| 1. |
- In ’t Veld, Sjors G.J.G., et al.
(författare)
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Detection and localization of early- and late-stage cancers using platelet RNA
- 2022
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Ingår i: Cancer Cell. - : Elsevier. - 1535-6108 .- 1878-3686. ; 40:9, s. 999-1009.e6
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Tidskriftsartikel (refereegranskat)abstract
- Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I–IV cancer patients and in half of 352 stage I–III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening.
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| 2. |
- Medema, M. H., et al.
(författare)
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Minimum Information about a Biosynthetic Gene cluster
- 2015
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Ingår i: Nature Chemical Biology. - : Springer Science and Business Media LLC. - 1552-4450 .- 1552-4469. ; 11:9, s. 625-631
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Forskningsöversikt (refereegranskat)abstract
- A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.
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| 3. |
- Downing, Andrea S., et al.
(författare)
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Coupled human and natural system dynamics as key to the sustainability of Lake Victoria's ecosystem services
- 2014
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Ingår i: Ecology and Society. - 1708-3087. ; 19:4, s. 31-
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Tidskriftsartikel (refereegranskat)abstract
- East Africa's Lake Victoria provides resources and services to millions of people on the lake's shores and abroad. In particular, the lake's fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria's system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake's social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks' vulnerability to exploitation but reduce society's vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.
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| 4. |
- Lewandowska, A. M., et al.
(författare)
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The influence of balanced and imbalanced resource supply on biodiversity-functioning relationship across ecosystems
- 2016
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Ingår i: Philosophical Transactions of the Royal Society B-Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 371:1694
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Tidskriftsartikel (refereegranskat)abstract
- Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity ecosystern functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common pattems and differences in biodiversity functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity.
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| 5. |
- Moss, B, et al.
(författare)
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The determination of ecological status in shallow lakes - a tested system (ECOFRAME) for implementation of the European Water Framework Directive
- 2003
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Ingår i: Aquatic Conservation: Marine and Freshwater Ecosystems. - : Wiley. - 1052-7613. ; 13:6, s. 507-549
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Tidskriftsartikel (refereegranskat)abstract
- 1. The European Water Framework Directive requires the determination of ecological status in European fresh and saline waters. This is to be through the establishment of a typology of surface water bodies, the determination of reference (high status) conditions in each element (ecotype) of the typology and of lower grades of status (good, moderate, poor and bad) for each ecotype. It then requires classification of the status of the water bodies and their restoration to at least 'good status' in a specified period. 2. Though there are many methods for assessing water quality, none has the scope of that defined in the Directive. The provisions of the Directive require a wide range of variables to be measured and give only general guidance as to how systems of classification should be established. This raises issues of comparability across States and of the costs of making the determinations. 3. Using expert workshops and subsequent field testing, a practicable pan-European typology and classification system has been developed for shallow lakes, which can easily be extended to all lakes. It is parsimonious in its choice of determinands, but based on current limnological understanding and therefore as cost-effective as possible. 4. A core typology is described, which can be expanded easily in particular States to meet local conditions. The core includes 48 ecotypes across the entire European climate gradient and incorporates climate, lake area, geology of the catchment and conductivity. 5. The classification system is founded on a liberal interpretation of Annexes in the Directive and uses variables that are inexpensive to measure and ecologically relevant. The need for taxonomic expertise is minimized. 6. The scheme has been through eight iterations, two of which were tested in the field on tranches of 66 lakes. The final version, Version 8, is offered for operational testing and further refinement by statutory authorities.
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| 6. |
- Frenken, T., et al.
(författare)
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Integrating chytrid fungal parasites into plankton ecology: research gaps and needs
- 2017
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912. ; 19:10, s. 3802-3822
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Forskningsöversikt (refereegranskat)abstract
- Chytridiomycota, often referred to as chytrids, can be virulent parasites with the potential to inflict mass mortalities on hosts, causing e.g. changes in phytoplankton size distributions and succession, and the delay or suppression of bloom events. Molecular environmental surveys have revealed an unexpectedly large diversity of chytrids across a wide range of aquatic ecosystems worldwide. As a result, scientific interest towards fungal parasites of phytoplankton has been gaining momentum in the past few years. Yet, we still know little about the ecology of chytrids, their life cycles, phylogeny, host specificity and range. Information on the contribution of chytrids to trophic interactions, as well as co-evolutionary feedbacks of fungal parasitism on host populations is also limited. This paper synthesizes ideas stressing the multifaceted biological relevance of phytoplankton chytridiomycosis, resulting from discussions among an international team of chytrid researchers. It presents our view on the most pressing research needs for promoting the integration of chytrid fungi into aquatic ecology.
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| 7. |
- Noges, P, et al.
(författare)
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Factors controlling hydrochemical and trophic state variables in 86 shallow lakes in Europe
- 2003
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Ingår i: Hydrobiologia. - 1573-5117 .- 0018-8158. ; 506:1-3, s. 51-58
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Konferensbidrag (refereegranskat)abstract
- In order to disentangle the causes of variations in water chemistry among European shallow lakes, we performed standardised sampling programs in 86 lakes along a latitudinal gradient from southern Spain to northern Sweden. Lakes with an area of 0.1 to 27000 ha and mean depth of 0.4-5.6 m located in low to high altitudes were investigated within the EC project ECOFRAME 1-4 times during June-October 2000-2001. Several variables like conductivity, alkalinity, abundance of submerged plants, concentrations of suspended solids, total nitrogen and phosphorus were latitude-dependent decreasing from south to north. Secchi depth, concentrations of total nitrogen, total phosphorus, suspended solids, and chlorophyll a correlated strongly with the presumed quality classes of the lakes. We came to the conclusion that the variability of shallow lakes in Europe is still mostly dependent on natural differences. Variables connected to lake morphometry, seasonality, basin geology and climate explained altogether nearly half of the total variability of lakes. The trophic state factor, describing mostly the human influence on lakes, was the strongest single factor responsible for nearly a quarter of the total variability of the studied European lakes.
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| 8. |
- Stephen, D, et al.
(författare)
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Continental-scale patterns of nutrient and fish effects on shallow lakes: introduction to a pan-European mesocosm experiment
- 2004
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 49:12, s. 1517-1524
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Tidskriftsartikel (refereegranskat)abstract
- 1. Shallow lake ecosystems are normally dominated by submerged and emergent plants. Biological stabilising mechanisms help preserve this dominance. The systems may switch to dominance by phytoplankton, however, with loss of submerged plants. This process usually takes place against a background of increasing nutrient loadings but also requires additional switch mechanisms, which damage the plants or interfere with their stabilising mechanisms. 2. The extent to which the details or even major features of this general model may change with geographical location are not clear. Manipulation of the fish community (biomanipulation) has often been used to clear the water of algae and restore the aquatic plants in northerly locations, but it is again not clear whether this is equally appropriate at lower latitudes. 3. Eleven parallel experiments (collectively the International Mesocosm Experiment, IME) were carried out in six lakes in Finland, Sweden, England, the Netherlands and Spain in 1998 and 1999 to investigate the between-year and large-scale spatial variation in relationships between nutrient loading and zooplanktivorous fish on submerged plant and plankton communities in shallow lakes. 4. Comparability of experiments in different locations was achieved to a high degree. Cross-laboratory comparisons of chemical analyses revealed some systematic differences between laboratories. These are unlikely to lead to major misinterpretations. 5. Nutrient addition, overall, had its greatest effect on water chemistry then substantial effects on phytoplankton and zooplankton. Fish addition had its major effect on zooplankton and did not systematically change the water chemistry. There was no trend in the relative importance of fish effects with latitude, but nutrient addition affected more variables with decreasing latitude. 6. The relative importance of top-down and bottom-up influences on the plankton differed in different locations and between years at the same location. The outcome of the experiments in different years was more predictable with decreasing latitude and this was attributed to more variable weather at higher latitudes that created more variable starting conditions for the experiments.
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| 9. |
- Zweegman, Sonja, et al.
(författare)
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Melphalan, prednisone, and lenalidomide versus melphalan, prednisone, and thalidomide in untreated multiple myeloma.
- 2016
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Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 127:9, s. 1109-1116
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Tidskriftsartikel (refereegranskat)abstract
- The combination of melphalan, prednisone and thalidomide (MPT) is considered standard therapy for newly diagnosed patients with multiple myeloma (NDMM) who are ineligible for stem-cell transplantation. Long term treatment with thalidomide is hampered by neurotoxicity. Melphalan, prednisone and lenalidomide, followed by lenalidomide maintenance therapy showed promising results, without severe neuropathy emerging. We randomly assigned 668 NDMM patients, ineligible for stem-cell transplantation, between nine 4-weekly cycles of MPT followed by thalidomide maintenance until disease progression or unacceptable toxicity (MPT-T) and the same MP regimen with thalidomide being replaced by lenalidomide (MPR-R). This multicenter, open-label, randomised phase 3 trial was undertaken by HOVON and the NMSG. The primary endpoint was progression-free survival (PFS). The accrual for the study was completed in October 19, 2012. 318 patients were randomly assigned to receive MPT-T and 319 MPR-R. After a median follow up of 36 months PFS with MPT-T was 20 months (95% CI 18-23 months) versus 23 months (95% CI 19-27 months) with MPR-R (HR 0.87 [0.72-1.04], p=0.12). Response rates were similar, with ≥VGPR 47% and 45% respectively. Hematological toxicity was more pronounced with MPR-R, especially grade 3 and 4 neutropenia: 64 versus 27%. Neuropathy ≥ grade 3 was significantly higher in the MPT-T arm; 16% versus 2% in MPR-R, resulting in a significant shorter duration of maintenance therapy (5 versus 17 months in MPR-R), irrespective of age. MPR-R has no advantage over MPT-T concerning efficacy. The toxicity profile differed with clinically significant neuropathy during thalidomide maintenance versus myelosuppression with MPR.
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| 10. |
- Moss, B, et al.
(författare)
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Continental-scale patterns of nutrient and fish effects on shallow lakes: synthesis of a pan-European mesocosm experiment
- 2004
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 49:12, s. 1633-1649
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Tidskriftsartikel (refereegranskat)abstract
- 1. Results are analysed from 11 experiments in which effects of fish addition and nutrient loading on shallow lakes were studied in mesocosms. The experiments, five in 1998, six in 1999, were carried out in six lakes, distributed from Finland to southern Spain, according to a standard protocol. 2. Effects of the treatments on 29 standard chemical, phytoplankton and zooplankton variables are examined to assess the relative importance of bottom-up (nutrient enrichment) and top-down (fish predation) effects. For each year, the experiments in different locations are treated as replicates in a meta-analysis. Results of individual experiments are then compared in terms of the patterns of significant influences of nutrient addition and fish predation with these overall results (the baseline), and between years in the same location. 3. The overall meta-analysis gave consistent results across the 2 years, with nutrient loading influencing all of the chemical variables, and on average 31% of primary producer and 39% of zooplankton variables. In contrast, fish influenced none of the chemical variables, 11% of the primary producer and 44% of the zooplankton variables. Nutrient effects on the system were thus about three times greater than fish effects, although fish effects were not inconsiderable. 4. The relative importance of nutrients and fish in individual experiments often differed between years at the same location and effects deviated to varying degrees from the baseline. These deviations were treated as measures of consistency (predictability) of conclusions in repeat experiments. Consistency increased southwards and this is interpreted as a consequence of more variable annual weather northwards. 5. The influence of nutrient loading was greater southwards and this was probably manifested through naturally greater annual macrophyte abundance in warmer locations in consequence of the longer plant growing-season. There was no trend in the relative importance of fish effects with latitude but this may partly be an artefact of the simple fish community used. These findings suggest that nutrient control should be a greater priority than biomanipulation in the restoration of eutrophicated shallow lakes in warm temperate regions. 6. Starting conditions affected the outcome of experiments. High initial concentrations of total phosphorus and planktonic chlorophyll a concentration (created by local conditions prior to the experiment) led to de-emphasis of the importance of nutrient loading in the experiment.
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