Constructing a representative in-silico population for paediatric simulations: Application to HIV-positive African children

AIMS: Simulations are an essential tool for investigating scenarios in pharmacokinetics-pharmacodynamics. The models used during simulation often include the effect of highly correlated covariates such as weight, height and sex, and for children also age, which complicates the construction of an in silico population. For this reason, a suitable and representative patient population is crucial for the simulations to produce meaningful results. For simulation in paediatric patients, international growth charts from the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) provide a reference, but these may not always be representative for specific populations, such as malnourished children with HIV or acutely unwell children. METHODS: We present a workflow to construct a virtual paediatric patient population using WHO and CDC growth charts, suggest piecewise linear functions to adjust the median of the growth charts by sex and age, and suggest visual diagnostics to compare with the target population. We applied this workflow in a population of 1206 HIV-positive African children, consisting of 19 742 observations with weight ranging from 3.8 to 79.7 kg, height from 55.5 to 180 cm, and an age between 0.40 and 18 years. RESULTS: Before adjustment, the WHO and CDC charts produced weights and heights higher compared to the observed data. After applying our methodology, we could simulate weight, height, sex and age combinations in good agreement with the observed data. CONCLUSION: The methodology presented here is flexible and may be applied to other scenarios where WHO and CDC growth standards might not be appropriate. In addition we provide R scripts and a large ready-to-use paediatric population

HIV-1 co-infection does not reduce exposure to rifampicin, isoniazid, and pyrazinamide in South African tuberculosis outpatients

There are contrasting data in the literature about antituberculosis plasma drug concentrations in HIV-1-coinfected patients. We report the pharmacokinetics of rifampin, isoniazid, and pyrazinamide in a cohort of patients being treated for active tuberculosis, the majority of whom were coinfected with HIV-1 and had commenced antiretroviral therapy within 2 months of starting antituberculosis treatment. We also examined the association between antituberculosis drug concentrations and reported drug side effects at the 2-month clinical review. One hundred patients with pulmonary tuberculosis (65% coinfected with HIV-1) were intensively sampled to determine rifampin, isoniazid, and pyrazinamide plasma concentrations after 7 to 8 weeks of a daily quadruple-therapy regimen dosed according to World Health Organization (WHO) weight bands. Pharmacokinetic parameters were determined for each patient by using nonlinear mixed-effects models. HIV-1-coinfected patients had lower clearance rates for rifampin (21% decrease) and isoniazid (23% decrease) than HIV-1-uninfected patients, with resulting higher areas under the concentration-time curve from 0 to 24 h (AUC0–24) and maximum concentrations of drug in serum (Cmax). Antiretroviral therapy (ART) that included double-standard-dose lopinavir/ritonavir further lowered rifampin clearance, by 46%, and increased the AUC0–24. The current uniform dosing (per kilogram of body weight) across WHO weight bands was associated with a trend of decreased pharmacokinetic exposures for the lowest weight band. Use of fat-free mass as opposed to total body weight for allometric scaling of clearance significantly improved the model. Ambulant HIV-1-coinfected patients, the majority of whom were coprescribed ART, did not have reduced antituberculosis drug concentrations compared to HIV-1-uninfected patients

A Horseshoe Pit mixture model for Bayesian screening with an application to light sheet fluorescence microscopy in brain imaging

Finding parsimonious models through variable selection is a fundamental problem in many areas of statistical inference. Here, we focus on Bayesian regression models, where variable selection can be implemented through a regularizing prior imposed on the distribution of the regression coefficients. In the Bayesian literature, there are two main types of priors used to accomplish this goal: the spike-and-slab and the continuous scale mixtures of Gaussians. The former is a discrete mixture of two distributions characterized by low and high variance. In the latter, a continuous prior is elicited on the scale of a zero-mean Gaussian distribution. In contrast to these existing methods, we propose a new class of priors based on discrete mixture of continuous scale mixtures providing a more general framework for Bayesian variable selection. To this end, we substitute the observation-specific local shrinkage parameters (typical of continuous mixtures) with mixture component shrinkage parameters. Our approach drastically reduces the number of parameters needed and allows sharing information across the coefficients, improving the shrinkage effect. By using half-Cauchy distributions, this approach leads to a cluster-shrinkage version of the Horseshoe prior. We present the properties of our model and showcase its estimation and prediction performance in a simulation study. We then recast the model in a multiple hypothesis testing framework and apply it to a neurological dataset obtained using a novel whole-brain imaging technique

Beads for Cell Immobilization: Comparison of Alternative Additive Manufacturing Techniques

The attachment or entrapment of microbial cells and enzymes are promising solutions for various industrial applications. When the traps are beads, they are dispersed in a fluidized bed in a vessel where a pump guarantees fresh liquid inflow and waste outflow without washing out the cells. Scientific papers report numerous types of cell entrapment, but most of their applications remain at the laboratory level. In the present research, rigid polymer beads were manufactured by two different additive manufacturing (AM) techniques in order to verify the economy, reusability, and stability of the traps, with a view toward a straightforward industrial application. The proposed solutions allowed for overcoming some of the drawbacks of traditional manufacturing solutions, such as the limited mechanical stability of gel traps, and they guaranteed the possibility of producing parts of constant quality with purposely designed exchange surfaces, which are unfeasible when using conventional processes. AM proved to be a viable manufacturing solution for beads with complex shapes of two different size ranges. A deep insight into the production and characteristics of beads manufactured by AM is provided. The paper provides biotechnologists with a manufacturing perspective, and the results can be directly applied to transit from the laboratory to the industrial scale

Population pharmacokinetics of lopinavir and ritonavir in combination with rifampicin-based antitubercular treatment in HIV-infected children

Children with HIV associated tuberculosis often require co-formulated lopinavir/ritonavir (LPV/RTV)-based antiretroviral treatment with rifampicin-based antitubercular treatment (ATT). Rifampicin (RIF), a potent inducer of drug-metabolizing systems, profoundly reduces the bioavailability of LPV. The aims of this study were to develop an integrated population pharmacokinetic (PK) model describing LPV and RTV PK in children with and without concomitant ATT using two different dosing approaches and to estimate doses of LPV/RTV achieving target exposures during ATT in young children

MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants

The amount of genetic variation discovered in human populations is growing rapidly leading to challenging computational tasks, such as variant calling. Standard methods for addressing this problem include read mapping, a computationally expensive procedure; thus, mapping-free tools have been proposed in recent years. These tools focus on isolated, biallelic SNPs, providing limited support for multi-allelic SNPs and short insertions and deletions of nucleotides (indels). Here we introduce MALVA, a mapping-free method to genotype an individual from a sample of reads. MALVA is the first mapping-free tool able to genotype multi-allelic SNPs and indels, even in high-density genomic regions, and to effectively handle a huge number of variants. MALVA requires one order of magnitude less time to genotype a donor than alignment-based pipelines, providing similar accuracy. Remarkably, on indels, MALVA provides even better results than the most widely adopted variant discovery tools. Biological Sciences; Genetics; Genomics; Bioinformatic

Tropospheric Ozone In A Mountain Forest Area: Spatial Distribution And Its Relation With Meteorology And Emission Sources

Biological injuries to forest ecosystems in two lateral valleys of Valtellina (Italy) have been studied. The selected areas are characterized by different forest novel decline symptoms and ozone concentration levels. Analyses of meteorological and air quality data collected by fixed and mobile stations located in the two valleys are presented. Ozone concentration has been measured both by passive samplers and continues analyzers and the ozone vertical gradient in one valley has been determined. In order to investigate the relation between emission sources, ambient ozone levels and plant biological injuries, a modeling research project has been started. As preliminary results the wind field obtained by the application of two diagnostic meteorological models, MINERVE and CALMET, and the computation of the biogenic emissions are presented. Some examples of spatial distribution and temporal trend of the most important pollutants emitted by plants are discussed

Effects of build orientation and element partitioning on microstructure and mechanical properties of biomedical Ti-6Al-4V alloy produced by laser sintering

Direct Metal Laser Sintering (DMLS) technology was used to produce tensile and flexural samples based on the Ti-6Al-4V biomedical composition. Tensile samples were produced in three different orientations in order to investigate the effect of building direction on the mechanical behavior. On the other hand, flexural samples were submitted to thermal treatments to simulate the firing cycle commonly used to veneer metallic devices with ceramics in dental applications. Roughness and hardness measurements as well as tensile and flexural mechanical tests were performed to study the mechanical response of the alloy while X-ray diffraction (XRD), electron microscopy (SEM, TEM, STEM) techniques and microanalysis (EDX) were used to investigate sample microstructure. Results evidenced a difference in the mechanical response of tensile samples built in orthogonal directions. In terms of microstructure, samples not submitted to the firing cycle show a single phase acicular α’ (hcp) structure typical of metal parts subject to high cooling rates. After the firing cycle, samples show a reduction of hardness and strength due to the formation of laths of the β (bcc) phase at the boundaries of the primary formed α’ plates as well as to lattice parameters variation of the hcp phase. Element partitioning during the firing cycle gives rise to high concentration of V atoms (up to 20 wt%) at the plate boundaries where the β phase preferentially forms

Concentration-dependent antagonism and culture conversion in pulmonary tuberculosis

Background There is scant evidence to support target drug exposures for optimal tuberculosis outcomes. We therefore assessed whether pharmacokinetic/pharmacodynamic (PK/PD) parameters could predict 2-month culture conversion. Methods One hundred patients with pulmonary tuberculosis (65% HIV-co-infected) were intensively sampled to determine rifampicin, isoniazid and pyrazinamide plasma concentrations after 7-8 weeks of therapy, and pharmacokinetic parameters determined using non-linear-mixed-effects models. Detailed clinical data and sputum for culture were collected at baseline, 2 and 5-6 months. Minimum inhibitory concentrations (MIC) were determined on baseline isolates. Multivariate logistic regression and the assumption-free multivariate adaptive regression splines (MARS) were used to identify clinical and PK/PD predictors of 2-month culture conversion. Potential PK/PD predictors included 24-hour-area-under-the-curve (AUC0-24), peak concentration (Cmax), AUC0-24/MIC, Cmax/MIC and % time that concentrations persisted above MIC (%TMIC). Results 26% of patients had Cmax (mg/L) of rifampicin4.6 mg/L, higher isoniazid exposures were associated with improved rates of culture conversion. Conclusions PK/PD analyses using MARS identified isoniazid Cmax and rifampicin Cmax/MIC thresholds below which there is concentration-dependent antagonism that reduces 2-month sputum culture conversion

Features of Vat-Photopolymerized Masters for Microfluidic Device Manufacturing

The growing interest in advancing microfluidic devices for manipulating fluids within micrometer-scale channels has prompted a shift in manufacturing practices, moving from single-component production to medium-size batches. This transition arises due to the impracticality of lab-scale manufacturing methods in accommodating the increased demand. This experimental study focuses on the design of master benchmarks 1–5, taking into consideration critical parameters such as rib width, height, and the relative width-to-height ratio. Notably, benchmarks 4 and 5 featured ribs that were strategically connected to the inlet, outlet, and reaction chamber of the master, enhancing their utility for subsequent replica production. Vat photopolymerization was employed for the fabrication of benchmarks 1–5, while replicas of benchmarks 4 and 5 were generated through polydimethylsiloxane casting. Dimensional investigations of the ribs and channels in both the master benchmarks and replicas were conducted using an optical technique validated through readability analysis based on the Michelson global contrast index. The primary goal was to evaluate the potential applicability of vat photopolymerization technology for efficiently producing microfluidic devices through a streamlined production process. Results indicate that the combination of vat photopolymerization followed by replication is well suited for achieving a minimum rib size of 25 μm in width and an aspect ratio of 1:12 for the master benchmark