| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
- Schael, S, et al.
(författare)
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Precision electroweak measurements on the Z resonance
- 2006
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Ingår i: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
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Forskningsöversikt (refereegranskat)abstract
- We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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| 4. |
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| 5. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 9. |
- Stanaway, Jeffrey D., et al.
(författare)
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Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017
- 2018
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Ingår i: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994
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Tidskriftsartikel (refereegranskat)abstract
- Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
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| 10. |
- Xie, Huaijun, et al.
(författare)
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Development and evaluation of diffusive gradients in thin films technique for measuring antibiotics in seawater
- 2018
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 618, s. 1605-1612
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Tidskriftsartikel (refereegranskat)abstract
- As coastal waters in many regions of the world have been polluted by organic micro-pollutants such as antibiotics that can promote the development of resistance genes, it is of importance to monitor the levels of antibiotics in coastal waters. For this purpose, a reliable and robust sampling approach based on diffusive gradients in thin films (DGT) was developed in this study. The DGT measurement can provide a time weighted average concentration of pollutants. A binding material (resin XDA-1) with a high adsorption capacity for antibiotics, which can resist the pH and ionic strength of seawaters, was selected. The DGT sampler exhibited linear accumulation for 20 antibiotics during a 12 h deployment. The antibiotic measurement by the sampler was not affected by pH in the range of 7.3 to 8.9 and ionic strength in the range of 0.5 to 0.8 M. After an 8-hour in situ DGT sampling, 10 antibiotics were detected in Dalian coastal seawaters with the concentrations ranging from 2.6 to 44.8 ngL(-1), which was comparable to the results measured by an active sampling method. This study can be a first attempt to construct DGT sampler for determining antibiotics in seawaters.
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| 11. |
- Xie, Huaijun, et al.
(författare)
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Investigation and application of diffusive gradients in thin-films technique for measuring endocrine disrupting chemicals in seawaters
- 2018
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 200, s. 351-357
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Tidskriftsartikel (refereegranskat)abstract
- Endocrine disrupting chemicals (EDCs) can be released to coastal waters and affect the endocrine system of marine organisms. To monitor their levels in seawaters, a simple, robust passive sampling method, the diffusive gradients in thin-films (DGT) technique, was developed with XDA-1 resin as a binding agent. Six EDCs (including three estrogens, two pesticides and bisphenol A) were used to assess the performance of the DGT. The XDA-1 binding gel showed adequate ability for adsorbing EDCs in seawaters. The DGT sampler exhibited linear accumulation for the EDCs during a 15-day deployment and diffusion coefficients and sampling rates were calculated. The DGT measurement was independent of pH in the range 7.0-9.0 and ionic strength in the range 0.4-0.8 M. Field applications of this DGT in a coast of Dalian (China) showed comparable results to those from grab sampling. Five EDCs were detected with concentrations ranging from 0.7 to 19.4 ng L-1. This study is a first attempt to apply DGT sampler for determining EDCs in seawaters.
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| 15. |
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| 16. |
- Bousquet, J, et al.
(författare)
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Nrf2-interacting nutrients and COVID-19: time for research to develop adaptation strategies
- 2020
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Ingår i: Clinical and translational allergy. - : Wiley. - 2045-7022. ; 10:1, s. 58-
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Tidskriftsartikel (refereegranskat)abstract
- There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPARγ:Peroxisome proliferator-activated receptor, NFκB: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2α:Elongation initiation factor 2α). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT1R axis (AT1R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity.
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| 17. |
- Chen, Chang-Er L., et al.
(författare)
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Deriving in Vivo Bioconcentration Factors of a Mixture of Fragrance Ingredients Using a Single Dietary Exposure and Internal Benchmarking
- 2018
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 52:9, s. 5227-5235
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Tidskriftsartikel (refereegranskat)abstract
- Chemicals in mixtures that are hydrophobic with Log K-OW > 4 are potentially bioaccumulative. Here, we evaluate an abbreviated and benchmarked in vivo BCF measurement methodology by exposing rainbow trout to a mixture of eight test chemicals found in fragrance substances and three benchmark chemicals (musk xylene (MX), hexachlorobenzene (HCB) and PCB52) via a single contaminated feeding event followed by a 28-day depuration period. Concentrations of HCB and PCB52 in fish did not decline significantly (their apparent depuration rate constants, k(T), were close to zero), whereas k(T) for MX was 0.022 d(-1). The test chemicals were eliminated much more rapidly than the benchmark chemicals (k(T) > 0.117 d(-1)). The bioconcentration factors (BCFA) for the test chemicals were in the range of 273 L kg(-1) (8-cyclohexadecen-1-one (globanone)) to 1183 L kg(-1) (alpha-pinene); the benchmarked BCFs (BCFG) calculated relative to HCB ranged from 238 L kg(-1) (globanone) to 1147 L kg(-1) (alpha-pinene). BCFG were not significantly different from BCFA but had smaller standard errors. BCFs derived here agreed well with values previously measured using the OECD 305 test protocol. We conclude that it will be feasible to derive BCFs of chemicals in mixtures using a single dietary exposure and chemical benchmarking.
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| 18. |
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| 19. |
- Ge, Linke, et al.
(författare)
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Aqueous multivariate phototransformation kinetics of dissociated tetracycline : implications for the photochemical fate in surface waters
- 2018
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Ingår i: Environmental Science and Pollution Research. - : Springer Science and Business Media LLC. - 0944-1344 .- 1614-7499. ; 25:16, s. 15726-15732
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Tidskriftsartikel (refereegranskat)abstract
- Antibiotics are ubiquitous pollutants in aquatic systems and can exist as different dissociated species depending on the water pH. New knowledge of their multivariate photochemical behavior (i.e., the photobehavior of different ionized forms) is needed to improve our understanding on the fate and possible remediation of these pharmaceuticals in surface and waste waters. In this study, the photochemical degradation of aqueous tetracycline (TC) and its dissociated forms (TCH20, TCH-, and TC2-) was investigated. Simulated sunlight experiments and matrix calculations indicated that the three dissociated species had dissimilar photolytic kinetics and photo-oxidation reactivities. TC2- photo-degraded the fastest due to apparent photolysis with a kinetic constant of 0.938 +/- 0.021 min(-1), followed by TCH- (0.020 +/- 0.005 min(-1)) and TCH20 (0.012 +/- 0.001 min(-1)), whereas Tar was found to be the most highly reactive toward center dot OH (105.78 +/- 3.40 M(-1 )s(-1)), and TC2- reacted the fastest with O-1(2) (344.96 +/- 45.07 M-1 s(-1)). Water with relatively high pH (e.g., similar to 8-9) favors the dissociated forms of TCH- and TC2- which are most susceptible to photochemical loss processes compared to neutral TC. The calculated corresponding environmental half-lives (t(1/2,E) ) in sunlit surface waters ranged from 0.05 h for pH = 9 in midsummer to 3.68 h for pH = 6 in midwinter at 45 degrees N latitude. The moms was dominated by apparent photolysis (especially in summer, 62-91%), followed by O-1(2) and center dot OH oxidation. Adjusting the pH to slightly alkaline conditions prior to UV or solar UV light treatment may be an effective way of enhancing the photochemical removal of TC from contaminated water.
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| 20. |
- Hu, Li-Xin, et al.
(författare)
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What is in Nigerian waters? Target and non-target screening analysis for organic chemicals
- 2021
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Ingår i: Chemosphere. - : Elsevier BV. - 0045-6535 .- 1879-1298. ; 284
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Tidskriftsartikel (refereegranskat)abstract
- Emerging organic contaminants (e.g., active pharmaceutical ingredients and personal care products ingredients) are ubiquitous in the environment and potentially harmful to ecosystems, have gained increasing public attention worldwide. Nevertheless, there is a scarcity of data on these contaminants in Africa. In this study, various types of water samples (wastewater, surface water and tap water) collected from Lagos, Nigeria were analyzed for these chemicals by both target and non-target analysis on an UHPLC-Orbitrap-MS/MS. In total, 109 compounds were identified by non-target screening using the online database mzCloud. Level 1 identification confidence was achieved for 13 compounds for which reference standards were available and level 2 was achieved for the rest. In the quantitative analysis, 18 of 38 target compounds were detected, including the parent compounds and their metabolites. Acetaminophen, sulfamethoxazole, acesulfame, and caffeine were detected in all samples with their highest concentrations at 8000, 5300, 16, and 7700 μg/L in wastewater, 140000, 3300, 7.7, and 12000 μg/L in surface water, and 66, 62, 0.17 and 1000 μg/L in tap water, respectively. The occurrence of psychoactive substances, anticancer treatments, antiretrovirals, antihypertensives, antidiabetics and their metabolites were reported in Nigeria for the first time. These results indicate poor wastewater treatment and management in Nigeria, and provide a preliminary profile of organic contaminants occurring in Nigerian waters. The findings from this study urge more future research on chemical pollution in the aquatic environments in Nigeria.
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| 21. |
- Lammel, Tobias, et al.
(författare)
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Mixture toxicity effects and uptake of titanium dioxide (TiO2) nanoparticles and 3,3 ',4,4 '-tetrachlorobiphenyl (PCB77) in juvenile brown trout following co-exposure via the diet
- 2019
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Ingår i: Aquatic Toxicology. - : Elsevier BV. - 0166-445X .- 1879-1514. ; 213
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Tidskriftsartikel (refereegranskat)abstract
- Titanium dioxide nanoparticles (n-TiO2) are among the man-made nanomaterials that are predicted to be found at high concentrations in the aquatic environment. There, they likely co-exist with other chemical pollutants. Thus, n-TiO2 and other chemical pollutants can be taken up together or accumulate independently from each other in prey organisms of fish. This can lead to dietary exposure of fish to n-TiO2-chemical pollutant mixtures. In this study, we examine if simultaneous dietary exposure to n-TiO2 and 3,3',4,4'-Tetrachlorobiphenyl (PCB77)-used as a model compound for persistent organic pollutants with dioxin-like properties-can influence the uptake and toxicological response elicited by the respective other substance. Juvenile brown trout (Salmo trutta) were fed custom-made food pellets containing n-TiO2, PCB77 or n-TiO2+PCB77 mixtures for 15 days. Ti and PCB77 concentrations in the liver were measured by ICP-MS and GC-MS, respectively. Besides, n-TiO2 uptake was assessed using TEM. Combination effects on endpoints specific for PCB77 (i.e., cytochrome P450 1A (CYP1A) induction) and endpoints shared by both PCB77 and n-TiO2 (i.e., oxidative stress-related parameters) were measured in intestine and liver using RT-qPCR and enzyme activity assays. The results show that genes encoding for proteins/enzymes essential for tight junction function (zo-1) and ROS elimination (sod-1) were significantly upregulated in the intestine of fish exposed to n-TiO2 and PCB77 mixtures, but not in the single-substance treatments. Besides, n-TiO2 had a potentiating effect on PCB77-induced CYP1A and glutathione reductase (GR) expression/enzyme activity in the liver. This study shows that simultaneous dietary exposure to nanomaterials and traditional environmental pollutants might result in effects that are larger than observed for the substances alone, but that understanding the mechanistic basis of such effects remains challenging.
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| 22. |
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| 23. |
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| 24. |
- Wilkinson, John L., et al.
(författare)
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Pharmaceutical pollution of the world's rivers
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:8
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Tidskriftsartikel (refereegranskat)abstract
- Environmental exposure to active pharmaceutical ingredients (APIs) can have negative effects on the health of ecosystems and humans. While numerous studies have monitored APIs in rivers, these employ different analytical methods, measure different APIs, and have ignored many of the countries of the world. This makes it difficult to quantify the scale of the problem from a global perspective. Furthermore, comparison of the existing data, generated for different studies/regions/continents, is challenging due to the vast differences between the analytical methodologies employed. Here, we present a global-scale study of API pollution in 258 of the world's rivers, representing the environmental influence of 471.4 million people across 137 geographic regions. Samples were obtained from 1,052 locations in 104 countries (representing all continents and 36 countries not previously studied for API contamination) and analyzed for 61 APIs. Highest cumulative API concentrations were observed in sub-Saharan Africa, south Asia, and South America. The most contaminated sites were in low- to middle-income countries and were associated with areas with poor wastewater and waste management infrastructure and pharmaceutical manufacturing. The most frequently detected APIs were carbamazepine, metformin, and caffeine (a compound also arising from lifestyle use), which were detected at over half of the sites monitored. Concentrations of at least one API at 25.7% of the sampling sites were greater than concentrations considered safe for aquatic organisms, or which are of concern in terms of selection for antimicrobial resistance. Therefore, pharmaceutical pollution poses a global threat to environmental and human health, as well as to delivery of the United Nations Sustainable Development Goals.
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| 25. |
- Yuan, Bo, et al.
(författare)
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Determination of Chlorinated Paraffins by Bromide-Anion Attachment Atmospheric-Pressure Chemical Ionization Mass Spectrometry
- 2018
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Ingår i: Environmental Science and Technology Letters. - : American Chemical Society (ACS). - 2328-8930. ; 5:6, s. 348-353
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Tidskriftsartikel (refereegranskat)abstract
- A novel method for the quantitative determination of chlorinated paraffins (CPs) was developed using bromide-anion attachment atmospheric-pressure chemical ionization mass spectrometry (APCI-MS). Bromoform was used to enhance ionization of CPs. Near exclusive formation of stable bromide adduct ions ([M + BR](-)) enabled accurate detection of individual CP congener groups (CnClm) with only a moderate-resolution quadrupole time-of-flight mass spectrometer. Furthermore, the method was free from interference commonly observed with chloride-anion attachment methods (e.g., decomposition ions [M + Cl - HCl](-)) that require deconvolution. Together with a CnClm-response-factor algorithm for quantifying short-chain CPs and a CnClm-pattern-reconstruction algorithm for quantifying medium- and long-chain CPs, method applicability was demonstrated on biota and sediment samples. These data were generated significantly faster and with improved selectivity and sensitivity versus those of conventional measurements by chloride-anion attachment APCI-MS.
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