exposures similar to the ones associated with therapeutic effect in the adult studies were identified via trial simulation. D-optimal design and power analysis were conducted to identify optimal pharmacokinetic sampling times and sample size, respectively.ResultsThe developed clinical trial design formed the basis of a phase I study to assess the safety and pharmacokinetics of loxapine for inhalation in children aged 10 years and older (ClinicalTrials.gov ID: NCT02184767).ConclusionThe results of the study indicated that overall loxapine exposures were consistent with what had been predicted by the trial simulations. The presented approach illustrates how modeling and simulation can assist in the design of informative clinical trials to identify safe and effective doses and dose ranges in children and adolescents.
| S-EPMC5557705 | biostudies-literature
Project description:Lack of data is an obvious limitation to what can be modelled. However, aggregate data in the form of means and possibly (co)variances, as well as previously published pharmacometric models, are often available. Being able to use all available data is desirable, and therefore this paper will outline several methods for using aggregate data as the basis of parameter estimation. The presented methods can be used for estimation of parameters from aggregate data, and as a computationally efficient alternative for the stochastic simulation and estimation procedure. They also allow for population PK/PD optimal design in the case when the data-generating model is different from the data-analytic model, a scenario for which no solutions have previously been available. Mathematical analysis and computational results confirm that the aggregate-data FO algorithm converges to the same estimates as the individual-data FO and yields near-identical standard errors when used in optimal design. The aggregate-data MC algorithm will asymptotically converge to the exactly correct parameter estimates if the data-generating model is the same as the data-analytic model. The performance of the aggregate-data methods were also compared to stochastic simulations and estimations (SSEs) when the data-generating model is different from the data-analytic model. The aggregate-data FO optimal design correctly predicted the sampling distributions of 200 models fitted to simulated datasets with the individual-data FO method.
| S-EPMC8405508 | biostudies-literature
Project description:Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article was to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS- and IBD-based allele sharing studies are considered. Furthermore, we propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log-ratios of IBS and IBD probabilities. We illustrate all graphical tools with genetic data from the HGDP-CEPH diversity panel, using mainly 377 microsatellites genotyped for 25 individuals from the Maya population of this panel. We enhance all graphics with convex hulls obtained by simulation and use these to confirm the documented relationships. The proposed compositional graphics are shown to be useful in relatedness research, as they also single out the most prominent related pairs. The ternary diagram is advocated for its ability to display all three allele sharing probabilities simultaneously. The log-ratio plots are advocated as an attempt to overcome the problems with the Euclidean distance interpretation in the classical graphics.
| S-EPMC5624821 | biostudies-literature
Project description:Supporting decision making in drug development is a key purpose of pharmacometric models. Pharmacokinetic models predict exposures under alternative posologies or in different populations. Pharmacodynamic models predict drug effects based on exposure to drug, disease, or other patient characteristics. Estimation uncertainty is commonly reported for model parameters; however, prediction uncertainty is the key quantity for clinical decision making. This tutorial reviews confidence and prediction intervals with associated calculation methods, encouraging pharmacometricians to report these routinely.
| S-EPMC6027739 | biostudies-literature
Project description:OBJECTIVE:The purpose of this study was to assess the relationship between an embodied sensory experience and the ability to translate the perception of this experience visually using modifiable motion graphics. METHODS:A custom-designed software was developed to enable users to modify a motion graphic in real-time. The motion graphics were designed to depict realistic visualizations of pain quality descriptors, such as tingling and burning. Participants (N = 34) received an electrical stimulation protocol known to elicit sensations of tingling. The protocol consisted of eight stimulation intensities ranging from 2-6mA delivered, in a randomized fashion and repeated three times, to the index finger. Immediately after each stimulus, participants drew the area of the evoked sensation on a digital body chart of the hand. Participants then modified the motion graphic of tingling by adjusting two parameters, namely the speed (rate of dots disappearing and re-appearing) and density of these dots in the drawn area. Then, participants rated the perceived intensity and selected the most appropriate pain quality descriptor. RESULTS:There was an increase in the area, density, and perceived intensity ratings as the electrical stimulation intensity increased (P<0.001). The density of the motion graphic, but not speed, correlated with perceived intensity ratings (0.69, P<0.001) and electrical stimulation intensities (0.63, P<0.01). The descriptor 'tingling' was predominantly selected in the range of 3-4.5mA and was often followed by 'stabbing' as the electrical intensity increased. DISCUSSION:The motion graphic tested was perceived to reflect a tingling sensation, the stimulation protocol elicited a tingling sensation, and participants adjusted one of the two motion graphic features systematically. In conclusion, an embodied sensation, such as tingling, maybe visually represented similarly between individuals. These findings create research, clinical, and commercial opportunities that utilize psychophysics to explore, visualize, and quantify changes in embodied sensory experiences in response to known stimuli.
| S-EPMC7039426 | biostudies-literature