| 1. |
- Messner, Christoph B., et al.
(författare)
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Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection
- 2020
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Ingår i: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 11:1, s. 11-24.E4
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Tidskriftsartikel (refereegranskat)abstract
- The COVID-19 pandemic is an unprecedented global challenge, and point-of-care diagnostic classifiers are urgently required. Here, we present a platform for ultra-high-throughput serum and plasma proteomics that builds on ISO13485 standardization to facilitate simple implementation in regulated clinical laboratories. Our low-cost workflow handles up to 180 samples per day, enables high precision quantification, and reduces batch effects for large-scale and longitudinal studies. We use our platform on samples collected from a cohort of early hospitalized cases of the SARS-CoV-2 pandemic and identify 27 potential biomarkers that are differentially expressed depending on the WHO severity grade of COVID-19. They include complement factors, the coagulation system, inflammation modulators, and pro-inflammatory factors upstream and downstream of interleukin 6. All protocols and software for implementing our approach are freely available. In total, this work supports the development of routine proteomic assays to aid clinical decision making and generate hypotheses about potential COVID-19 therapeutic targets.
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| 2. |
- Henneberger, Paul K, et al.
(författare)
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Development of an Asthma-Specific Job Exposure Matrix for Use in the United States.
- 2020
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Ingår i: Annals of work exposures and health. - : Oxford University Press (OUP). - 2398-7316 .- 2398-7308. ; 64:1, s. 82-95
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Tidskriftsartikel (refereegranskat)abstract
- Existing asthma-specific job-exposure matrices (JEMs) do not necessarily reflect current working conditions in the USA and do not directly function with occupational coding systems commonly used in the USA. We initiated a project to modify an existing JEM to address these limitations, and to apply the new JEM to the entire US employed population to estimate quantitatively the extent of probable work-related asthma exposures nationwide.We started with an asthma-specific JEM that was developed for northern Europe (the N-JEM) and modified it to function with the 2010 US Standard Occupational Classification (SOC-2010) codes and to reflect working conditions in the USA during the post-2000 period. This involved cross walking from the 1988 International Standard Classification of Occupations (ISCO-88) codes used in the N-JEM to the SOC-2010 codes, transferring the N-JEM exposure assignments to the SOC-2010 codes, and modifying those assignments to reflect working conditions in the USA. The new US asthma JEM (USA-JEM) assigns exposures to 19 agents organized into five categories. The USA-JEM and N-JEM were applied to the same sample of working adults with asthma to compare how they performed, and the USA-JEM was also applied to the entire 2015 US working population to estimate the extent of occupational asthma exposures nationally.The USA-JEM assigns at least one asthma-related probable exposure to 47.5% and at least one possible exposure to 14.9% of the 840 SOC-2010 detailed occupations, and 9.0% of the occupations have both probable exposure to at least one agent and possible exposure to at least one other agent. The USA-JEM has greater sensitivity for cleaning products, highly reactive disinfectants and sterilants, and irritant peak exposures than the N-JEM. When applied to the entire 2015 US working population, the USA-JEM determined that 42.6% of workers had probable exposure to at least one type of occupational asthma agent.A new asthma-specific JEM for application in the USA was developed. Additional work is needed to compare its performance to similar JEMs and, if possible, to exposure assessments generated on a case-by-case basis.
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| 3. |
- Viljur, Mari-Liis, et al.
(författare)
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The effect of natural disturbances on forest biodiversity : an ecological synthesis
- 2022
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Ingår i: Biological Reviews. - : Wiley. - 1464-7931 .- 1469-185X. ; 97:5, s. 1930-1947
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Tidskriftsartikel (refereegranskat)abstract
- Disturbances alter biodiversity via their specific characteristics, including severity and extent in the landscape, which act at different temporal and spatial scales. Biodiversity response to disturbance also depends on the community characteristics and habitat requirements of species. Untangling the mechanistic interplay of these factors has guided disturbance ecology for decades, generating mixed scientific evidence of biodiversity responses to disturbance. Understanding the impact of natural disturbances on biodiversity is increasingly important due to human-induced changes in natural disturbance regimes. In many areas, major natural forest disturbances, such as wildfires, windstorms, and insect outbreaks, are becoming more frequent, intense, severe, and widespread due to climate change and land-use change. Conversely, the suppression of natural disturbances threatens disturbance-dependent biota. Using a meta-analytic approach, we analysed a global data set (with most sampling concentrated in temperate and boreal secondary forests) of species assemblages of 26 taxonomic groups, including plants, animals, and fungi collected from forests affected by wildfires, windstorms, and insect outbreaks. The overall effect of natural disturbances on α-diversity did not differ significantly from zero, but some taxonomic groups responded positively to disturbance, while others tended to respond negatively. Disturbance was beneficial for taxonomic groups preferring conditions associated with open canopies (e.g. hymenopterans and hoverflies), whereas ground-dwelling groups and/or groups typically associated with shady conditions (e.g. epigeic lichens and mycorrhizal fungi) were more likely to be negatively impacted by disturbance. Across all taxonomic groups, the highest α-diversity in disturbed forest patches occurred under moderate disturbance severity, i.e. with approximately 55% of trees killed by disturbance. We further extended our meta-analysis by applying a unified diversity concept based on Hill numbers to estimate α-diversity changes in different taxonomic groups across a gradient of disturbance severity measured at the stand scale and incorporating other disturbance features. We found that disturbance severity negatively affected diversity for Hill number q = 0 but not for q = 1 and q = 2, indicating that diversity–disturbance relationships are shaped by species relative abundances. Our synthesis of α-diversity was extended by a synthesis of disturbance-induced change in species assemblages, and revealed that disturbance changes the β-diversity of multiple taxonomic groups, including some groups that were not affected at the α-diversity level (birds and woody plants). Finally, we used mixed rarefaction/extrapolation to estimate biodiversity change as a function of the proportion of forests that were disturbed, i.e. the disturbance extent measured at the landscape scale. The comparison of intact and naturally disturbed forests revealed that both types of forests provide habitat for unique species assemblages, whereas species diversity in the mixture of disturbed and undisturbed forests peaked at intermediate values of disturbance extent in the simulated landscape. Hence, the relationship between α-diversity and disturbance severity in disturbed forest stands was strikingly similar to the relationship between species richness and disturbance extent in a landscape consisting of both disturbed and undisturbed forest habitats. This result suggests that both moderate disturbance severity and moderate disturbance extent support the highest levels of biodiversity in contemporary forest landscapes.
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