| 1. |
- Abarenkov, Kessy, et al.
(författare)
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The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered
- 2024
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Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 52:D1, s. D791-D797
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Tidskriftsartikel (refereegranskat)abstract
- UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into similar to 2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms. Graphical Abstract
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| 2. |
- Ahlborg, Helene, 1980, et al.
(författare)
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Theorizing power in political ecology: the where of power in resource governance projects
- 2018
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Ingår i: Journal of Political Ecology. - : University of Arizona. - 1073-0451. ; 25:1, s. 381-401
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Tidskriftsartikel (refereegranskat)abstract
- Power and politics have been central topics from the early days of Political Ecology. There are different and sometimes conflicting conceptualizations of power in this field that portray power alternatively as a resource, personal attribute or relation. The aim of this article is to contribute to theorizations of power by probing contesting views regarding its role in societal change and by presenting a specific conceptualization of power, one which draws on both political ecology and sociotechnical approaches in science and technology studies. We review how power has been conceptualized in the political ecology field and identify three trends that shaped the current discussion. We then develop our conceptual discussion and explicitly ask where power emerges in processes of resource governance projects. We identify four locations that we illustrate empirically through an example of rural electrification in Tanzania that aimed at catalyzing social and economic development by providing renewable energy-based electricity services to people. Our analysis supports the argument that power is relational and productive, and it draws on science and technology studies to bring to the fore the critical role of non-human elements in co-constitution of society—technology—nature. This leads us to see power exercise as having contradictory and ambiguous effects. We conclude that by exploring the tension between human agency and constitutive power, we keep the politics alive throughout the analysis and are able to show why intentional choices and actions really matter for how resource governance projects play out in everyday life.
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| 3. |
- Andersson-Sköld, Yvonne, et al.
(författare)
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A framework for assessing urban greenery's effects and valuing its ecosystem services
- 2018
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Ingår i: Journal of Environmental Management. - : Academic Press. - 0301-4797 .- 1095-8630. ; 205, s. 274-285
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Tidskriftsartikel (refereegranskat)abstract
- Ongoing urban exploitation is increasing pressure to transform urban green spaces, while there is increasing awareness that greenery provides a range of important benefits to city residents. In efforts to help resolve associated problems we have developed a framework for integrated assessments of ecosystem service (ES) benefits and values provided by urban greenery, based on the ecosystem service cascade model. The aim is to provide a method for assessing the contribution to, and valuing, multiple ES provided by urban greenery that can be readily applied in routine planning processes. The framework is unique as it recognizes that an urban greenery comprises several components and functions that can contribute to multiple ecosystem services in one or more ways via different functional traits (e.g. foliage characteristics) for which readily measured indicators have been identified. The framework consists of five steps including compilation of an inventory of indicator; application of effectivity factors to rate indicators' effectiveness; estimation of effects; estimation of benefits for each ES; estimation of the total ES value of the ecosystem. The framework was applied to assess ecosystem services provided by trees, shrubs, herbs, birds, and bees, in green areas spanning an urban gradient in Gothenburg, Sweden. Estimates of perceived values of ecosystem services were obtained from interviews with the public and workshop activities with civil servants. The framework is systematic and transparent at all stages and appears to have potential utility in the existing spatial planning processes.
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| 4. |
- Asker, Noomi, 1968, et al.
(författare)
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A gene to organism approach-assessing the impact of environmental pollution in eelpout (Zoarces viviparus) females and larvae
- 2015
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Ingår i: Environmental Toxicology and Chemistry. - : Wiley. - 0730-7268 .- 1552-8618. ; 34:7, s. 1511-1523
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Tidskriftsartikel (refereegranskat)abstract
- A broad biomarker approach was applied to study the effects of marine pollution along the Swedish west coast using the teleost eelpout (Zoarces viviparus) as the sentinel species. Measurements were performed on different biological levels, from the molecular to the organismal, including measurements of messenger RNA (mRNA), proteins, cellular and tissue changes, and reproductive success. Results revealed that eelpout captured in Stenungsund had significantly higher hepatic ethoxyresorufin O-deethylase activity, high levels of both cytochrome P4501A and diablo homolog mRNA, and high prevalence of dead larvae and nuclear damage in erythrocytes. Eelpout collected in Göteborg harbor displayed extensive macrovesicular steatosis, whereby the majority of hepatocytes were affected throughout the liver, which could indicate an effect on lipid metabolism. Results also indicate that eelpouts collected at polluted sites might have an affected immune system, with lower mRNA expression of genes involved in the innate immune system and a higher number of lymphocytes. Biomarker assessment also was performed on livers dissected from unborn eelpout larvae collected from the ovary of the females. No significant differences were noted, which might indicate that the larvae to some extent are protected from effects of environmental pollutants. In conclusion, usage of the selected set of biological markers, covering responses from gene to organism, has demonstrated site-specific biomarker patterns that provided a broad and comprehensive picture of the impact of environmental stressors.
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| 5. |
- Asker, Noomi, 1968, et al.
(författare)
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Biomarker responses in eelpouts from four coastal areas in Sweden, Denmark and Germany
- 2016
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Ingår i: Marine Environmental Research. - : Elsevier BV. - 0141-1136 .- 1879-0291. ; 120, s. 32-43
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Tidskriftsartikel (refereegranskat)abstract
- To increase our understanding of possible chemical impacts on coastal fish populations in the Baltic Sea, Kattegat and Skagerrak, the viviparous eelpout (Zoarces viviparus) was used as sentinel species in two major sampling campaigns (spring and autumn) in 16 different coastal sites. Condition factor (CF), liver somatic index (LSI), gonad somatic index (GSI) were measured and the activity of the hepatic enzymes ethoxyresorufin-O-deethylase (EROD), glutathione reductase GR), glutathione S-transferase (GST), catalase (CAT) and muscular activity of acetylcholinesterase (AChE) were assessed. PAH metabolites in bile were also analyzed. The most notable finding in the data set was the low EROD activity in eelpouts collected at the relatively polluted region in Germany compared to the other regions, which could be due to an inhibition of the CYP1A-system or to adaptation to chronic exposure of pollutants in this area. Additionally, low AChE activity was noted in the German region in the autumn campaign and low AChE activity detected in the Danish region in the spring campaign. These differences suggest possible season-specific differences in the use and release of AChE-inhibiting chemicals in the Danish and German regions. Clustering of biomarkers on site level indicated a relationship between CF and GSI and suggested that sites with a high CF contained eelpout that put a larger effort into their larvae development. Clustering of the oxidative stress markers GR, GST and CAT on the individual level reflected a possible coordinated regulation of these enzymes. Overall, the results support the importance of taking into account general regional differences and seasonal variation in biomarker activity when monitoring and assessing the effects of pollution. Despite the expected seasonal variation for most of the measured endpoint, several markers (GSI, EROD and CF) vary similarly between all selected sites in both spring and autumn. This suggests that the differences between sites for these endpoints are independent of season.
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| 6. |
- Bernin, Diana, 1979, et al.
(författare)
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Multi-scale characterization of pasta during cooking using microscopy and real-time magnetic resonance imaging
- 2014
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Ingår i: Food Research International. - : Elsevier BV. - 0963-9969 .- 1873-7145. ; 66, s. 132-139
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Tidskriftsartikel (refereegranskat)abstract
- Macroscopic properties of pasta, such as the texture, are formed during cooking by a complex interplay of water and heat with the structuring agents starch and gluten. The impact of the starch-to-gluten ratio on microstructure and water distribution in pasta was analyzed by a multi-scale approach combining magnetic resonance imaging (MRI) and light microscopy. The cooking process and thus the water distribution was monitored non-invasively using 1H MRI in real-time with a temporal resolution of 45s. Our MRI set-up allowed following the water ingress by imaging the reduction of the uncooked core. The water ingress rate was neither dependent on pasta composition nor on the presence of salt in the cooking media (0.7% NaCl). Starch-rich samples showed a more homogeneous water distribution in the gelatinized zone, which was mirrored in a more homogeneous microstructure. In contrast, gluten-rich samples showed both a heterogeneous water distribution and microstructure. Thus, the gluten content affected local water content in the gelatinized zone but not the water ingress. © 2014 Elsevier Ltd.
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| 7. |
- Blanck, Hans, 1950, et al.
(författare)
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A retrospective analysis of contamination and periphyton PICT patterns for the antifoulant irgarol 1051, around a small marina on the Swedish west coast
- 2009
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Ingår i: Marine Pollution Bulletin. - : Elsevier BV. - 0025-326X .- 1879-3363. ; 58, s. 230-237
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Tidskriftsartikel (refereegranskat)abstract
- Irgarol is a triazine photosystem II (PSII) inhibitor that has been used in Sweden as an antifouling ingredient since the 1990s. Early microcosm studies indicated that periphyton was sensitive to irgarol at concentrations regularly found in harbours and marinas. However, field studies of irgarol effects on the Swedish west coast in 1994, using the pollution-induced community tolerance (PICT) approach, failed to detect any effects of the toxicant in the field. A PICT study involves sampling of replicate communities in a gradient of contamination, and a comparison of their community tolerance levels, with an increase being an indication that sensitive species have been eliminated and replaced by more tolerant ones. Typically, short-term assays are used to quantify the community tolerance levels. Later PICT studies in the same area over a 10 year period demonstrate that irgarol tolerance levels have increased, although the contamination pattern has been stable. Our results support the hypothesis that that the PICT potential was low initially, due to a small differential sensitivity between the community members, and that a persistent selection pressure was required to favour and enrich irgarol-tolerant species or genotypes. © 2008 Elsevier Ltd. All rights reserved.
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| 8. |
- Brunius, Carl, 1974, et al.
(författare)
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Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data
- 2017
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1460-2059 .- 1367-4811. ; 33:22, s. 3567-3574
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Tidskriftsartikel (refereegranskat)abstract
- Biobanks are important infrastructures for life science research. Optimal sample handling regarding e.g. collection and processing of biological samples is highly complex, with many variables that could alter sample integrity and even more complex when considering multiple study centers or using legacy samples with limited documentation on sample management. Novel means to understand and take into account such variability would enable high-quality research on archived samples. This study investigated whether pre-analytical sample variability could be predicted and reduced by modeling alterations in the plasma metabolome, measured by NMR, as a function of pre-centrifugation conditions (1-36 h pre-centrifugation delay time at 4 A degrees C and 22 A degrees C) in 16 individuals. Pre-centrifugation temperature and delay times were predicted using random forest modeling and performance was validated on independent samples. Alterations in the metabolome were modeled at each temperature using a cluster-based approach, revealing reproducible effects of delay time on energy metabolism intermediates at both temperatures, but more pronounced at 22 A degrees C. Moreover, pre-centrifugation delay at 4 A degrees C resulted in large, specific variability at 3 h, predominantly of lipids. Pre-analytical sample handling error correction resulted in significant improvement of data quality, particularly at 22 A degrees C. This approach offers the possibility to predict pre-centrifugation delay temperature and time in biobanked samples before use in costly downstream applications. Moreover, the results suggest potential to decrease the impact of undesired, delay-induced variability. However, these findings need to be validated in multiple, large sample sets and with analytical techniques covering a wider range of the metabolome, such as LC-MS.
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| 9. |
- Cardilin, Tim, 1989, et al.
(författare)
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Evaluation and translation of combination therapies in oncology – A quantitative approach
- 2018
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Ingår i: European Journal of Pharmacology. - : Elsevier BV. - 0014-2999 .- 1879-0712. ; 834, s. 327-336
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Tidskriftsartikel (refereegranskat)abstract
- Quantitative techniques improve our understanding of tumor volume data for combination treatments and its translation across in vivo models and species. The focus of this paper is therefore on understanding in vivo data, highlighting key structural elements of pharmacodynamic tumor models, and challenging these methods from a translational point of view. We introduce the concept of Tumor Static Exposure (TSE) both for single and multiple combined anticancer agents. The TSE curve separates all possible exposure combinations into regions of tumor growth and tumor shrinkage. Moreover, the degree of curvature of the TSE curve indicates the degree of synergy or antagonism. We demonstrate the TSE approach by two case studies. The first examines a combination of the drugs cetuximab and cisplatin. The TSE curve associated with this combination reveals a weak synergistic effect, suggesting only modest gains from combination therapy. The second case study examines combinations of ionizing radiation and a radiosensitizing agent. In this case, the TSE curve exhibits a pronounced curvature, indicating a strong synergistic effect; tumor regression can be achieved at significantly lower exposure levels and/or radiation doses. Finally, an allometric approach to human dose prediction demonstrates the translational power of the model and the TSE concept. We conclude that the TSE approach, which embodies model-based measures of both drug (potency) and target properties (tumor growth rate), has a strong potential for ranking of compounds, supporting compound selection, and translating preclinical findings to humans.
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| 10. |
- Cardilin, Tim, 1989, et al.
(författare)
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Model-based evaluation of radiation and radiosensitizing agents in oncology
- 2018
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Ingår i: CPT: Pharmacometrics and Systems Pharmacology. - : Wiley. - 2163-8306. ; 7:1, s. 51-58
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Tidskriftsartikel (refereegranskat)abstract
- © 2017 ASCPT. Radiotherapy is one of the major therapy forms in oncology, and combination therapies involving radiation and chemical compounds can yield highly effective tumor eradication. In this paper, we develop a tumor growth inhibition model for combination therapy with radiation and radiosensitizing agents. Moreover, we extend previous analyses of drug combinations by introducing the tumor static exposure (TSE) curve. The TSE curve for radiation and radiosensitizer visualizes exposure combinations sufficient for tumor regression. The model and TSE analysis are then tested on xenograft data. The calibrated model indicates that the highest dose of combination therapy increases the time until tumor regrowth 10-fold. The TSE curve shows that with an average radiosensitizer concentration of 1.0μg/mL the radiation dose can be decreased from 2.2 Gy to 0.7 Gy. Finally, we successfully predict the effect of a clinically relevant treatment schedule, which contributes to validating both the model and the TSE concept.
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