Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have reanalyzed publicly available mass spectrometry proteomics data sets enriched for phosphopeptides from Asian rice (). In total we identified 15,565 phosphosites on serine, threonine, and tyrosine residues on rice proteins.

A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome.

Phosphorylation is the most studied post-translational modification, and has multiple biological functions. In this study, we have re-analysed publicly available mass spectrometry proteomics datasets enriched for phosphopeptides from Asian rice (). In total we identified 15,522 phosphosites on serine, threonine and tyrosine residues on rice proteins.

Assessing Multiple Evidence Streams to Decide on Confidence for Identification of Post-Translational Modifications, within and Across Data Sets.

Phosphorylation is a post-translational modification of great interest to researchers due to its relevance in many biological processes. LC-MS/MS techniques have enabled high-throughput data acquisition, with studies claiming identification and localization of thousands of phosphosites. The identification and localization of phosphosites emerge from different analytical pipelines and scoring algorithms, with uncertainty embedded throughout the pipeline.

Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.

Phosphoproteomic methods are commonly employed to identify and quantify phosphorylation sites on proteins. In recent years, various tools have been developed, incorporating scores or statistics related to whether a given phosphosite has been correctly identified or to estimate the global false localization rate (FLR) within a given data set for all sites reported. These scores have generally been calibrated using synthetic datasets, and their statistical reliability on real datasets is largely unknown, potentially leading to studies reporting incorrectly localized phosphosites, due to inadequate statistical control.

A randomised study to assess the nicotine pharmacokinetics of an oral nicotine pouch and two nicotine replacement therapy products.

Nicotine replacement therapies (NRTs) are intended for short-term use to help cigarette smokers to quit. Some smokers find NRTs ineffective or seek a more satisfactory source of nicotine. Tobacco-free oral nicotine pouch (NP) products have emerged as a potential reduced risk product compared with cigarettes and other tobacco products.

A Randomised Study to Investigate the Nicotine Pharmacokinetics of Oral Nicotine Pouches and a Combustible Cigarette.

Background And Objectives: Nicotine pouches (NPs) are a relatively new type of oral smokeless tobacco-free nicotine product. Currently, few data are available on the nicotine pharmacokinetics or subjective effects of NP use. The objective of this study was to determine and compare the pharmacokinetics of nicotine absorption into the blood from different NP variants and a combustible cigarette.

Investigating the Health Effects of 3 Coexisting Tobacco-Related Products Using System Dynamics Population Modeling: An Italian Population Case Study.

With the proliferation of tobacco products, there might be a need for more complex models than current two-product models. We have developed a three-product model able to represent interactions between three products in the marketplace. We also investigate if using several implementations of two-product models could provide sufficient information to assess 3 coexisting products.

Changes in biomarkers after 180 days of tobacco heating product use: a randomised trial.

The aim of this study was to investigate whether biomarkers of exposure (BoE) and potential harm (BoPH) are modified when smokers switch from smoking cigarettes to exclusive use of a tobacco heating product (THP) in an ambulatory setting. Participants in this randomised, controlled study were healthy volunteer smokers assigned either to continue smoking or switch to a THP, and a control group of smokers who abstained from cigarette smoking. Various BoE and BoPH related to oxidative stress, cardiovascular and respiratory diseases, and cancer were assessed at baseline and up to 180 days.

A randomized controlled study in healthy participants to explore the exposure continuum when smokers switch to a tobacco heating product or an E-cigarette relative to cessation.

Background: Cigarette smoking is associated with a number of diseases, such as cancer and cardiovascular diseases. Recently, there has been an increase in the use of electronic cigarettes (ECs) and tobacco-heating products (THPs) as an alternative to cigarettes, which may reduce the health burden associated with smoking. However, an exposure continuum when smokers switch to ECs or THPs compared to complete smoking cessation is not well established.

The development of an in vitro 3D model of goblet cell hyperplasia using MUC5AC expression and repeated whole aerosol exposures.

Goblet cell hyperplasia and overproduction of airway mucin are characteristic features of the lung epithelium of smokers and COPD patients. Tobacco heating products (THPs) are a potentially less risky alternative to combustible cigarettes, and through continued use solus THPs may reduce smoking-related disease risk. Using the MucilAir™ in vitro lung model, a 6-week feasibility study was conducted investigating the effect of repeated cigarette smoke (1R6F), THP aerosol and air exposure.

A randomised controlled single-centre open-label pharmacokinetic study to examine various approaches of nicotine delivery using electronic cigarettes.

Smokers who switch completely to e-cigarettes may reduce their relative risk of tobacco-related disease. Effective nicotine delivery from e-cigarettes is important in consumer acceptance. We assessed whether protonated nicotine and e-cigarette devices delivering greater aerosol mass increase nicotine delivery and product liking.

Changes in Biomarkers of Exposure on Switching From a Conventional Cigarette to the glo Tobacco Heating Product: A Randomized, Controlled Ambulatory Study.

Introduction: Tobacco heating products (THPs) generate lower machine yields of toxicants compared to those found in conventional cigarette smoke. During use, these products are likely to expose users to lower levels of particulate matter and harmful and potentially harmful compounds compared with smoking cigarettes.

Aims And Methods: This randomized, controlled study is investigating whether biomarkers of exposure (BoE) to smoke toxicants are reduced when smokers switch from smoking cigarettes to using the glo THP in a naturalistic, ambulatory setting.

Evaluation of a high-throughput in vitro endothelial cell migration assay for the assessment of nicotine and tobacco delivery products.

Endothelial cell migration is a critical process in the maintenance of healthy blood vessels. Impaired endothelial migration is reportedly associated with the development of cardiovascular diseases. Here, we report on the development of a 96-well in vitro endothelial migration assay for the purpose of comparative toxicological assessment of a novel THP relative to cigarette smoke, to be able to rapidly inform regulatory decision making.

Results from a 2018 cross-sectional survey in Tokyo, Osaka and Sendai to assess tobacco and nicotine product usage after the introduction of heated tobacco products (HTPs) in Japan.

Background: For novel tobacco products that potentially reduce the risk of tobacco harm, post-market surveillance is important to observe population usage and behaviours associated with everyday use. This pilot study was performed to examine the use of tobacco products in three Japanese urban regions.

Methods: This study was a cross-sectional epidemiological survey administered in Sendai, Tokyo and Osaka, Japan, from May 19th to June 25th, 2018.

Statistical analysis plan for "A randomised, controlled study to evaluate the effects of switching from cigarette smoking to using a tobacco heating product on health effect indicators in healthy subjects".

Tobacco harm reduction strategies aim to substitute smoking with potentially reduced risk products (PRRPs) such as e-cigarettes and tobacco-heating products (THPs). The health benefits of switching from smoking to PRRPs is unknown. A randomised controlled trial is being conducted to increase understanding of the health effects of switching from smoking to a THP in a 12-month long ambulatory study (ISRCTN81075760).

Proteome Bioinformatics Methods for Studying Histidine Phosphorylation.

In this chapter, we introduce the bioinformatics methods associated with studying histidine phosphorylation (pHis) by LC-MS/MS. We describe methods for converting and preprocessing raw data from MS instruments, the method of searching MS data against a sequence database and scoring the confidence associated with localizing the modification site on the peptide sequence. We also describe methods for performing pathway enrichment once a set of pHis-containing proteins have been identified to understand the putative functions of modified proteins.

Evaluating the effects of switching from cigarette smoking to using a heated tobacco product on health effect indicators in healthy subjects: study protocol for a randomized controlled trial.

Tobacco heating products (THPs) are a potentially safer alternative to combustible cigarette smoking. Through continued use, THPs may reduce smoking-related disease risk, whilst maintaining the sensorial experience and nicotine delivery sought by smokers. While literature evidence of the biological effects of THP aerosol exposure is increasing, there remains a knowledge gap with respect to substantiation of THP reduced risk potential in longer term real-life use.

Changes in Biomarkers of Exposure on Switching From a Conventional Cigarette to Tobacco Heating Products: A Randomized, Controlled Study in Healthy Japanese Subjects.

Background: Smoking is a leading cause of numerous human disorders including pulmonary disease, cardiovascular disease, and cancer. Disease development is primarily caused by exposure to cigarette smoke constituents, many of which are known toxicants. Switching smokers to modified risk tobacco products (MRTPs) has been suggested as a potential means to reduce the risks of tobacco use, by reducing such exposure.

A randomised, controlled, two-Centre open-label study in healthy Japanese subjects to evaluate the effect on biomarkers of exposure of switching from a conventional cigarette to a tobacco heating product.

Background: Smoking is a leading cause of numerous human disorders including lung cancer, chronic obstructive pulmonary disease, and atherosclerotic cardiovascular disease. The development of modified risk tobacco products (MRTPs) has been suggested as a possible way to reduce the risks of tobacco smoking by reducing exposure to cigarette smoke toxicants. This study is designed to investigate whether biomarkers of such exposure are reduced when smokers switch from smoking commercial cigarettes to using either a novel or a commercially-available tobacco heating product (THP).

A system dynamics modelling approach to assess the impact of launching a new nicotine product on population health outcomes.

In 2012 the US FDA suggested the use of mathematical models to assess the impact of releasing new nicotine or tobacco products on population health outcomes. A model based on system dynamics methodology was developed to project the potential effects of a new nicotine product at a population level. A model representing traditional smoking populations (never, current and former smokers) and calibrated using historical data was extended to a two-product model by including electronic cigarettes use statuses.

E-cigarette Nicotine Delivery: Data and Learnings from Pharmacokinetic Studies.

Objectives: E-cigarettes could potentially play a major role in tobacco harm reduction by delivering nicotine in a vapor containing significantly fewer toxicants than cigarette smoke and may aid smoking behavior changes such as reduction or cessation.

Methods: We examined blood nicotine levels in smokers who were non-accustomed to e-cigarette use (Study 1) and accustomed e-cigarette users (Study 2). We compared nicotine levels when participants used a closed modular system e-cigarette to those when participants smoked a cigarette.

Electronic cigarette aerosol induces significantly less cytotoxicity than tobacco smoke.

Electronic cigarettes (E-cigarettes) are a potential means of addressing the harm to public health caused by tobacco smoking by offering smokers a less harmful means of receiving nicotine. As e-cigarettes are a relatively new phenomenon, there are limited scientific data on the longer-term health effects of their use. This study describes a robust in vitro method for assessing the cytotoxic response of e-cigarette aerosols that can be effectively compared with conventional cigarette smoke.

Reference change values in concentrations of urinary and salivary biomarkers of exposure and mouth level exposure in individuals participating in an ambulatory smoking study.

Background: Modified-risk tobacco products (MRTPs) are being developed that may contribute to tobacco harm reduction. To support reduced exposure or risk claims, a scientific framework needs to be developed to assess the validity of claims and monitor consumers after product launch. We calculated reference change values (RCVs) for biomarker of exposure (BoE): salivary cotinine and hydroxycotinine; and urinary total nicotine equivalents, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) and creatinine.

Cigarette smoke induced genotoxicity and respiratory tract pathology: evidence to support reduced exposure time and animal numbers in tobacco product testing.

Many laboratories are working to develop in vitro models that will replace in vivo tests, but occasionally there remains a regulatory expectation of some in vivo testing. Historically, cigarettes have been tested in vivo for 90 days. Recently, methods to reduce and refine animal use have been explored.