Application of Physiologically Based Pharmacokinetic (PBPK) Modeling to Support Dose Selection: Report of an FDA Public Workshop on PBPK

The US Food and Drug Administration (FDA) public workshop, entitled "Application of Physiologically-based Pharmacokinetic (PBPK) Modeling to Support Dose Selection focused on the role of PBPK in drug development and regulation. Representatives from industry, academia, and regulatory agencies discussed the issues within plenary and panel discussions. This report summarizes the discussions and provides current perspectives on the application of PBPK in different areas, including its utility, predictive performance, and reporting for regulatory submissions.

Atmospheric benzenoid emissions from plants rival those from fossil fuels

Despite the known biochemical production of a range of aromatic compounds by plants and the presence of benzenoids in floral scents, the emissions of only a few benzenoid compounds have been reported from the biosphere to the atmosphere. Here, using evidence from measurements at aircraft, ecosystem, tree, branch and leaf scales, with complementary isotopic labeling experiments, we show that vegetation (leaves, flowers, and phytoplankton) emits a wide variety of benzenoid compounds to the atmosphere at substantial rates. Controlled environment experiments show that plants are able to alter their metabolism to produce and release many benzenoids under stress conditions. The functions of these compounds remain unclear but may be related to chemical communication and protection against stress. We estimate the total global secondary organic aerosol potential from biogenic benzenoids to be similar to that from anthropogenic benzenoids (~10 Tg y⁻¹), pointing to the importance of these natural emissions in atmospheric physics and chemistry.

PBPK model describes the effects of comedication and genetic polymorphism on systemic exposure of drugs that undergo multiple clearance pathways

An important goal in drug development is to understand the effects of intrinsic and/or extrinsic factors (IEFs) on drug pharmacokinetics. Although clinical studies investigating a given IEF can accomplish this goal, they may not be feasible for all IEFs or for situations when multiple IEFs exist concurrently. Physiologically based pharmacokinetic (PBPK) models may serve as a complementary tool for forecasting the effects of IEFs. We developed PBPK models for four drugs that are eliminated by both cytochrome P450 (CYP)3A4 and CYP2D6, and evaluated model prediction of the effects of comedications and/or genetic polymorphism on drug exposure. PBPK models predicted 100 and ≥70% of the observed results when the conventional "twofold rule" and the more conservative 25% deviation cut point were applied, respectively. These findings suggest that PBPK models can be used to infer effects of individual or combined IEFs and should be considered to optimize studies that evaluate these factors, specifically drug interactions and genetic polymorphism of drug-metabolizing enzymes.

The future is now: model-based clinical trial design for Alzheimer's disease

Failures in trials for Alzheimer's disease (AD) may be attributable to inadequate dosing, population selection, drug inefficacy, or insufficient design optimization. The Coalition Against Major Diseases (CAMD) was formed in 2008 to develop drug development tools (DDT) to expedite drug development for AD and Parkinson's disease. CAMD led a process that successfully advanced a clinical trial simulation (CTS) tool for AD through the formal regulatory review process at the US Food and Drug Administration (FDA) and European Medicines Agency (EMA).

Oral Colon-Specific Drug Delivery of Protein and Peptide Drugs

With the advent of new technologies and radical growth in the field of biotechnology, dozens of protein and peptide drugs have been marketed. However, there are several challenges for successful delivery of such molecules. A number of routes have been used for the delivery of these fragile molecules by exploring various novel delivery technologies, including microspheres, liposomes, gel spheres, nano-spheres, niosomes, microemulsions, use of permeation enhancers, use of protease inhibitors, etc. But the route that has attracted the attention of worldwide drug delivery scientists is the oral route due to its various advantages. Even though the proteolytic activity is higher in a few segments of the gastrointestinal tract (GIT), this route has certain segments that have lower proteolytic activity, for example, the colon. The colon has captured attention as a site for the delivery of these molecules because of its greater responsiveness to absorption enhancers, protease inhibitors, and novel bioadhesive and biodegradable polymers. Although the success rate of these approaches, when used alone is pretty low, when used in combinations, these agents have demonstrated wonders in increasing the drug bioavailability. This review focuses on the challenges, pharmaceutical concepts, and approaches involved in the delivery of these fragile molecules, specifically to the colon. This review also includes studies conducted on colonic targeting of such drugs. Further studies may lead to improvements in therapy using protein/peptide drugs and refinements in the technology of colon-specific drug delivery.

Consensus statement from the international consensus meeting on post-traumatic cranioplasty

Background

Due to the lack of high-quality evidence which has hindered the development of evidence-based guidelines, there is a need to provide general guidance on cranioplasty (CP) following traumatic brain injury (TBI), as well as identify areas of ongoing uncertainty via a consensus-based approach.

Methods

The international consensus meeting on post-traumatic CP was held during the International Conference on Recent Advances in Neurotraumatology (ICRAN), in Naples, Italy, in June 2018. This meeting was endorsed by the Neurotrauma Committee of the World Federation of Neurosurgical Societies (WFNS), the NIHR Global Health Research Group on Neurotrauma, and several other neurotrauma organizations. Discussions and voting were organized around 5 pre-specified themes: (1) indications and technique, (2) materials, (3) timing, (4) hydrocephalus, and (5) paediatric CP.

Results

The participants discussed published evidence on each topic and proposed consensus statements, which were subject to ratification using anonymous real-time voting. Statements required an agreement threshold of more than 70% for inclusion in the final recommendations.

Conclusions

This document is the first set of practical consensus-based clinical recommendations on post-traumatic CP, focusing on timing, materials, complications, and surgical procedures. Future research directions are also presented.

Physiologically based pharmacokinetic modeling: from regulatory science to regulatory policy

Assessment of controllable sources of intra- and interpatient variability in drug response is of critical importance in the regulatory evaluation of new drugs.(1) Although determinants of response variability would ideally be understood and accounted for before approval of a new pharmaceutical product, this is rarely the case for all; clinical trials in specific populations that definitively test optimal dosing in patient management strategies are not routinely performed prior to drug approval.

How Much Does Large-Scale Crop Residue Burning Affect the Air Quality in Delhi?

Elevated PM_2.5 concentrations frequently cause severe air pollution events in Delhi. Till recently, the effect of crop residue burning on the air quality in Delhi has not been fully quantified and the approaches to control the impact of fire emissions have not been effective. In this study, for the first time, we quantified the statewise contribution of post-monsoon crop residue burning in the northwestern states of India to surface PM_2.5 concentrations in Delhi using several sensitivity experiments with the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) and FINNv1.5 fire emission inventory. Results were evaluated with ground-based observations in Delhi (21 stations), Punjab, and Haryana (14 stations). On average, ∼20% of PM_2.5 concentration in Delhi during the post-monsoon season (October-November) was found to be contributed by nonlocal fire emissions. However, on typical air pollution events, fire emissions contributed as high as 50-75% (80-120 μg/m³) to PM_2.5 in Delhi, highlighting the importance of both external transport and local emissions to PM_2.5 pollution in Delhi.

A population approach to enzyme characterization and identification: application to phenacetin O-deethylation

PURPOSE

To determine the enzyme kinetics (EK) and identify the human cytochrome(s) P450 (CYP) involved in the deethylation of phenacetin to acetaminophen using a population-based method.

METHODS

A sparse data set was generated from incubations containing human liver microsomes (n = 19) with phenacetin. Estimates of the EK parameters were obtained by fitting the concentration-velocity data to Michaelis-Menten models by using nonlinear mixed effects modeling. Relationships between the EK parameters and the CYP activities determined for these liver microsomes were examined.

RESULTS

A two-enzyme kinetic model with a saturated, low KM enzyme and an unsaturated, high KM enzyme capable of forming acetaminophen best fit the data. The population estimates of the EK parameters were Vmax1, 911 pmol/min/mg protein; KM1, 11.3 microM; and Cl(int2), 0.4 microl/min/mg. The coefficients of variation for interliver variability in Vmax1 and residual error of the model were 39% and 15%, respectively. When the selective catalytic activities were examined as potential covariates, 7-ethoxyresorufin O-deethylation (CYP1A2) activity was found to be associated with the low KM enzyme, however, the high KM enzyme(s) could not be identified.

CONCLUSIONS

The population approach characterized the EK parameters and identified the low KM enzyme responsible for phenacetin O-deethylation as CYP1A2. Population modeling of EK provides valuable information on inter- and intraliver variability in CYP dependent activities.

A multiscale modelling approach to elucidate the mechanism of the oxygen evolution reaction at the hematite-water interface

Photoelectrochemical (PEC) splitting of water to make hydrogen is a promising clean-energy technology. The oxygen evolution reaction (OER) largely determines the energy efficiency in PEC water-splitting. Hematite, which is a cheap and sustainable semiconductor material with excellent chemical properties, a favourable band gap (2.1 eV) and composed of earth abundant elements is a suitable model photoanode material for studying OER. To understand the design of energy efficient anodes, it is highly desirable to have mechanistic insight into OER at an atomistic level which can be directly connected to experimentally measured quantities. We present a multiscale computational model of OER which connects the thermodynamics and kinetics of elementary charge transfer reactions in OER to kinetics of OER at laboratory length and time scales. We couple density functional theory (DFT) and DFT based molecular dynamics (DFT-MD) simulations with solvent effects at an atomistic level with kinetic Monte Carlo (kMC) simulations at a coarse-grained level in our multiscale model. The time and applied bias potential dependent surface coverage, which are experimentally not known, and the O₂ evolution rate during OER at the hematite-water interface are calculated by the multiscale model. Furthermore, the multiscale model demonstrates the effect of explicitly modelling the interaction of water with the electrode surface via direct adsorption.

Chronic suppurative osteomyelitis of mandible: a case report

Osteomyelitis is an inflammatory disease of the bone that usually begins as an infection of the medullary cavity, rapidly involves the haversian system, and quickly extends to the periosteum of the area. It develops in the jaws after a chronic odontogenic infection or for a variety of other reasons such as trauma, inadequate treatment of fracture, or irradiation to the mandible. When antimicrobial agents or drainage prove unsuccessful, acute osteomyelitis may become chronic. Conventional radiography, culture, bone biopsy, radioisotope bone scan, laser Doppler flowmetry, computed tomography, and magnetic resonance imaging are used for its diagnosis. We present a case of chronic suppurative osteomyelitis associated with a draining extraoral sinus, which was successfully treated with surgical debridement and stabilization with a 10-hole reconstruction plate and bicortical screws using AO principles.

A simplified isolated perfused rat liver apparatus: characterization and measurement of extraction ratios of selected compounds

A simplified isolated perfused rat liver (IPRL) preparation has been developed and evaluated. The liver is briefly perfused in situ prior to being placed into a 37 degrees C oven and suspended from a stand. This set-up takes about 5 min. A non-recirculatory or one-pass perfusion approach has been used. The performance of the apparatus was evaluated with use of three model compounds: antipyrine, lidocaine and ethanol. In addition, oxygen extraction was determined. The steady-state extraction ratio (ER) was determined for each compound (and oxygen) as a function of perfusate flow rate (15-35 ml/min) during sequential 45 min perfusion periods. Perfusion experiments lasted for up to 3 hr. The ERs (at 15 ml/min) of ethanol (0.65 +/- 0.15), lidocaine (0.91 +/- 0.01) and oxygen (0.65 +/- 0.10) were dependent upon perfusate flow; whereas, antipyrine ER (0.07 +/- 0.01) was independent of flow. The corresponding values for unbound intrinsic clearances (CLu,int) for antipyrine, ethanol, lidocaine and oxygen were: 1.6, 31.0, 158.0 and 27.5 ml/min, respectively. These findings are consistent with the known hepatic ER values for those compounds reported in the literature.

OUP accepted manuscript

Conflicts between transcription and replication machinery are a potent source of replication stress and genome instability; however, no technique currently exists to identify endogenous genomic locations prone to transcription–replication interactions. Here, we report a novel method to identify genomic loci prone to transcription–replication interactions termed transcription–replication immunoprecipitation on nascent DNA sequencing, TRIPn-Seq. TRIPn-Seq employs the sequential immunoprecipitation of RNA polymerase 2 phosphorylated at serine 5 (RNAP2s5) followed by enrichment of nascent DNA previously labeled with bromodeoxyuridine. Using TRIPn-Seq, we mapped 1009 unique transcription–replication interactions (TRIs) in mouse primary B cells characterized by a bimodal pattern of RNAP2s5, bidirectional transcription, an enrichment of RNA:DNA hybrids, and a high probability of forming G-quadruplexes. TRIs are highly enriched at transcription start sites and map to early replicating regions. TRIs exhibit enhanced Replication Protein A association and TRI-associated genes exhibit higher replication fork termination than control transcription start sites, two marks of replication stress. TRIs colocalize with double-strand DNA breaks, are enriched for deletions, and accumulate mutations in tumors. We propose that replication stress at TRIs induces mutations potentially contributing to age-related disease, as well as tumor formation and development.

Datasets acquired with correlative microscopy method for delineation of prior austenite grain boundaries and characterization of prior austenite grain size in a low-alloy high-performance steel

Prior studies on martensitic steel microstructures have either delineated the prior austenite grain boundaries via chemical etching or reconstructed the prior austenite grains from crystallographic orientations measured with electron backscattered diffraction (EBSD). To appropriately validate the reconstruction algorithms, the EBSD data need to be collected on martensitic microstructures, where the prior austenite grain boundaries are delineated with techniques such as chemical etching that can serve as ground truth for comparison with the reconstructed prior austenite grains. In this article, the method of correlative microscopy is employed to collect scanning electron microscope (SEM) image and automated EBSD scan data from the same region of an appropriately etched steel specimen. The SEM images and automated EBSD scan data are presented for five different fields of view in the specimen. These datasets are analyzed and discussed in the accompanying article titled "Correlative microscopy for quantification of prior austenite grain size in AF9628 steel" [1].

Study of betasatellite molecule from leaf curl disease of sunn hemp (Crotalaria juncea) in India

Leaves of sunn hemp (Crotalaria juncea) showing geminiviral symptoms were collected from Lucknow, India during rainy season in 2008. DNA template isolated from the symptomatic leaf tissues were subjected to polymerase chain reaction (PCR) using specific primers to amplify coat protein (CP) gene of DNA-A as well as betasatellite DNA associated with the leaf curl disease. CP gene showed 97% sequence identity with that of Cotton leaf curl Burewala virus (CLCuBwV). Further, the betasatellite DNA molecule revealed sequence similarity with previously characterized betasatellite DNA of begomoviruses affecting malvaceous crops from different regions of India and Pakistan. Maximum similarity (>90%) of betasatellite DNA under study was observed with Cotton leaf curl Multan betasatellite (CLCuMB-[Pak: Mul17:08) and other betasatellite DNA from Pakistan thus confirming possible infection of C. juncea with begomovirus. A complementary sense open reading frame (ORF) βC1 is present at nucleotide position 194-550. Sequence comparison of this ORF with other members of begomoviruses further confirmed association of a begomovirus with C. juncea. The betasatellite DNA when expressed under the control of CaMV35S promoter Nicotiana tabacum, showed leaf deformities. Our results demonstrated that a malvaceous betasatellite is adapted by a nonmalvaceous host and causes similar disease symptoms.

Nocturnal Atmospheric Oxidative Processes in the Indo-Gangetic Plain and Their Variation During the COVID-19 Lockdowns

This study investigates selected secondary atmospheric responses to the widely reported emission change attributed to COVID-19 lockdowns in the highly polluted Indo-Gangetic Plain (IGP) using ground-based measurements of trace gases and particulate matter. We used a chemical box-model to show that production of nighttime oxidant, NO₃, was affected mainly by emission decrease (average nighttime production rates 1.2, 0.8 and 1.5 ppbv hr^-1 before, during and relaxation of lockdown restrictions, respectively), while NO₃ sinks were sensitive to both emission reduction and seasonal variations. We have also shown that the maximum potential mixing ratio of nitryl chloride, a photolytic chlorine radical source which has not been previously considered in the IGP, is as high as 5.5 ppbv at this inland site, resulting from strong nitrate radical production and a potentially large particulate chloride mass. This analysis suggests that air quality measurement campaigns and modeling explicitly consider heterogeneous nitrogen oxide and halogen chemistry.

Scale for Assessment of Thought, Language and Communication in psychotic in-patients

The reliability and usefulness of the Scale for Assessment of Thought, Language and Communication was evaluated in a group of psychotic in-patients. A very high interrater reliability (0.75-1.0) and an optimum rate-rerate reliability (0.50-1.0) were found on the individual items of the scale as well as the global rating. Since the scale has a good scope in different clinical and research settings, it was necessary to evaluate its reliability at a place other than where it originated. This study confirms its usefulness in the field of both clinical practice and research.

Volatile organic compound measurements point to fog-induced biomass burning feedback to air quality in the megacity of Delhi

We report the first ambient measurements of thirteen VOCs for investigations of emissions and air quality during fog and non-fog wintertime conditions at a tower site (28.57° N, 77.11° E, 220 m amsl) in the megacity of Delhi. Measurements of acetonitrile (biomass burning (BB) tracer), isoprene (biogenic emission tracer in daytime), toluene (a traffic exhaust tracer) and benzene (emitted from BB and traffic), together with soluble and reactive oxygenated VOCs such as methanol, acetone and acetaldehyde were performed during the winters of 2015-16 and 2016-17, using proton transfer reaction mass spectrometry. Remarkably, ambient VOC composition changes during fog were not governed by solubility. Acetaldehyde, toluene, sum of C8-aromatics (e.g. xylenes), sum of C9-aromatics (e.g. trimethyl benzenes) decreased by ≥30% (>95% confidence interval), whereas acetonitrile and benzene showed significant increases by 20% (>70% confidence interval), even after accounting for boundary layer dilution. During fog, the lower temperatures appeared to induce an emissions feedback from enhanced open BB within Delhi for warming, releasing both gaseous and aerosol pollutants with consequences for fog chemistry, sustenance and intensity. The potential feedback is important to consider for improving current emission parametrizations in models used for predicting air quality and fog in such atmospheric environments.

The efficacy of antisense-based construct for inducing resistance against Croton yellow vein mosaic virus in Nicotiana tabacum

Begomoviruses have increased pathogenicity because of their adaptation to a wide host range; consequently, these viruses cause a major loss to agroeconomic crops worldwide. In this study, we designed a gene construct representing an antisense coat protein gene. We also analyzed the efficacy of the induced resistance against Croton yellow vein mosaic virus (CrYVMV) affecting papaya in Nicotiana tabacum plants. Positive control plants developed typical leaf curl symptoms, whereas transgenic plants were symptomless. Moreover, the key component (i.e., short interfering RNA) of the antisense pathway was upregulated in transgenic plants. This finding demonstrates the activation of the gene silencing mechanism in transgenic plants. Thus, these results confirm that our construct is functional and effectively induces transient resistance against CrYVMV infections.

Cropland trees need to be included for accurate model simulations of land-atmosphere heat fluxes, temperature, boundary layer height, and ozone

Trees significantly impact land-atmosphere feedbacks through evapotranspiration, photosynthesis and isoprene emissions. These processes influence the local microclimate, air quality and can mitigate temperature extremes and sequester carbon dioxide. Despite such importance, currently only 5 out of 15 atmospheric chemistry climate models even partially account for the presence of cropland trees. We first show that the tree cover over intensely farmed regions in Asia, Australia and South America is significantly underestimated (e.g. only 1-3% tree cover over north-India) in the Model of Emissions of Gases and Aerosol from Nature (MEGAN) and absent in Noah land-surface module of the Weather Research and Forecasting (WRF-Chem) Model. By including the actual tree cover (~10%) over the north-west Indo Gangetic Plain in the Noah land-surface module of the WRF-Chem and the MEGAN module, during the rice growing monsoon season in August, we find that the latent heat flux alone increases by 100%-300% while sensible heat flux reduces by 50%-100%, leading to a reduction in daytime boundary layer height by 200-400 m. This greatly improves agreement between the modelled and measured temperature, boundary layer height and surface ozone, which were earlier overestimated and isoprene and its oxidation products which were earlier underestimated. Mitigating peak daytime temperatures and ozone improves rice production by 10 to 20%. Our findings from north west Indo-Gangetic Plain establish that such plantations mitigate heat stress, and have beneficial effects on crop yields while also sequestering carbon. Expanding agroforestry practices to 50% of the cropland area could result in up to 40% yield gain regionally. Implementing such strategies globally could increase crop production and sequester 0.3-30 GtC per year, and therefore future climate mitigation and food security efforts should consider stakeholder participation for increased cropland agroforestry in view of its beneficial effects.