| 1. |
- Householder, John Ethan, et al.
(författare)
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One sixth of Amazonian tree diversity is dependent on river floodplains
- 2024
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Ingår i: NATURE ECOLOGY & EVOLUTION. - 2397-334X.
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Tidskriftsartikel (refereegranskat)abstract
- Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.
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| 2. |
- Luize, Bruno Garcia, et al.
(författare)
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Geography and ecology shape the phylogenetic composition of Amazonian tree communities
- 2024
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Ingår i: JOURNAL OF BIOGEOGRAPHY. - 0305-0270 .- 1365-2699.
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Tidskriftsartikel (refereegranskat)abstract
- Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and v & aacute;rzea forest types, the phylogenetic composition varies by geographic region, but the igap & oacute; and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R-2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R-2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions.
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| 3. |
- ter Steege, Hans, et al.
(författare)
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Mapping density, diversity and species-richness of the Amazon tree flora
- 2023
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Ingår i: COMMUNICATIONS BIOLOGY. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution. A study mapping the tree species richness in Amazonian forests shows that soil type exerts a strong effect on species richness, probably caused by the areas of these forest types. Cumulative water deficit, tree density and temperature seasonality affect species richness at a regional scale.
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| 4. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 6. |
- Bruneau, Anne, et al.
(författare)
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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
- 2024
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Ingår i: PhytoKeys. - Sofia : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 240, s. 1-552
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Tidskriftsartikel (refereegranskat)abstract
- Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Cera-tonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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| 7. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 8. |
- Crous, P. W., et al.
(författare)
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Fungal Planet description sheets : 785-867
- 2018
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Ingår i: Persoonia. - : Naturalis Biodiversity Center. - 0031-5850 .- 1878-9080. ; 41, s. 238-417
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Tidskriftsartikel (refereegranskat)abstract
- Novel species of fungi described in this study include those from various countries as follows: Angola, Gnomoniopsis angolensis and Pseudopithomyces angolensis on unknown host plants. Australia, Dothiora cotymbiae on Corymbia citriodora, Neoeucasphaeria eucalypti (incl. Neoeucasphaeria gen. nov.) on Eucalyptus sp., Fumagopsis stellae on Eucalyptus sp., Fusculina eucalyptorum (incl. Fusculinaceae fam. nov.) on Eucalyptus socialis, Harknessia cotymbiicola on Corymbia maculata, Neocelosporium eucalypti (incl. Neocelosporium gen. nov., Neocelosporiaceae fam. nov. and Neocelosporiales ord. nov.) on Eucalyptus cyanophylla, Neophaeomoniella corymbiae on Corymbia citriodora, Neophaeomoniefia eucalyptigena on Eucalyptus pilularis, Pseudoplagiostoma corymbiicola on Corymbia citriodora, Teratosphaeria gracilis on Eucalyptus gracilis, Zasmidium corymbiae on Corymbia citriodora. Brazil, Calonectria hemileiae on pustules of Hemileia vastatrix formed on leaves of Coffea arabica, Calvatia caatinguensis on soil, Cercospora solani-betacei on Solanum betaceum, Clathrus natalensis on soil, Diaporthe poincianellae on Poincianella pyramidalis, Geastrum piquiriunense on soil, Geosmithia carolliae on wing of Carollia perspicillata, Henningsia resupinata on wood, Penicillium guaibinense from soil, Periconia caespitosa from leaf litter, Pseudocercospora styracina on Styrax sp., Simplicillium filiforme as endophyte from Citrullus lanatus, Thozetella pindobacuensis on leaf litter, Xenosonderhenia coussapoae on Coussapoa floccosa. Canary Islands (Spain), Orbilia amarilla on Euphorbia canariensis, Cape Verde Islands, Xylodon jacobaeus on Eucalyptus camaldulensis. Chile, Colletotrichum arboricola on Fuchsia magellanica. Costa Rica, Lasiosphaeria miniovina on tree branch. Ecuador, Ganoderma chocoense on tree trunk. France, Neofitzroyomyces nerii (incl. Neofitzroyomyces gen. nov.) on Nerium oleander. Ghana, Castanediella tereticornis on Eucalyptus tereticornis, Falcocladium africanum on Eucalyptus brassiana, Rachicladosporium corymbiae on Corymbia citriodora. Hungary, Entoloma silvae-frondosae in Carpinus betulus-Pinus sylvestris mixed forest. Iran, Pseudopyricularia persiana on Cyperus sp. Italy, lnocybe roseascens on soil in mixed forest. Laos, Ophiocordyceps houaynhangensis on Coleoptera larva. Malaysia, Monilochaetes melastomae on Melastoma sp. Mexico, Absidia terrestris from soil. Netherlands, Acaulium pannemaniae, Conioscypha boutwelliae, Fusicolla septimanifiniscientiae, Gibellulopsis simonii, Lasionectria hilhorstii, Lectera nordwiniana, Leptodiscella rintelii, Parasarocladium debruynii and Sarocladium dejongiae (incl. Sarocladiaceae fam. nov.) from soil. New Zealand, Gnomoniopsis rosae on Rosa sp. and Neodevriesia metrosideri on Metrosideros sp. Puerto Rico, Neodevriesia coccolobae on Coccoloba uvifera, Neodevriesia tabebuiae and Alfaria tabebuiae on Tabebuia chrysantha. Russia, Amanita paludosa on bogged soil in mixed deciduous forest, Entoloma tiliae in forest of Tilia x europaea, Kwoniella endophytica on Pyrus communis. South Africa, Coniella diospyri on Diospyros mespiliformis, Neomelanconiella combreti (incl. Neomelanconiellaceae fam. nov. and Neomelanconiella gen. nov.) on Combretum sp., Polyphialoseptoria natalensis on unidentified plant host, Pseudorobillarda bolusanthi on Bolusanthus speciosus, Thelonectria pelargonii on Pelargonium sp. Spain, Vermiculariopsiella lauracearum and Anungitopsis lauri on Laurus novocanariensis, Geosmithia xerotolerans from a darkened wall of a house, Pseudopenidiella gallaica on leaf litter. Thailand, Corynespora thailandica on wood, Lareunionomyces loeiensis on leaf litter, Neocochlearomyces chromolaenae (incl. Neocochlearomyces gen. nov.) on Chromolaena odorata, Neomyrmecridium septatum (incl. Neomyrmecridium gen. nov.), Pararamichloridium caricicola on Carex sp., Xenodactylaria thailandica (incl. Xenodactylariaceae fam. nov. and Xenodactylaria gen. nov.), Neomyrmecridium asiaticum and Cymostachys thailandica from unidentified vine. USA, Carolinigaster bonitoi (incl. Carolinigaster gen. nov.) from soil, Penicillium fortuitum from house dust, Phaeotheca shathenatiana (incl. Phaeothecaceae fam. nov.) from twig and cone litter, Pythium wohlseniorum from stream water, Superstratomyces tardicrescens from human eye, Talaromyces iowaense from office air. Vietnam, Fistulinella olivaceoalba on soil. Morphological and culture characteristics along with DNA barcodes are provided.
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| 9. |
- Scaramboni, Caroline, et al.
(författare)
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Characterization of cross-continental PM2.5: Insights into emissions and chemical composition
- 2024
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Ingår i: Atmospheric research. - 0169-8095 .- 1873-2895. ; , s. 107423-107423
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric fine particulate matter (PM2.5) is a critical indicator of air quality, with substantial implications for human health. Understanding the emission sources and chemical composition of PM2.5 is crucial for mitigating possible adverse health effects. This study spans five diverse cities on three continents from north and south hemisphere: Stockholm (Sweden), Kyoto (Japan), Limeira, Ribeirão Preto, and Cáceres (Brazil). Our objective was to assess PM2.5 chemical composition and regional and long-range transport influences to identify the main sources of particulate air pollution at these cities during the winter/dry seasons. All studied cities but Kyoto exhibited PM2.5 levels above World Health Organization (WHO) guidelines, with the Brazilian cities experiencing the highest fine particle pollution levels, implying increased adverse health risks. We observed significant variations in concentrations of polycyclic aromatic compounds (PACs), monosaccharide anhydrides (MAs), and inorganic elements. Limeira exhibited the highest levels of total PACs (median level of 12.4 ng m−3), while Cáceres displayed high variability of PACs, most likely due to episodic regional wildfire events. MA concentrations were significantly higher in Limeira and Ribeirão Preto and together with elevated levels of retene and potassium (K) they suggested a substantial influence of biomass burning. Backward air mass trajectory analysis suggested widespread Amazon and Savanna wildfires along with local fires as main contributors for these sites. All source identification approaches highlighted differences among the cities, with Stockholm and Kyoto showing influence of sources related to traffic emissions, waste burning, and long-range transport, and Brazilian cities traffic, industrial, biogenic, and more evident biomass burning. This cross-continental study provides valuable insights into PM2.5 composition and emission sources, emphasizing the impact of different emissions on air quality. Our findings underscore the importance of local strategies to mitigate air pollution and protect public health, especially in regions where PM2.5 levels consistently exceed recommended guidelines.
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| 10. |
- Colomé, Núria, et al.
(författare)
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Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
- 2022
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Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 251
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Tidskriftsartikel (refereegranskat)abstract
- Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
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| 11. |
- Poorter, Lourens, et al.
(författare)
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Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
- 2019
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Ingår i: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 3:6, s. 928-934
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Tidskriftsartikel (refereegranskat)abstract
- Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.
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| 12. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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Ingår i: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Tidskriftsartikel (refereegranskat)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 13. |
- Bernal, Ximena E., et al.
(författare)
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Empowering Latina scientists
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 363:6429, s. 825-826
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 14. |
- Dominguez, Mev, et al.
(författare)
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Characterization of germline mutations of MLH1 and MSH2 in unrelated south American suspected Lynch syndrome individuals
- 2011
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Ingår i: Familial Cancer. - : Springer Science and Business Media LLC. - 1389-9600 .- 1573-7292. ; 10:4, s. 641-647
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Tidskriftsartikel (refereegranskat)abstract
- Lynch syndrome (LS) is an autosomal dominant syndrome that predisposes individuals to development of cancers early in life. These cancers are mainly the following: colorectal, endometrial, ovarian, small intestine, stomach and urinary tract cancers. LS is caused by germline mutations in DNA mismatch repair genes (MMR), mostly MLH1 and MSH2, which are responsible for more than 85% of known germline mutations. To search for germline mutations in MLH1 and MSH2 genes in 123 unrelated South American suspected LS patients (Bethesda or Amsterdam Criteria) DNA was obtained from peripheral blood, and PCR was performed followed by direct sequencing in both directions of all exons and intron-exon junctions regions of the MLH1 and MSH2 genes. MLH1 or MSH2 pathogenic mutations were found in 28.45% (34/123) of the individuals, where 25/57 (43.85%) fulfilled Amsterdam I, II and 9/66 (13.63%) the Bethesda criteria. The mutations found in both genes were as follows: nonsense (35.3%), frameshift (26.47%), splicing (23.52%), and missense (9%). Thirteen alterations (35.14%) were described for the first time. The data reported in this study add new information about MLH1 and MSH2 gene mutations and contribute to better characterize LS in Brazil, Uruguay and Argentina. The high rate of novel mutations demonstrates the importance of defining MLH1 and MSH2 mutations in distinct LS populations.
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| 15. |
- Poorter, Lourens, et al.
(författare)
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Functional recovery of secondary tropical forests
- 2021
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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 (PNAS). - 0027-8424 .- 1091-6490. ; 118:49, s. e2003405118-e2003405118
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Tidskriftsartikel (refereegranskat)abstract
- One-third of all Neotropical forests are secondary forests that regrow naturally after agricultural use through secondary succession. We need to understand better how and why succession varies across environmental gradients and broad geographic scales. Here, we analyze functional recovery using community data on seven plant characteristics (traits) of 1,016 forest plots from 30 chronosequence sites across the Neotropics. By analyzing communities in terms of their traits, we enhance understanding of the mechanisms of succession, assess ecosystem recovery, and use these insights to propose successful forest restoration strategies. Wet and dry forests diverged markedly for several traits that increase growth rate in wet forests but come at the expense of reduced drought tolerance, delay, or avoidance, which is important in seasonally dry forests. Dry and wet forests showed different successional pathways for several traits. In dry forests, species turnover is driven by drought tolerance traits that are important early in succession and in wet forests by shade tolerance traits that are important later in succession. In both forests, deciduous and compound-leaved trees decreased with forest age, probably because microclimatic conditions became less hot and dry. Our results suggest that climatic water availability drives functional recovery by influencing the start and trajectory of succession, resulting in a convergence of community trait values with forest age when vegetation cover builds up. Within plots, the range in functional trait values increased with age. Based on the observed successional trait changes, we indicate the consequences for carbon and nutrient cycling and propose an ecologically sound strategy to improve forest restoration success.
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| 16. |
- Almeida, Rafael M., et al.
(författare)
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High Primary Production Contrasts with Intense Carbon Emission in a Eutrophic Tropical Reservoir
- 2016
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies from temperate lakes indicate that eutrophic systems tend to emit less carbon dioxide (Co-2) and bury more organic carbon (OC) than oligotrophic ones, rendering them CO2 sinks in some cases. However, the scarcity of data from tropical systems is critical for a complete understanding of the interplay between eutrophication and aquatic carbon (C) fluxes in warm waters. We test the hypothesis that a warm eutrophic system is a source of both CO2 and CH4 to the atmosphere, and that atmospheric emissions are larger than the burial of OC in sediments. This hypothesis was based on the following assumptions: (i) OC mineralization rates are high in warm water systems, so that water column CO2 production overrides the high C uptake by primary producers, and (ii) increasing trophic status creates favorable conditions for CH4 production. We measured water-air and sediment-water CO2 fluxes, CH4 diffusion, ebullition and oxidation, net ecosystem production (NEP) and sediment OC burial during the dry season in a eutrophic reservoir in the semiarid northeastern Brazil. The reservoir was stratified during daytime and mixed during nighttime. In spite of the high rates of primary production (4858 +/- 934 mg C m(-2) d(-1)), net heterotrophy was prevalent due to high ecosystem respiration (5209 +/- 992 mg C m(-2) d(-1)). Consequently, the reservoir was a source of atmospheric CO2 (518 +/- 182 mg C m(-2) d(-1)). In addition, the reservoir was a source of ebullitive (17 +/- 10 mg C m(-2) d(-1)) and diffusive CH4 (11 +/- 6 mg C m(-2) d(-1)). OC sedimentation was high (1162 mg C m(-2) d(-1)), but our results suggest that the majority of it is mineralized to CO2 (722 +/- 182 mg C m(-2) d(-1)) rather than buried as OC (440 mg C m(-2) d(-1)). Although temporally resolved data would render our findings more conclusive, our results suggest that despite being a primary production and OC burial hotspot, the tropical eutrophic system studied here was a stronger CO2 and CH4 source than a C sink, mainly because of high rates of OC mineralization in the water column and sediments.
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| 17. |
- de Oliveira Galvão, Marcos Felipe, et al.
(författare)
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DNA damage signaling and genotoxic effects induced by complex mixtures of PAHs generated by biomass burning air particulate matter in human lung cells
- 2019
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Ingår i: Toxicology Letters. - : Elsevier BV. - 0378-4274 .- 1879-3169. ; 314:SI, s. S132-S133
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Tidskriftsartikel (refereegranskat)abstract
- Most research concerning the effects of air pollutants on human health focuses on urban centers and on the role of vehicular and industrial emissions as major sources of pollution. However, approximately 3 billion people world-wide are exposed to air pollution from biomass burning [1]. Herein, particulate matter (PM) emitted from artisanal cashew nut roasting, an important economic and social activity worldwide [2,3], was investigated. This study focused on: i) chemical characterization of polycyclic aromatic hydrocarbons (PAHs) and their oxy-PAH derivatives; ii) time-dependent activation of DNA damage signaling and genotoxic effects, and iii) differential expression of genes involved in xenobiotic metabolism, inflammation, cell cycle arrest and DNA repair using A549 lung cells. Among the PAHs, chrysene, benzo[a]pyrene (B[a]P), benzo[b]fluoranthene, and benz[a]anthracene showed the highest concentrations (7.8-10 ng/m3), while among oxy-PAHs, benzanthrone and 9,10-anthraquinone were the most abundant. Testing of PM extracts was based on B[a]P equivalent doses (B[a]Peq). IC50 values for viability was 5.7 and 3.0 nM B[a]Peq at 24 h and 48 h, respectively. Based on this, all other experiments were conducted at doses up to 2 nM B[a]Peq. At these low doses, we observed a dose-dependent activation of DNA damage signaling (phosphorylation of Chk1) and genotoxicity (double strand breaks). In comparison, effects of B[a]P alone was observed at micromolar range. To our knowledge, no other study has demonstrated an activation of pChk1, a biomarker used to estimate the carcinogenic potency of PAHs in vitro [4], in lung cells exposed to biomass burning extracts. Persistent increased gene expression of several important stress response mediators of xenobiotic metabolism (CYP1A1, CYP1B1), inflammation (IL-8, TNF-α), cell cycle arrest (CDKN1A), and DNA repair (DDB2) was also identified. In conclusion, our data show high potency of biomass burning PM to induce cellular stress including genotoxicity, and more potently so when compared to B[a]P alone. Our study provides new data that will help elucidate the mechanism of lung cancer development associated with biomass burning. In addition, the results of this study support the establishment of new guidelines for human health protection in regions strongly impacted by biomass burning.
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| 18. |
- de Oliveira Galvão, Marcos Felipe, et al.
(författare)
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Genotoxicity and DNA damage signaling in response to complex mixtures of PAHs in biomass burning particulate matter from cashew nut roasting
- 2020
-
Ingår i: Environmental Pollution. - : Elsevier BV. - 0269-7491 .- 1873-6424. ; 256
-
Tidskriftsartikel (refereegranskat)abstract
- Approximately 3 billion people world-wide are exposed to air pollution from biomass burning. Herein, particulate matter(PM) emitted from artisanal cashew nut roasting, an important economic activity worldwide, was investigated. This study focused on: i) chemical characterization of polycyclic aromatic hydrocarbons (PAHs) and oxygenated (oxy-) PAHs; ii) intracellular levels of reactive oxygen species (ROS); iii) genotoxic effects and time- and dose-dependent activation of DNA damage signaling, and iv) differential expression of genes involved in xenobiotic metabolism, inflammation, cell cycle arrest and DNA repair, using A549 lung cells. Among the PAHs, chrysene, benzo[a]pyrene (B[a]P), benzo[b]fluoranthene, and benz[a]anthracene showed the highest concentrations (7.8–10 ng/m3), while benzanthrone and 9,10-anthraquinone were the most abundant oxy-PAHs. Testing of PM extracts was based on B[a]P equivalent doses (B[a]Peq). IC50 values for viability were 5.7 and 3.0 nM B[a]Peq at 24 h and 48 h, respectively. At these low doses, we observed a time- and dose-dependent increase in intracellular levels of ROS, genotoxicity (DNA strand breaks) and DNA damage signaling (phosphorylation of the protein checkpoint kinase 1 – Chk1). In comparison, effects of B[a]P alone was observed at micromolar range. To our knowledge, no previous study has demonstrated an activation of pChk1, a biomarker used to estimate the carcinogenic potency of PAHs in vitro, in lung cells exposed to cashew nut roasting extracts. Sustained induction of expression of several important stress response mediators of xenobiotic metabolism (CYP1A1, CYP1B1), ROS and pro-inflammatory response (IL-8, TNF-α, IL-2,COX2), and DNA damage response (CDKN1A and DDB2) was also identified. In conclusion, our data show high potency of cashew nut roasting PM to induce cellular stress including genotoxicity, and more potently when compared to B[a]P alone. Our study provides new data that will help elucidate the toxic effects of low-levels of PAH mixtures from air PM generated by cashew nut roasting.
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| 19. |
- Pinotti, Felipe Eduardo, et al.
(författare)
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Use of a Non-Crosslinked Collagen Membrane During Guided Bone Regeneration Does Not Interfere With the Bone Regenerative Capacity of the Periosteum
- 2018
-
Ingår i: Journal of oral and maxillofacial surgery (Print). - : Elsevier. - 0278-2391 .- 1531-5053. ; 76:11
-
Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: To assess whether the use of a non-crosslinked porcine collagen type I and III bi-layered membrane inter-positioned between the periosteum and a bone defect would interfere with the bone regenerative capacity of the periosteum. MATERIALS AND METHODS: Sixty rats, each with 1 critical-size calvarial defect (CSD; diameter, 5 mm) in the parietal bone, were randomly allocated to 1 of 3 equal-size groups after CSD creation: 1) the periosteum was excised and the flap was repositioned without interposition of a membrane (no-periosteum [NP] group); 2) the flap including the periosteum was repositioned (periosteum [P] group); and 3) a non-crosslinked collagen membrane was inter-positioned between the flap, including the periosteum, and the bone defect (membrane [M] group). Micro-computed tomography, qualitative histology, immunohistochemistry, and reverse transcription real-time quantitative polymerase chain reaction were performed at 3, 7, 15, and 30 days postoperatively. RESULTS: A markedly increased radiographic residual defect length was observed in the NP group compared with the P group at 30 days. The NP group also presented a smaller radiographic bone fill area than the P group at 15 and 30 days and then the M group at 30 days. The P and M groups exhibited considerably greater expression of bone morphogenetic protein-2 and osteocalcin than the NP group at 7 days; expression of transforming growth factor-beta1 was considerably greater in the NP group at 15 days. Further, the P group presented considerably higher gene expression levels of Runx2 and Jagged1 at 7 days and of alkaline phosphatase at 3 and 15 days compared with the M and NP groups. CONCLUSION: Interposition of this specific non-crosslinked collagen membrane between the periosteum and the bone defect during guided bone regeneration interferes only slightly, if at all, with the bone regenerative capacity of the periosteum.
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| 20. |
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| 21. |
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| 22. |
- Bitencourt de Oliveira, Felipe, 1982, et al.
(författare)
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Assessing Metal Use and Scarcity Impacts of Vehicle Gliders
- 2024
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Ingår i: Circular Economy and Sustainability. - 2730-597X .- 2730-5988. ; In Press
-
Tidskriftsartikel (refereegranskat)abstract
- This study assesses the metal composition of two vehicle gliders, configured with different equipment levels and evaluates the risk of short and long-term metal scarcity. Entropy analysis is also used for insights on secondary metal recovery strategies. Fifty-five metals are evaluated, with gold, copper, bismuth, lead, molybdenum, and certain rare-earth metals (REMs) subject to the largest supply risks. Differences in equipment levels significantly impact the short-term supply risk for specific metals. Entertainment and communications equipment contain significant amounts of REMs, whereas mirrors and electrical infrastructure contain considerable shares of gold, silver and copper. Some metals are concentrated in a few components while some are dispersed across thousands, impacting recycling opportunities. The broad metal demand of the gliders underscores the automotive industry's role in supply risks for its own manufacturing needs and other societal domains. This emphasizes the significance of comprehensively evaluating metal requirements beyond powertrains for informed resource management.
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| 23. |
- Bitencourt de Oliveira, Felipe, 1982, et al.
(författare)
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Exploring automotive supplier data in life cycle assessment – Precision versus workload
- 2022
-
Ingår i: Transportation Research Part D: Transport and Environment. - : Elsevier BV. - 1361-9209. ; 105
-
Tidskriftsartikel (refereegranskat)abstract
- The International Material Data System (IMDS) can be used as data source for life cycle assessments (LCAs) in the automotive industry. The level of data aggregation and degree of completeness affect precision of LCA results and required workload. This paper assesses this trade-off. Life cycle impact assessment scores for an engine, modelled as detailed as possible, were compared to results for seven simplified modelling options. The study concludes that: (1) employing IMDS data with lower resolution reduced the workload marginally; (2) cutting-off materials below 1 wt-% greatly decreased workload while maintaining reasonable precision; (3) decreasing the number of substances representing each material largely affected scores for most impact categories except a few, including the climate change category, while (4) excluding complementary data for manufacturing significantly impacted greenhouse gas emissions. Since modelling choices affect the impact categories differently, aligning choices with the purpose of the study and available workload is paramount.
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| 24. |
- Bitencourt de Oliveira, Felipe, 1982
(författare)
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Leveraging supplier material data to inform LCA modelling and resource assessment in the automotive industry
- 2023
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis investigates the application of supplier material composition data from the automotive industry's International Material Data System (IMDS) to inform sustainability assessments. A methodology is developed to systematically extract and process IMDS data for use in life cycle assessment (LCA) modelling. The implications of using IMDS data at varying levels of aggregation and completeness on the accuracy of LCA results are quantitatively evaluated through an LCA case study on an automotive engine. Compared to a highly detailed reference model, simplified modelling options reduced workload but compromised accuracy, especially for impacts related to resource use. A material mass cut-off of one percent of weight maintained reasonable precision while significantly decreasing effort. Decreasing the number of substances representing each material largely affected scores for most impact categories except a few, including the climate change category. Excluding manufacturing data notably impacted greenhouse gas emissions. Additionally, this thesis performs an in-depth compositional analysis focusing on metals present in two vehicle "gliders" (the car excluding the powertrain) with distinct equipment levels. Over 50 metals are documented, and their contributions to short and long-term metal scarcity examined. Gold, copper, bismuth, lead, molybdenum, and certain rare-earth metals (REMs) face substantial supply risks. The analysis of metals across the gliders subsystems and components indicates that equipment levels significantly affect short-term supply risks for some metals. Entropy analysis is also used to gather insights into the effectiveness of different substitution and secondary metal recovery strategies revealing significant challenges for the recovery and substitution of certain metals like copper and rare earths. Overall, this thesis demonstrates the potential of leveraging IMDS data to expedite sustainability assessments in the automotive industry. However, balancing model complexity and precision remains essential. The extensive reliance of vehicles on diverse metals, even excluding the powertrain, highlights the sector's substantial resource dependence. This underscores the need for sustainable metal management in automotive manufacturing.
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| 25. |
- de Oliveira, Felipe, 1984-, et al.
(författare)
-
Autoimmunity detection via proximity assays
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Since autoantibodies are recognized as valuable biomarkers for clinical diagnostics and prognostics in autoimmune diseases such as Stiff Person Syndrome (SPS) and Type 1 diabetes, detection of such markers at improved sensitivity and specificity could be of significant interest. In addition, as proximity assays have been shown to offer highly sensitive and specific detection of multiple proteins, the technique could be expanded to applications for autoimmunity detection. In the present study, we have applied the newly developed proximity ligation assay with rolling circle amplification (PLARCA), and proximity extension assay (PEA) for the detection of GADA, autoantibodies specific for glutamic acid decarboxylase 65 (GAD65). Through the use of oligonucleotide conjugated autoantigen GAD65 and anti-human antibodies, as proximity probes, we were able to apply these proximity assays to detect GADA in a set of SPS patient samples. In summary, we have applied and established both PLARCA and PEA, as a proof of concept, for the use of the specific and sensitive autoimmune detection.
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| 26. |
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| 27. |
- de Oliveira, Felipe Marques Souza, et al.
(författare)
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Detection of post-translational modifications using solid-phase proximity ligation assay.
- 2018
-
Ingår i: New biotechnology. - : Elsevier BV. - 1876-4347 .- 1871-6784. ; 45:October, s. 51-59
-
Tidskriftsartikel (refereegranskat)abstract
- Post-translational modifications (PTMs) regulate protein activities to help orchestrate and fine-tune cellular processes. Dysregulation of PTMs is often related with disorders and malignancies, and may serve as a precise biomarker of disease. Developing sensitive tools to measure and monitor low-abundant PTMs in tissue lysates or serum will be instrumental for opening up new PTM-based diagnostic avenues. Here, we investigate the use of solid-phase proximity ligation assay (SP-PLA) for detection of different PTMs. The assay depends on the recognition of the target protein molecule and its modification by three affinity binders. Using antibodies and lectins, we applied the method for detection of glycosylated CD44 and E-Cadherin, and phosphorylated p53 and EGFR. The assay was found to have superior dynamic range and limit of detection compared to standard ELISAs. In summary, we have established the use of SP-PLA as an appropriate method for sensitive detection of PTMs in lysates and sera, which may provide a basis for future PTM-based diagnostic and prognostic biomarkers.
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| 28. |
- de Oliveira, Felipe Marques Souza
(författare)
-
Development and Application of Proximity Assays for Proteome Analysis in Medicine
- 2018
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Along with proteins, a myriad of different molecular biomarkers, such as post-translational modifications and autoantibodies, could be used in an attempt to improve disease detection and progression. In this thesis, I build on several iterations of the proximity ligation assay to develop and apply new adaptable methods to facilitate detection of proteins, autoantibodies and post-translational modifications.In paper I, we present an adaptation of the solid-phase proximity ligation assay (SP-PLA) for the detection of post-translational modification of proteins (PTMs). The assay was adapted for the detection of two of the most commons PTMs present in proteins, glycosylation and phosphorylation, offering the encouraging prospect of using detection of PTMs in a diagnostic or prognostic capacity. In paper II, we developed a variant of the proximity ligation assay using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer, termed PLARCA. With a detection limit considerably lower than ELISA, PLARCA detected femtomolar levels of these proteins in patient samples.In paper III, we aim to compare detection values of samples collected from earlobe capillary, venous plasma, as well as capillary plasma stored in dried plasma spots (DPS) assessed with a 92-plex inflammation panel using multiplex proximity extension assay (PEA). Despite the high variability in protein measurements between the three sample sources, we were able to conclude that earlobe capillary sampling is a suitable less invasive alternative, to venipuncture.In paper IV, we describe the application of PLARCA and proximity extension assay (PEA) for the detection of GAD65 autoantibodies (GADA). Thus, offering highly sensitive and specific autoimmunity detection.
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| 29. |
- Dominguez, Mev, et al.
(författare)
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Evaluation of MLH1 I219V Polymorphism in Unrelated South American Individuals Suspected of Having Lynch Syndrome.
- 2012
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Ingår i: Anticancer research. - 1791-7530. ; 32:10, s. 4347-4351
-
Tidskriftsartikel (refereegranskat)abstract
- Some single-nucleotide polymorphisms are associated with higher risk of colorectal cancer development and are suggested to explain part of the genetic contribution to Lynch syndrome. Aim: To evaluate the mutL homolog 1 (MLH1) I219V polymorphism in 124 unrelated South American individuals suspected of having Lynch syndrome, based on frequency, association with pathogenic MLH1 and mutS homolog 2 (MSH2) mutation and clinical features.
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| 30. |
- Dotto, Guilherme Luiz, et al.
(författare)
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Adsorption of rare earth elements (Ce3+, La3+, and Nd3+) and recovery from phosphogypsum leachate using a novel ZSM-5 zeolite
- 2024
-
Ingår i: Colloids and Surfaces A. - : Elsevier. - 0927-7757 .- 1873-4359. ; 698
-
Tidskriftsartikel (refereegranskat)abstract
- ZSM-5 zeolite is a multifunctional material highly efficient for adsorbing ions. Our ZSM-5 was synthesized by employing a nucleating gel as a structure-directing agent, followed by homogenization and hydrothermal treatment. The as-prepared ZSM-5 was physicochemically characterized to assess its properties. Next, the as-prepared zeolite was employed as an adsorbent to remove rare earth elements, REEs from synthetic solutions and real phosphogypsum leachate under batch mode operation. As expected, the ZSM-5 adsorbent was discovered to be highly microporous with abundant surface functionalities, which could positively impact REE adsorption. The adsorption data indicated a high affinity between ZSM-5 and all three REEs with rapid kinetics and high adsorption capacities. The modeling study suggested that the adsorption kinetic data were well fitted by Avrami-fractional order, and Liu described the equilibrium data. The maximum adsorption capacity for Ce3+, La3+, and Nd3+ were 99.42 mg g−1, 96.43 mg g−1, 118.10 mg g−1, respectively. Further, the thermodynamic analysis revealed that the interaction between ZSM-5 and Ce3+, La3+, and Nd3+ was favorable, spontaneous, and endothermic. The efficiency of ZSM-5 adsorbent was also studied in recovering several REEs from leachate of phosphogypsum wastes, and the data results proved its potency to do so. The findings reported in this work support the idea that ZSM-5 can be successfully used as an adsorbent to recover REEs from synthetic and real samples.
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| 31. |
- Ebai, Tonge, et al.
(författare)
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Analytically Sensitive Protein Detection in Microtiter Plates by Proximity Ligation with Rolling Circle Amplification
- 2017
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Ingår i: Clinical Chemistry. - : Oxford University Press (OUP). - 0009-9147 .- 1530-8561. ; 63:9, s. 1497-1505
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Detecting proteins at low concentrations in plasma is crucial for early diagnosis. Current techniques in clinical routine, such as sandwich ELISA, provide sensitive protein detection because of a dependence on target recognition by pairs of antibodies, but detection of still lower protein concentrations is often called for. Proximity ligation assay with rolling circle amplification (PLARCA) is a modified proximity ligation assay (PLA) for analytically specific and sensitive protein detection via binding of target proteins by 3 antibodies, and signal amplification via rolling circle amplification (RCA) in microtiter wells, easily adapted to instrumentation in use in hospitals.METHODS: Proteins captured by immobilized antibodies were detected using a pair of oligonucleotide-conjugated antibodies. Upon target recognition, these PLA probes guided oligonucleotide ligation, followed by amplification via RCA of circular DNA strands that formed in the reaction. The RCA products were detected by horseradish peroxidase-labeled oligonucleotides to generate colorimetric reaction products with readout in an absorbance microplate reader.RESULTS: We compared detection of interleukin (IL)-4, IL-6, IL-8, p53, and growth differentiation factor-15 by PLARCA and conventional sandwich ELISA or immuno RCA. PLARCA detected lower concentrations of proteins and exhibited a broader dynamic range compared ELISA and iRCA using the same antibodies. IL-4 and IL-6 were detected in clinical samples at femtomolar concentrations, considerably lower than for ELISA.CONCLUSIONS: PLARCA offers detection of lower protein levels and increased dynamic ranges compared to ELISA. The PLARCA procedure may be adapted to routine instrumentation available in hospitals and research laboratories.
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| 32. |
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| 33. |
- Felipe de Oliveira Galvão, Marcos, et al.
(författare)
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Determination of whole mixture-based potency factors for cancer risk assessment of complex environmental mixtures by in vitro testing of standard reference materials
- 2022
-
Ingår i: Environment International. - : Elsevier BV. - 0160-4120 .- 1873-6750. ; 63, s. 98-98
-
Tidskriftsartikel (refereegranskat)abstract
- Whole mixture-based testing using in vitro new approach methodologies (NAMs) has been suggested to facilitate the hazard and risk assessment of complex environmental mixtures. Previous studies have shown that phosphorylation of DNA damage signaling proteins checkpoint kinase 1 (pChk1) and histone 2AX (γH2AX) are sensitive markers that can be used for estimating carcinogenicity potencies in vitro. Here, and with the aim to better validate the applicability, in vitro-based Mixture Potency Factors (MPFs) of Standard Reference Materials (SRMs) from environmental polycyclic aromatic hydrocarbon (PAH)-containing mixtures were determined and compared to published mutagenicity and tumorigenicity data. Also, genotoxicity was assessed by a flow cytometry-based micronucleus (MN) assay which showed that only benzo[a]pyrene (B[a]P) and coal tar SRM (SRM1597a) caused dose-dependent increases of MN formation, while extracts of diesel particulate matter (SRM1650b), diesel particulate extract (SRM1975), and urban dust (SRM1649b) did not. However, a dose-dependent activation of DNA damage signaling was observed for all PAHs and SRMs. The results demonstrated that all SRMs were more potent than B[a]P, at B[a]P-equivalent concentrations, to induce pChk1 and γH2AX, and that western blot was more sensitive than the In-Cell Western assay in detecting their activation in response to these complex mixtures. Relative MPFs, based on dose–response modelling of pChk1 and γH2AX, ranged 113 – 5270 for the SRMs, indicating several orders of magnitude higher genotoxic potential than B[a]P. Moreover, these MPFs were in good agreement with potency values based on published data from Salmonella mutagenicity and in vivo carcinogenicity studies. In conclusion, these comparisons further validate the feasibility of applying in vitro NAMs, such as whole-mixture based MPFs, in cancer risk assessment of complex mixtures.
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| 34. |
- Koos, Björn, et al.
(författare)
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Proximity-dependent initiation of hybridization chain reaction
- 2015
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
-
Tidskriftsartikel (refereegranskat)abstract
- Sensitive detection of protein interactions and post-translational modifications of native proteins is a challenge for research and diagnostic purposes. A method for this, which could be used in point-of-care devices and high-throughput screening, should be reliable, cost effective and robust. To achieve this, here we design a method (proxHCR) that combines the need for proximal binding with hybridization chain reaction (HCR) for signal amplification. When two oligonucleotide hairpins conjugated to antibodies bind in close proximity, they can be activated to reveal an initiator sequence. This starts a chain reaction of hybridization events between a pair of fluorophore-labelled oligonucleotide hairpins, generating a fluorescent product. In conclusion, we show the applicability of the proxHCR method for the detection of protein interactions and posttranslational modifications in microscopy and flow cytometry. As no enzymes are needed, proxHCR may be an inexpensive and robust alternative to proximity ligation assays.
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| 35. |
- Kwon, Hyuk Sung, et al.
(författare)
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Early increment of soluble triggering receptor expressed on myeloid cells 2 in plasma might be a predictor of poor outcome after ischemic stroke
- 2020
-
Ingår i: Journal of clinical neuroscience. - : ELSEVIER SCI LTD. - 0967-5868 .- 1532-2653. ; 73, s. 215-218
-
Tidskriftsartikel (refereegranskat)abstract
- Soluble triggering receptor expressed on myeloid cells 2 (sTREM2) is derived from cleavage of TREM2, which is expressed on the cell surface of microlgia and other tissue-specific macrophages. In the present study, the changes in the sTREM2 levels after ischemic stroke (IS) and their association with clinical outcomes were evaluated. A total of 43 patients diagnosed with non-cardioembolic IS between June 2011 and May 2014 were consecutively included in this study. Patients treated with intravenous thrombolysis or intra-arterial thrombectomy were excluded. Plasma samples were collected three times (days 1, 7, and 90) after ictus. The sTREM2 level was measured in the samples using the highly sensitive solid-phase proximity ligation assay (SP-PLA). Among the 43 subjects, higher initial NIH stroke scale (NIHSS) score (P = 0.005), early increment of sTREM2 (P < 0.001), and late decrement of sTREM2 (P = 0.002), were more common in patients with poor outcome. Based on multivariate analysis, initial NIHSS score (P = 0.015) and early increment of sTREM2 (P = 0.032) were independently associated with poor outcome. The results from the present study indicate that increment of sTREM2 level at the early phase was a predictor of poor outcome. Serial follow-up of sTREM2 may aid prognosis after stroke.
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| 36. |
- Lavers Westin, Alexandra, 1986, et al.
(författare)
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Combining material flow analysis with life cycle assessment to identify environmental hotspots of urban consumption
- 2019
-
Ingår i: Journal of Cleaner Production. - : Elsevier. - 0959-6526 .- 1879-1786. ; 226, s. 526-539
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding the global environmental impacts of local consumption is an area of growing interest among policymakers and consumers. By knowing what products comprise urban consumption “hotspots,” municipalities and consumers alike could take deliberate actions to target and discourage consumption of high-impact products. In this paper, a new method for identifying environmental hotspots of consumption is presented. The main methodological advances are the following: i) material flow analysis of urban areas and life cycle assessment are combined; ii) a 16-year time-series of urban consumption data is used for selection of the most suitable representative products and for trend analysis; iii) representative products are selected systematically from consumption data of 1000 product types; iv) representative products are scaled up to represent consumption of the product groups; v) hotspots are identified by simultaneously evaluating six environmental impacts - acidification, climate change, eutrophication (marine and freshwater), photochemical ozone formation, and resource use; vi) for the case study, hotspots are connected to the city's profiles. The method was applied to the Swedish cities Stockholm, Gothenburg and Malmo and to Sweden in total. Electronics is a hotspot for all the studied areas and all the studied impacts and should be a prioritized product group for action. Fuel is a hotspot shared by all the areas while vehicles is a hotspot in Gothenburg. Meat is a nationwide hotspot, but not for the cities investigated. Gothenburg and Stockholm could collaborate to find effective measures for their common hotspot machinery. Thus, the method can be used to identify hotspots and find which product types could be part of national versus local programs.
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| 37. |
- Law, Chi Yan, 1990, et al.
(författare)
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Polarized Light from Massive Protoclusters (POLIMAP). I. Dissecting the Role of Magnetic Fields in the Massive Infrared Dark Cloud G28.37+0.07
- 2024
-
Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 967:2
-
Tidskriftsartikel (refereegranskat)abstract
- Magnetic fields may play a crucial role in setting the initial conditions of massive star and star cluster formation. To investigate this, we report SOFIA-HAWC+ 214 μm observations of polarized thermal dust emission and high-resolution GBT-Argus C18O(1-0) observations toward the massive Infrared Dark Cloud (IRDC) G28.37+0.07. Considering the local dispersion of B-field orientations, we produce a map of the B-field strength of the IRDC, which exhibits values between ∼0.03 and 1 mG based on a refined Davis-Chandrasekhar-Fermi method proposed by Skalidis & Tassis. Comparing to a map of inferred density, the IRDC exhibits a B-n relation with a power-law index of 0.51 ± 0.02, which is consistent with a scenario of magnetically regulated anisotropic collapse. Consideration of the mass-to-flux ratio map indicates that magnetic fields are dynamically important in most regions of the IRDC. A virial analysis of a sample of massive, dense cores in the IRDC, including evaluation of magnetic and kinetic internal and surface terms, indicates consistency with virial equilibrium, sub-Alfvénic conditions, and a dominant role for B-fields in regulating collapse. A clear alignment of magnetic field morphology with the direction of the steepest column density gradient is also detected. However, there is no preferred orientation of protostellar outflow directions with the B-field. Overall, these results indicate that magnetic fields play a crucial role in regulating massive star and star cluster formation, and therefore they need to be accounted for in theoretical models of these processes.
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| 38. |
- Lim, Hwanmi, et al.
(författare)
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Polycyclic aromatic compounds in particulate matter and indoor dust at preschools in Stockholm, Sweden : Occurrence, sources and genotoxic potential in vitro
- 2021
-
Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 755
-
Tidskriftsartikel (refereegranskat)abstract
- Children spend a significant amount of their day in preschool; thus, environmental quality at preschools may have an impact on children’s health. In the present study, we analyzed polycyclic aromatic compounds (PACs), including PAHs, alkylated PAHs and oxygenated PAHs (OPAHs), in indoor and outdoor air particulate matter (PM10) and indoor dust at preschools in Stockholm, Sweden. There were significant correlations between PAC levels in outdoor and indoor PM10, with in general higher PAC levels outdoors. Fluoranthene and pyrene were detected at highest levels in all sample types, although phenanthrene and methylated phenanthrene derivatives also were found at high levels in indoor dust. In addition, the highly carcinogenic PAHs 7H-benzo[c]fluorene, 7,12-dimethylbenz[a]anthracene, benz[j]aceanthrylene, and dibenzo[a,l]pyrene were detected in some samples. Benzanthrone was the most prevalent OPAH in PM10 samples and 9,10-anthraquinone in indoor dust. Based on diagnostic ratios and Positive Matrix Factorization we identified vehicle emission and biomass burning as important PAC sources for all samples analyzed. However, poor correlation between PAC levels in indoor PM10 and indoor dust suggested additional sources for the latter. Measuring activation of DNA damage signaling in human cells exposed to organic extracts of the samples indicated substantial genotoxic potential of outdoor PM10 and indoor dust. Determination of benzo[a]pyrene equivalents demonstrated that the highly potent PAHs benz[j]aceanthrylene and dibenz[a,h]anthracene contributed more than 20% to the total carcinogenic potency of the samples. We conclude that PAC levels at Stockholm preschools are relatively low but that outdoor air quality may impact on the indoor environment.
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| 39. |
- Lopes, Melina Savioli, et al.
(författare)
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Reduction in the amount of sulfur in waste oil using reactive molecular distillation
- 2021
-
Ingår i: Petroleum Science and Technology. - : Informa UK Limited. - 1091-6466 .- 1532-2459. ; 39:13-14, s. 471-483
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Tidskriftsartikel (refereegranskat)abstract
- Petroleum, contains proportions of contaminants such as sulfur, nitrogen, oxygen, and metals, such as nickel, iron, copper, sodium, and vanadium. Particularly, contaminants containing sulfur cause problems during handling, transportation, and the use of the their derivatives. This work had the goal of cracking the heavy crude oil molecules by reacting these molecules with tetralin and simultaneously promoting the separation of the low-mass and high-mass fractions, aiming to obtain a product of high value. The process to be studied is Reactive Molecular Distillation (RMD). It was developed at the laboratory LDPS-FEQ-UNCAMP, in order to perform the molecular distillation with chemical reaction using tetralin, which, at high temperatures (210 to 330 °C) and high vacuum (10-3 mmHg), suffers the cracking of molecules, providing protons that help the disaggregation of asphaltene; consequently, the residues will suffer physicochemical alterations and, therefore, the reduction in the amount of sulfur in the oil waste. The sample to be studied is a petroleum waste, named JU 560 °C. This oil is a residue from the vaccuum column of an oil distillery. With the processing of petroleum waste JU 560 °C with 5% of tetralin, a reduction of 49% in the sulfur content of the original sample was achieved.
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| 40. |
- Marnissi, Boutheina, et al.
(författare)
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Accurate detection of Newcastle disease virus using proximity-dependent DNA aptamer ligation assays
- 2021
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Ingår i: FEBS Open Bio. - : John Wiley & Sons. - 2211-5463. ; 11:4, s. 1122-1131
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Tidskriftsartikel (refereegranskat)abstract
- Detecting viral antigens at low concentrations in field samples can be crucial for early veterinary diagnostics. Proximity ligation assays (PLAs) in both solution and solid-phase formats are widely used for high-performance protein detection in medical research. However, the affinity reagents used, which are mainly poly- and monoclonal antibodies, play an important role in the performance of PLAs. Here, we have established the first homogeneous and solid-phase proximity-dependent DNA aptamer ligation assays for rapid and accurate detection of Newcastle disease virus (NDV). NDV is detected by a pair of extended DNA aptamers that, upon binding in proximity to proteins on the envelope of the virus, are joined by enzymatic ligation to form a unique amplicon that can be sensitively detected using real-time PCR. The sensitivity, specificity, and reproducibility of the assays were validated using 40 farm samples. The results demonstrated that the developed homogeneous and solid-phase PLAs, which use NDV-selective DNA aptamers, are more sensitive than the sandwich enzymatic-linked aptamer assay (ELAA), and have a comparable sensitivity to real-time reverse transcription PCR (rRT-PCR) as the gold standard detection method. In addition, the solid-phase PLA was shown to have a greater dynamic range with improved lower limit of detection, upper- and lower limit of quantification, and minimal detectable dose as compared with those of ELAA and rRT-PCR. The specificity of PLA is shown to be concordant with rRT-PCR.
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| 41. |
- Nordelöf, Anders, 1975, et al.
(författare)
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Methodological Approaches to End-Of-Life Modelling in Life Cycle Assessments of Lithium-Ion Batteries
- 2019
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Ingår i: Batteries. - : MDPI AG. - 2313-0105. ; 5:51, s. 1-15
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Forskningsöversikt (refereegranskat)abstract
- This study presents a review of how the end-of-life (EOL) stage is modelled in life cycle assessment (LCA) studies of lithium-ion batteries (LIBs). Twenty-five peer-reviewed journal and conference papers that consider the whole LIB life cycle and describe their EOL modelling approach sufficiently were analyzed. The studies were categorized based on two archetypal EOL modelling approaches in LCA: The cutoff (no material recovery, possibly secondary material input) and EOL recycling (material recovery, only primary material input) approaches. It was found that 19 of the studies followed the EOL recycling approach and 6 the cutoff approach. In addition, almost a third of the studies deviated from the expected setup of the two methods by including both material recovery and secondary material input. Such hybrid approaches may lead to double counting of recycling benefits by both including secondary input (as in the cutoff approach) and substituting primary materials (as in the EOL recycling approach). If the archetypal EOL modelling approaches are not followed, it is imperative that the modelling choices are well-documented and motivated to avoid double counting that leads to over- or underestimations of the environmental impacts of LIBs. Also, 21 studies model hydrometallurgical treatment, and 17 completely omit waste collection.
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| 42. |
- Sadiktsis, Ioannis, 1982-, et al.
(författare)
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A yearlong monitoring campaign of polycyclic aromatic compounds and other air pollutants at three sites in Sweden : Source identification, in vitro toxicity and human health risk assessment
- 2023
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Ingår i: Chemosphere. - 0045-6535 .- 1879-1298. ; 332
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Tidskriftsartikel (refereegranskat)abstract
- Air pollution is a complex mixture of gases and particulate matter (PM) with local and non-local emission sources, resulting in spatiotemporal variability in concentrations and composition, and thus associated health risks. To study this in the greater Stockholm area, a yearlong monitoring campaign with in situ measurements of PM10, PM1, black carbon, NOx, O3, and PM10-sampling was performed. The locations included an Urban and a Rural background site and a Highway site. Chemical analysis of PM10 was performed to quantify monthly levels of polycyclic aromatic compounds (PACs), which together with other air pollution data were used for source apportionment and health risk assessment. Organic extracts from PM10 were tested for oxidative potential in human bronchial epithelial cells. Strong seasonal patterns were found for most air pollutants including PACs, with higher levels during the winter months than summer e.g., highest levels of PM10 were detected in March at the Highway site (33.2 μg/m3) and lowest in May at the Rural site (3.6 μg/m3). In general, air pollutant levels at the sites were in the order Highway > Urban > Rural. Multivariate analysis identified several polar PACs, including 6H-Benzo[cd]pyren-6-one, as possible discriminatory markers for these sites. The main sources of particulate pollution for all sites were vehicle exhaust and biomass burning emissions, although diesel exhaust was an important source at the Highway site. In vitro results agreed with air pollutant levels, with higher oxidative potential from the winter samples. Estimated lung cancer cases were in the order PM10 > NO2 > PACs for all sites, and with less evident seasonal differences than in vitro results. In conclusion, our study presents novel seasonal data for many PACs together with air pollutants more traditionally included in air quality monitoring. Moreover, seasonal differences in air pollutant levels correlated with differences in toxicity in vitro.
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| 43. |
- Shen, Qiujin, et al.
(författare)
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A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer
- 2019
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Ingår i: EBioMedicine. - : Elsevier. - 2352-3964. ; 44, s. 322-333
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Tidskriftsartikel (refereegranskat)abstract
- Background: Gastric cancer (GC) is the third leading cause of cancer death. Early detection is a key factor to reduce its mortality. Methods: We retrospectively collected pre- and postoperative serum samples as well as tumour tissues and adjacent normal tissues from 100 GC patients. Serum samples from non-cancerous patients were served as controls (n = 50). A high-throughput protein detection technology, multiplex proximity extension assays (PEA), was applied to measure levels of over 300 proteins. Alteration of each protein was analysed by univariate analysis. Elastic-net logistic regression was performed to select serum proteins into the diagnostic model. Findings: We identified 19 serum proteins (CEACAM5, CA9, MSLN, CCL20, SCF, TGF-alpha, MMP-1, MMP-10, IGF-1, CDCPI, PPIA, DDAH-1, HMOX-1, FLI1, IL-7, ZBTB-17, APBB1IP, KAZALD-1, and ADAMTS-15) that together distinguish GC cases from controls with a diagnostic sensitivity of 93%, specificity of 100%, and area under receiver operating characteristic curve (AUC) of 0.99 (95% CI: 0.98-1). Moreover, the 19-serum protein signature pro-vided an increased diagnostic capacity in patients at TNMI-II stage (sensitivity 89%, specificity 100%, AUC 0.99) and in patients with high miaosatellite instability (MSI) (91%. 98%, and 0.99) compared to individual proteins. These promising results will inspire a large-scale independent cohort study to be pursued for validating the proposed protein signature. Interpretation: Based on targeted proteomics and elastic-net logistic regression, we identified a 19-serum protein signature which could contribute to clinical GC diagnosis, especially for patients at early stage and those with high MSI. (C) 2019 The Authors. Published by Elsevier B.V.
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| 44. |
- Siart, Benjamin, et al.
(författare)
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Measurements ofinflammation protein biomarkers in venous plasma, earlobe capillary plasma andin capillary plasma stored on filter paper
- 2017
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Ingår i: Cytokine. - 1043-4666 .- 1096-0023.
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Multiplex panels for protein biomarkers are increasingly used to analyze blood samples in various fields of clinical research. However, they are rarely used in studies performed outside of a clinical setting. This may in part be due to the relative invasiveness of drawing blood from the vein and because of problems associated with the separation and transport of plasma. Samples collected from the earlobe would be less invasive and could be collected more conveniently. Transportation and storage of such samples could be made easier by blotting plasma on filter paper as dried plasma spots (DPS). The objective of this study was to compare values of multiple protein biomarkers for inflammation measured from three different sources (1) venous plasma, (2) plasma derived from capillary blood from the earlobe and (3) from capillary plasma stored as DPS. Samples from twelve male individuals were assessed with a panel of 92 inflammation related proteins using multiplex proximity extension assay technology. Correlations between the three sample types varied greatly between analytes. In general, a high correlation was observed between capillary plasma and DPS, with 33 analytes showing a correlation value of ρ > 0.8 in the two sample types. At this level of correlation (ρ > 0.8) 14 analytes correlated between venous and capillary plasma in contrast to only six analytes in the comparison of venous blood with DPS. We conclude that collecting samples from the earlobe is a feasible and less invasive alternative to venipuncture, but that the comparability with measures obtained from venous samples varies greatly between proteins.
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| 45. |
- Siart, Benjamin, et al.
(författare)
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Protein measurements in venous plasma, earlobe capillary plasma and in plasma stored on filter paper
- 2019
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Ingår i: Analytical Biochemistry. - : ACADEMIC PRESS INC ELSEVIER SCIENCE. - 0003-2697 .- 1096-0309. ; 566, s. 146-150
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Tidskriftsartikel (refereegranskat)abstract
- In this study, levels of inflammatory protein biomarkers in venous plasma, plasma derived from capillary blood from the earlobe, and capillary plasma stored as dried plasma spots (DPS) were compared. Samples from 12 male individuals were assessed with a panel of 92 inflammation-related proteins using multiplex proximity extension assay. Correlations between sample types varied greatly between analytes. A high correlation of rho > 0.8 was observed between capillary plasma and DPS for 32 analytes. At this level of correlation, 13 analytes correlated between venous and capillary plasma and 5 analytes in the comparison of venous blood with DPS.
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| 46. |
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