Here we introduce graphPAF, a comprehensive R package designed for estimation, inference and display of population attributable fractions (PAF) and impact fractions. In addition to allowing inference for standard population attributable fractions and impact fractions, graphPAF facilitates display of attributable fractions over multiple risk factors using fan-plots and nomograms, calculations of attributable fractions for continuous exposures, inference for attributable fractions appropriate for specific risk factor → mediator → outcome pathways (pathway-specific attributable fractions) and Bayesian network-based calculations and inference for joint, sequential and average population attributable fractions in multi-risk factor scenarios. This article can be used as both a guide to the theory of attributable fraction estimation and a tutorial regarding how to use graphPAF in practical examples.

Most previous studies have focused on the continuous exposure of aquatic organisms to nanoplastics. However, persistent pollutants in natural aquatic surroundings are a threat, and their concentrations are continuously increasing. The discussion and research into the effects of accumulative exposure to these materials are limited. Therefore, this study aimed to compare the effects of continuous and accumulative exposure to polystyrene (PS) nanoplastics (80 nm) on Chlorella pyrenoidosa during chronic toxicity. The results indicated that under conditions of continuous exposure, this alga exhibited self-recovery to defend against the negative effects of PS nanoplastics during 15-21 days of exposure (the 21-d inhibitory rate was 1.41%). However, one unanticipated finding was that during the same period of accumulative exposure, nanoplastics retained a substantial and stable inhibitory effect on the algal growth (the 21-d inhibitory rate was 6.79% in accumulative exposure for twice), indicating the invalid self-recovery of algae. The results of scanning electron microscopy demonstrated that on day 21, the degree of damage to the algal cells under accumulative exposure was more severe than that under continuous exposure. Hence, nanoplastics exerted an irreversibly negative effect on aquatic organisms depending on the pattern, frequency, concentration, and duration of exposure. This project evaluated the practical significance of nanoplastics in aquatic ecosystems.

Large datasets of hundreds to thousands of individuals measuring RNA-seq in observational studies are becoming available. Many popular software packages for analysis of RNA-seq data were constructed to study differences in expression signatures in an experimental design with well-defined conditions (exposures). In contrast, observational studies may have varying levels of confounding transcript-exposure associations; further, exposure measures may vary from discrete (exposed, yes/no) to continuous (levels of exposure), with non-normal distributions of exposure. We compare popular software for gene expression-DESeq2, edgeR and limma-as well as linear regression-based analyses for studying the association of continuous exposures with RNA-seq. We developed a computation pipeline that includes transformation, filtering and generation of empirical null distribution of association P-values, and we apply the pipeline to compute empirical P-values with multiple testing correction. We employ a resampling approach that allows for assessment of false positive detection across methods, power comparison and the computation of quantile empirical P-values. The results suggest that linear regression methods are substantially faster with better control of false detections than other methods, even with the resampling method to compute empirical P-values. We provide the proposed pipeline with fast algorithms in an R package Olivia, and implemented it to study the associations of measures of sleep disordered breathing with RNA-seq in peripheral blood mononuclear cells in participants from the Multi-Ethnic Study of Atherosclerosis.

Studies that assess the connection between the prevalence of chronic diseases and continuous exposure to air pollution are scarce in developing countries, mainly due to data limitations. Largely overcoming data limitations, this study aimed to investigate the association between the likelihood of reporting a set of chronic diseases (diabetes, cancer, stroke and myocardial infarction, asthma, and hypertension) and continuous exposure to carbon monoxide (CO), nitrogen dioxide (NO2), ozone (O3), and coarse particulate matter (PM10). Using the estimated associations, the disease burden and economic costs of continuous exposure to air pollutants were also approximated. A 2011 Health Equity Assessment and Response Tool survey from Tehran, Iran, was used in the main analyses. A sample of 67,049 individuals who had not changed their place of residence for at least 2 years before the survey and reported all relevant socioeconomic information was selected. The individuals were assigned with the average monthly air pollutant levels of the nearest of 16 air quality monitors during the 2 years leading to the survey. Both single- and multi-pollutant analyses were conducted. The country\'s annual household surveys from 2002 to 2011 were used to calculate the associated economic losses. The single-pollutant analysis showed that a one-unit increase in monthly CO (ppm), NO2 (ppb), O3 (ppb), and PM10 (μg/m3) during the 2 years was associated with 751 [confidence interval (CI): 512-990], 18 (CI: 12-24), 46 (CI: -27-120), and 24 (CI: 13-35) more reported chronic diseases in 100,000, respectively. The disease-specific analyses showed that a unit change in average monthly CO was associated with 329, 321, 232, and 129 more reported cases of diabetes, hypertension, stroke and myocardial infarction, and asthma in 100,000, respectively. The measured associations were greater in samples with older individuals. Also, a unit change in average monthly O3 was associated with 21 (in 100,000) more reported cases of asthma. The multi-pollutant analyses confirmed the results from single-pollutant analyses. The supplementary analyses showed that a one-unit decrease in monthly CO level could have been associated with about 208 (CI: 147-275) years of life gained or 15.195 (CI: 10.296-20.094) thousand US dollars (USD) in life-time labor market income gained per 100,000 30-plus-year-old Tehranis.

The effects of asbestos fibers on human immune cells have not been well documented. We have developed a continuously exposed cell line model using the human T-lymphotropic virus 1 (HTLV-1)-immortalized human T cell line MT-2. Sublines continuously exposed to chrysotile (CH) or crocidolite (CR) showed acquired resistance to asbestos-induced apoptosis following transient and high-dose re-exposure with fibers. These sublines in addition to other immune cells such as natural killer cells or cytotoxic T lymphocytes exposed to asbestos showed a reduction in anti-tumor immunity. In this study, the expression of genes and molecules related to antioxidative stress was examined. Furthermore, complexes related to oxidative phosphorylation were investigated since the production of reactive oxygen species (ROS) is important when considering the effects of asbestos in carcinogenesis and the mechanisms involved in resistance to asbestos-induced apoptosis. In sublines continuously exposed to CH or CR, the expression of thioredoxin decreased. Interestingly, nicotinamide nucleotide transhydrogenase (NNT) expression was markedly enhanced. Thus, knockdown of NNT was then performed. Although the knockdown clones did not show any changes in proliferation or occurrence of apoptosis, these clones showed recovery of ROS production with returning NADPH/NADP+ ratio that increased with decreased production of ROS in continuously exposed sublines. These results indicated that NNT is a key factor in preventing ROS-induced cytotoxicity in T cells continuously exposed to asbestos. Considering that these sublines showed a reduction in anti-tumor immunity, modification of NNT may contribute to recovery of the anti-tumor effects in asbestos-exposed T cells.

Silver nanoparticles (AgNPs) are widely used in commercial applications as antimicrobial agents, but there have recently been increasing concerns raised about their possible environmental and health impacts. In this study, zebrafish embryos were exposed to two sizes of AgNP, 4 and 10 nm, through a continuous exposure from 4 to 96 h post-fertilisation (hpf), to study their uptake, impact and molecular defense responses. Results showed that zebrafish embryos were significantly impacted by 72 hpf when continuously exposed to 4 nm AgNPs. At concentrations above 0.963 mg/L, significant in vivo uptake and delayed yolk sac absorption was evident; at 1.925 mg/L, significantly reduced body length was recorded compared to control embryos. Additionally, 4 nm AgNP treatment at the same concentration resulted in significantly upregulated hypoxia inducible factor 4 (HIF4) and peroxisomal membrane protein 2 (Pxmp2) mRNA expression in exposed embryos 96 hpf. In contrast, no significant differences in terms of larvae body length, yolk sac absorption or gene expression levels were observed following exposure to 10 nm AgNPs. These results demonstrated that S4 AgNPs are available for uptake, inducing developmental (measured as body length and yolk sac area) and transcriptional (specifically HIF4 and Pxmp2) perturbations in developing embryos. This study suggests the importance of particle size as one possible factor in determining the developmental toxicity of AgNPs in fish embryos.

Methods based on cosmic-ray produced nuclides are key to improve our understanding of the Earth surface dynamic. Measuring multiple cosmogenic nuclides in the same rock sample has a great potential, but data interpretation requires rigorous and often complex mathematical treatments. In order to make progress on this topic, this paper presents two easy-to-use MATLAB© programs permitting to derive information from pairs of cosmogenic nuclides (26Al-10Be or 10Be-21Ne) measured in rock samples that have been exposed to cosmic rays in the past: \"Paleoaltitude.m\" and \"Burial.m\". •\"Paleoaltitude.m\" computes paleoelevations from a sample whose burial age is known. This new paleoaltimetry method is presented in detail in Blard et al. [1]. The present article also develops the mathematical approach.•Since the elevation of exposure may affect the accuracy of a burial age [1], the second MATLAB© script \"Burial.m\" is designed to compute burial ages from 26Al-10Be or 10Be-21Ne pairs, taking into account the position of a sample (elevation and latitude) during its preburial exposure history.

Titanium dioxide nanoparticles (TiO2 NPs) find applications in our day-to-day life because of unique physicochemical properties. Their release into the aquatic environment poses a possible risk to the organisms. However, the continuing exposure of NPs might reduce their bioavailability to marine organisms owing to aggregation and sedimentation in the aqueous systems thus significantly reducing their toxic impact. In this regard, the present study investigates the effect of continuous exposure of TiO2 NPs to marine microalgae Chlorella sp. under UV-A irradiation through \"tanks in series\" mode of experiments. In a three-cycle experiment, concentration of TiO2 NPs in the first cycle was fixed at 62.6 μM, and the interacted nanoparticles was subsequently exposed to fresh batches of algae in the next two cycles. After the interaction, the NPs underwent severe aggregation (mean hydrodynamic diameter 3000 ± 18.2 nm after cycle I) leading to gravitational settling in the medium and thus decreased bioavailability. The aggregation can be attributed to interactions between the particles themselves (homo-aggregation) further aggravated by the presence of the algal cells (hetero-aggregation). Cellular viability after cycle I was found to be only 24.2 ± 2.5%, and it was enhanced to 96.5 ± 2.8% after the cycle III in the course of continuous exposure. The results were validated with estimation of oxidative stress markers such as intracellular ROS (total ROS, superoxide and hydroxyl radicals) and LPO after each cycle of exposure. The continuing decrease in the EPS across the cycles further confirmed the diminishing toxicity of the NPs.

BACKGROUND: Several statistical approaches have been proposed to assess and correct for exposure measurement error. We aimed to provide a critical overview of the most common approaches used in nutritional epidemiology.
METHODS: MEDLINE, EMBASE, BIOSIS and CINAHL were searched for reports published in English up to May 2016 in order to ascertain studies that described methods aimed to quantify and/or correct for measurement error for a continuous exposure in nutritional epidemiology using a calibration study.
RESULTS: We identified 126 studies, 43 of which described statistical methods and 83 that applied any of these methods to a real dataset. The statistical approaches in the eligible studies were grouped into: a) approaches to quantify the relationship between different dietary assessment instruments and \"true intake\", which were mostly based on correlation analysis and the method of triads; b) approaches to adjust point and interval estimates of diet-disease associations for measurement error, mostly based on regression calibration analysis and its extensions. Two approaches (multiple imputation and moment reconstruction) were identified that can deal with differential measurement error.
CONCLUSIONS: For regression calibration, the most common approach to correct for measurement error used in nutritional epidemiology, it is crucial to ensure that its assumptions and requirements are fully met. Analyses that investigate the impact of departures from the classical measurement error model on regression calibration estimates can be helpful to researchers in interpreting their findings. With regard to the possible use of alternative methods when regression calibration is not appropriate, the choice of method should depend on the measurement error model assumed, the availability of suitable calibration study data and the potential for bias due to violation of the classical measurement error model assumptions. On the basis of this review, we provide some practical advice for the use of methods to assess and adjust for measurement error in nutritional epidemiology.

Exposure to ethanol during critical period of development can cause severe impairments in the central nervous system (CNS). This study was conducted to assess the neurotoxic effects of chronic embryonic exposure to ethanol in the zebrafish, taking into consideration the time dependent effect. Two types of exposure regimen were applied in this study. Withdrawal exposure group received daily exposure starting from gastrulation until hatching, while continuous exposure group received daily exposure from gastrulation until behavioural assessment at 6dpf (days post fertilization). Chronic embryonic exposure to ethanol decreased spontaneous tail coiling at 24hpf (hour post fertilization), heart rate at 48hpf and increased mortality rate at 72hpf. The number of apoptotic cells in the embryos treated with ethanol was significantly increased as compared to the control. We also measured the morphological abnormalities and the most prominent effects can be observed in the treated embryos exposed to 1.50% and 2.00%. The treated embryos showed shorter body length, larger egg yolk, smaller eye diameter and heart edema as compared to the control. Larvae received 0.75% continuous ethanol exposure exhibited decreased swimming activity and increased anxiety related behavior, while withdrawal ethanol exposure showed increased swimming activity and decreased anxiety related behavior as compared to the respective control. Biochemical analysis exhibited that ethanol exposure for both exposure regimens altered proteins, lipids, carbohydrates and nucleic acids of the zebrafish larvae. Our results indicated that time dependent effect of ethanol exposure during development could target the biochemical processes thus leading to induction of apoptosis and neurobehavioral deficits in the zebrafish larvae. Thus it raised our concern about the safe limit of alcohol consumption for pregnant mother especially during critical periods of vulnerability for developing nervous system.