| 1. |
- Ofverholm, Ingegerd, et al.
(författare)
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Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma
- 2024
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Ingår i: Clinical Cancer Research. - : American Association for Cancer Research (AACR). - 1078-0432 .- 1557-3265. ; 30:12, s. 2647-2658
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Tumor classification is a key component in personalized cancer care. For soft-tissue and bone tumors, this classification is currently based primarily on morphology assessment and IHC staining. However, these standard-of-care methods can pose challenges for pathologists. We therefore assessed how whole-genome and whole-transcriptome sequencing (WGTS) impacted tumor classification and clinical management when interpreted together with histomorphology.Experimental Design: We prospectively evaluated WGTS in routine diagnostics of 200 soft-tissue and bone tumors suspicious for malignancy, including DNA and RNA isolation from the tumor, and DNA isolation from a peripheral blood sample or any non-tumor tissue.Results: On the basis of specific genomic alterations or absence of presumed findings, WGTS resulted in reclassification of 7% (13/197) of the histopathologic diagnoses. Four cases were downgraded from low-grade sarcomas to benign lesions, and two cases were reclassified as metastatic malignant melanomas. Fusion genes associated with specific tumor entities were found in 30 samples. For malignant soft-tissue and bone tumors, we identified treatment relevant variants in 15% of cases. Germline pathogenic variants associated with a hereditary cancer syndrome were found in 22 participants (11%).Conclusions: WGTS provides an important dimension of data that aids in the classification of soft-tissue and bone tumors, correcting a significant fraction of clinical diagnoses, and identifies molecular targets relevant for precision medicine. However, genetic findings need to be evaluated in their morphopathologic context, just as germline findings need to be evaluated in the context of patient phenotype and family history.
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| 2. |
- Akselsson, Cecilia, et al.
(författare)
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Weathering rates in Swedish forest soils
- 2019
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 16:22, s. 4429-4450
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Forskningsöversikt (refereegranskat)abstract
- Soil and water acidification was internationally recognised as a severe environmental problem in the late 1960s. The interest in establishing “critical loads” led to a peak in weathering research in the 1980s and 1990s, since base cation weathering is the long-term counterbalance to acidification pressure. Assessments of weathering rates and associated uncertainties have recently become an area of renewed research interest, this time due to demand for forest residues to provide renewable bioenergy. Increased demand for forest fuels increases the risk of depleting the soils of base cations produced in situ by weathering. This is the background to the research programme Quantifying Weathering Rates for Sustainable Forestry (QWARTS), which ran from 2012 to 2019. The programme involved research groups working at different scales, from laboratory experiments to modelling. The aims of this study were to (1) investigate the variation in published weathering rates of base cations from different approaches in Sweden, with consideration of the key uncertainties for each method; (2) assess the robustness of the results in relation to sustainable forestry; and (3) discuss the results in relation to new insights from the QWARTS programme and propose ways to further reduce uncertainties. In the study we found that the variation in estimated weathering rates at single-site level was large, but still most sites could be placed reliably in broader classes of weathering rates. At the regional level, the results from the different approaches were in general agreement. Comparisons with base cation losses after stem-only and whole-tree harvesting showed sites where whole-tree harvesting was clearly not sustainable and other sites where variation in weathering rates from different approaches obscured the overall balance. Clear imbalances appeared mainly after whole-tree harvesting in spruce forests in southern and central Sweden. Based on the research findings in the QWARTS programme, it was concluded that the PROFILE/ForSAFE family of models provides the most important fundamental understanding of the contribution of weathering to long-term availability of base cations to support forest growth. However, these approaches should be continually assessed against other approaches. Uncertainties in the model approaches can be further reduced, mainly by finding ways to reduce uncertainties in input data on soil texture and associated hydrological parameters but also by developing the models, e.g. to better represent biological feedbacks under the influence of climate change.
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| 3. |
- Almeida, Juan Pablo, et al.
(författare)
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Ectomycorrhizal community composition and function in a spruce forest transitioning between nitrogen and phosphorus limitation
- 2019
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Ingår i: Fungal ecology. - : Elsevier. - 1754-5048 .- 1878-0083. ; 40, s. 20-31
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogen is the main limiting nutrient in boreal ecosystems, but studies in southwest Sweden suggest that certain forests approach phosphorus (P) limitation driven by nitrogen (N) deposition. We added N, P or N + P to a Norway spruce forest in this region, to push the system to N or P limitation. Tree growth and needle nutrient concentrations indicated that the trees are P limited. EMF biomass was reduced only by N + P additions. Soil EMF communities responded more strongly to P than to N. Addition of apatite to ingrowth meshbags altered EMF community composition and enhanced the abundance of Imleria badia in the control and N plots, but not when P was added. The ecological significance of this species is discussed. Effects on tree growth, needle chemistry, and EMF communities indicate a dynamic interaction between EMF fungi and the nutrient status of trees and soils. (C) 2018 Elsevier Ltd and British Mycological Society. All rights reserved.
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| 4. |
- Andersson, Malte, 1941, et al.
(författare)
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Kin selection and reciprocity in flight formation?
- 2004
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Ingår i: Behavioral Ecology. - 1045-2249. ; 15:1, s. 158-162
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Tidskriftsartikel (refereegranskat)abstract
- The reasons for conspicuous "V" and other flight formations in birds are debated. Theory and recent empirical advances show that energy saving is one important function of flight formations, but some aspects remain poorly understood. Combining theories of animal flight and sociality, we suggest that some of the variation in flight formations has its base in kin selection and reciprocation. The bird leading an acute V formation saves less energy than does the trailing participants. The disadvantage of leading is reduced in more obtuse formations, and when the longitudinal distance between neighbors is small, the leading bird can save about as much energy as others. Therefore, acute V formations are predicted to occur mainly in circumstances conducive to kin selection or reciprocity. These mechanisms seem possible, for example, in small flocks of adults with offspring, such as in swans, geese, and cranes. Inclusive fitness advantages may then favor an energetically expensive leader role for adults. In small groups, reciprocity is also possible among unrelated adults that recognize each other and take turns leading the V formation. In contrast, obtuse formations are expected in large flocks of unrelated individuals, such as spring flocks of waders migrating long distances. Possibilities for testing these ideas are discussed.
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| 5. |
- Andersson, Malte, 1941, et al.
(författare)
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Predator perches: a visual search perspective
- 2009
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Ingår i: Functional Ecology. - : Wiley. - 1365-2435 .- 0269-8463. ; 23, s. 373-379
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Tidskriftsartikel (refereegranskat)abstract
- 1. Predators hunting by sight often search for prey from elevated perches or hovering positions above the prey habitat. Theory suggests that prey visibility depends strongly on predator perch height and distance, but their quantitative effects have not been experimentally tested in natural habitats. 2. We estimate for the first time how prey visibility depends on predator perch height, distance and vegetation height in an open natural habitat, based on visibility measurements of two targets: a mounted bird and a graduated plate, from five perch heights (0·2–8 m) and six distances (5–120 m). 3. For both targets, their proportion visible increases strongly with observer perch height and proximity. From the lowest perch, visibility of the target bird declines to < 5% beyond 20 m distance, but 40% of it remains visible from the highest perch even at 120 m. 4. Models of predator search suggest that hunting success and predation rate depend strongly on the prey detection rate, which is expected to decline with distance r approximately as r−d. However, d, the distance decay parameter, has not previously been empirically estimated in natural predator habitats. For distance – prey visibility relationships similar to those observed here, we find a realistic estimate of d to be 2·1–2·4. 5. The results demonstrate the crucial role of relative perch and vegetation height for prey visibility, which is of relevance for habitat management. The strong increase of prey visibility with predator search height suggests that removal of predator perches can improve the survival of endangered prey populations in open habitats. Conversely, perch preservation or addition can improve habitat suitability for some predator species where perches are rare or lacking.
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| 6. |
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| 7. |
- Bahr, Adam, et al.
(författare)
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Nitrogen leaching and ectomycorrhizal nitrogen retention capacity in a Norway spruce forest fertilized with nitrogen and phosphorus
- 2015
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Ingår i: Plant and Soil. - : Springer Science and Business Media LLC. - 0032-079X .- 1573-5036. ; 390:1-2, s. 323-335
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Tidskriftsartikel (refereegranskat)abstract
- To estimate the production of external ectomycorrhizal mycelia (EMM) in Norway spruce forests with varying nitrogen (N) and phosphorus (P) levels, and to relate this to the N retention capacity of ectomycorrhizal fungi (EMF) and N leaching. Seasonal changes in EMF production (in ingrowth mesh bags) and soil water N (in suction lysimeters) were analyzed after fertilization with N or N combined with P. The EMF N retention capacity was estimated by the addition of isotopically labeled N to the mesh bags. No relationship was found between the seasonal variation in EMF growth and N leakage from the soil. However, in the mesh bags, the total assimilation of N-15 by EMF was almost halved by N fertilization, while twice as much N-15 leached through. We found a high specific N assimilation capacity per unit weight of EMF mycelia. This was unaffected by N fertilization, but the total assimilation of N by EMF was drastically reduced due to reduced production of EMM. However, N-retaining processes other than N assimilation by EMF must be taken into account to explain the losses of N after fertilization.
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| 8. |
- Duraj, Frans, et al.
(författare)
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Tarmtransplantation : Första svenska tunntarmstransplantationen till en vuxen patient med pseudoobstruktion
- 1998
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Ingår i: Läkartidningen. - 0023-7205 .- 1652-7518. ; 95:28-29, s. 3172-3176
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Tidskriftsartikel (refereegranskat)abstract
- Recent advances, first and foremost the development of new immunosuppressive agents, have markedly improved the outcome of intestinal transplantation, which is a treatment option for patients with serious intestinal diseases who have become dependent on total parenteral nutrition. The first small bowel transplantation in Sweden was performed at Huddinge Hospital in 1997, in the adult patient with intestinal pseudo-obstruction. The article reports the course of this patient and an update of international progress in intestinal transplantation.
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| 9. |
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| 10. |
- Gericke, Sabrina Maria, et al.
(författare)
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In Situ H2 Reduction of Al2O3-Supported Ni- and Mo-Based Catalysts
- 2022
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Ingår i: Catalysts. - : MDPI. - 2073-4344. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- Nickel (Ni)-promoted Molybdenum (Mo)-based catalysts are used for hydrotreatment processes in the chemical industry where the catalysts are exposed to high-pressure H2 at elevated temperature. In this environment, the catalyst transforms into the active phase, which involves the reduction of the oxide. Here, we report on the first in situ study on the reduction of alumina supported Ni- and Mo-based catalysts in 1 mbar H2 using ambient-pressure X-ray photoelectron spectroscopy (APXPS). The study confirms that mixing Ni and Mo lowers the reduction temperature of both Ni- and Mo-oxide as compared to the monometallic catalysts and shows that the MoO3 reduction starts at a lower temperature than the reduction of NiO in NiMo/Al2O3 catalysts. Additionally, the reduction of Ni and Mo foil was directly compared to the reduction of the Al2O3-supported catalysts and it was observed that the reduction of the supported catalysts is more gradual than the reduction of the foils, indicating a strong interaction between the Ni/Mo and the alumina support. © 2022 by the authors.
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