| 1. |
- Tuomi, Maria, et al.
(författare)
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Stomping in silence : Conceptualizing trampling effects on soils in polar tundra
- 2021
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Ingår i: Functional Ecology. - : Wiley. - 0269-8463 .- 1365-2435. ; 35:2, s. 306-317
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Forskningsöversikt (refereegranskat)abstract
- Ungulate trampling modifies soils and interlinked ecosystem functions across biomes. Until today, most research has focused on temperate ecosystems and mineral soils while trampling effects on cold and organic matter-rich tundra soils remain largely unknown. We aimed to develop a general model of trampling effects on soil structure, biota, microclimate and biogeochemical processes, with a particular focus on polar tundra soils. To reach this goal, we reviewed literature about the effects of trampling and physical disturbances on soils across biomes and used this to discuss the knowns and unknowns of trampling effects on tundra soils. We identified the following four pathways through which trampling affects soils: (a) soil compaction; (b) reductions in soil fauna and fungi; (c) rapid losses in vegetation biomass and cover; and (d) longer term shifts in vegetation community composition. We found that, in polar tundra, soil responses to trampling pathways 1 and 3 could be characterized by nonlinear dynamics and tundra-specific context dependencies that we formulated into testable hypotheses. In conclusion, trampling may affect tundra soil significantly but many direct, interacting and cascading responses remain unknown. We call for research to advance the understanding of trampling effects on soils to support informed efforts to manage and predict the functioning of tundra systems under global changes. A free Plain Language Summary can be found within the Supporting Information of this article.
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| 2. |
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| 3. |
- Söderlund, Z, et al.
(författare)
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Controlled release of growth factors using synthetic glycosaminoglycans in a modular macroporous scaffold for tissue regeneration
- 2022
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Healthy regeneration of tissue relies on a well-orchestrated release of growth factors. Herein, we show the use of synthetic glycosaminoglycans for controlled binding and release of growth factors to induce a desired cellular response. First, we screened glycosaminoglycans with growth factors of interest to determine kon (association rate constant), koff (dissociation rate constant), and Kd (equilibrium rate constant). As proof-of-concept, we functionalized an elastin-like recombinamer (ELR) hydrogel with a synthetic glycosaminoglycan and immobilized fibroblast growth factor 2 (FGF2), demonstrating that human umbilical vein endothelial cells cultured on top of ELR hydrogel differentiated into tube-like structures. Taking this concept further, we developed a tunable macroporous ELR cryogel material, containing a synthetic glycosaminoglycan and FGF2 that showed increased blood vessel formation and reduced immune response compared to control when implanted in a subcutaneous mouse model. These results demonstrated the possibility for specific release of desired growth factors in/from a modular 3D scaffold in vitro and in vivo.
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| 4. |
- Tuma, Katja, 1991, et al.
(författare)
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Finding security threats that matter: Two industrial case studies
- 2021
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Ingår i: Journal of Systems and Software. - : Elsevier BV. - 0164-1212. ; 179
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Tidskriftsartikel (refereegranskat)abstract
- In the past decade, speed has become an essential trait of software development (e.g., agile, continuous integration, DevOps) and any inefficiency is considered unaffordable time waster. Such a fast pace causes challenges for architectural threat analysis. Leading techniques for threat analysis, like STRIDE, have the advantage of being systematic. However, they are not equipped to discern between important and less critical threats, while the threats are being discovered. Consequently, many threats are discarded at a later time, when their risk value is assessed. An alternative technique, called eSTRIDE, promises to remove these inefficiencies by focusing the analysis on the critical parts of the architecture. Yet, no empirical evidence exists about the actual effect of trading off systematicity, for a more focused attention on high-priority threats. This paper contributes with an empirical study comparing these two approaches in the context of two industrial case studies. We found that the two approaches yield the same number of security threats during a given time frame. However, participants using eSTRIDE found twice as many high-priority threats. The underlying analysis procedures cause similarities and differences in the execution. In addition, security expertise has an effect (albeit small) on the quality of analysis outcomes and execution. (C) 2021 Elsevier Inc. All rights reserved.
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| 5. |
- van der Have, Oscar, et al.
(författare)
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Aggrecan accumulates at sites of increased pulmonary arterial pressure in idiopathic pulmonary arterial hypertension
- 2023
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Ingår i: Pulmonary Circulation. - : Wiley. - 2045-8932 .- 2045-8940. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Expansion of extracellular matrix occurs in all stages of pulmonary angiopathy associated with pulmonary arterial hypertension (PAH). In systemic arteries, dysregulation and accumulation of the large chondroitin-sulfate proteoglycan aggrecan is associated with swelling and disruption of vessel wall homeostasis. Whether aggrecan is present in pulmonary arteries, and its potential roles in PAH, has not been thoroughly investigated. Here, lung tissue from 11 patients with idiopathic PAH was imaged using synchrotron radiation phase-contrast microcomputed tomography (TOMCAT beamline, Swiss Light Source). Immunohistochemistry for aggrecan core protein in subsequently sectioned lung tissue demonstrated accumulation in PAH compared with failed donor lung controls. RNAscope in situ hybridization indicated ACAN expression in vascular endothelium and smooth muscle cells. Based on qualitative histological analysis, aggrecan localizes to cellular, rather than fibrotic or collagenous, lesions. Interestingly, ADAMTS15, a potential aggrecanase, was upregulated in pulmonary arteries in PAH. Aligning traditional histological analysis with three-dimensional renderings of pulmonary arteries from synchrotron imaging identified aggrecan in lumen-reducing lesions containing loose, cell-rich connective tissue, at sites of intrapulmonary bronchopulmonary shunting, and at sites of presumed elevated pulmonary blood pressure. Our findings suggest that ACAN expression may be an early response to injury in pulmonary angiopathy and supports recent work showing that dysregulation of aggrecan turnover is a hallmark of arterial adaptations to altered hemodynamics. Whether cause or effect, aggrecan and aggrecanase regulation in PAH are potential therapeutic targets.
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| 6. |
- Wijk, Sofia C., et al.
(författare)
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Ciliated (FOXJ1+) Cells Display Reduced Ferritin Light Chain in the Airways of Idiopathic Pulmonary Fibrosis Patients
- 2022
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Ingår i: Cells. - : MDPI AG. - 2073-4409. ; 11:6
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Tidskriftsartikel (refereegranskat)abstract
- Cell-based therapies hold great promise in re-establishing organ function for many diseases, including untreatable lung diseases such as idiopathic pulmonary fibrosis (IPF). However, many hurdles still remain, in part due to our lack of knowledge about the disease-driving mechanisms that may affect the cellular niche and thereby possibly hinder the function of any transplanted cells by imposing the disease phenotype onto the newly generated progeny. Recent findings have demonstrated increased ciliation of lung cells from IPF patients, but how this affects ciliated cell function and the airway milieu is not well-known. Here, we performed single-cell RNA sequencing on primary ciliated (FOJ1+) cells isolated from IPF patients and from healthy control donors. The sequencing identified multiple biological processes, such as cilium morphogenesis and cell signaling, that were significantly changed between IPF and healthy ciliated cells. Ferritin light chain (FTL) was downregulated in IPF, which suggests that iron metabolism may be affected in the IPF ciliated cells. The RNA expression was confirmed at the protein level with histological localization in lung tissue, prompting future functional assays to reveal the potential role of FTL. Taken together, our data demonstrate the importance of careful analyses in pure cell populations to better understand the IPF disease mechanism.
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| 7. |
- Wijk, Sofia C, et al.
(författare)
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Human Primary Airway Basal Cells Display a Continuum of Molecular Phases from Health to Disease in Chronic Obstructive Pulmonary Disease
- 2021
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Ingår i: American Journal of Respiratory Cell and Molecular Biology. - 1535-4989. ; 65:1, s. 103-113
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Tidskriftsartikel (refereegranskat)abstract
- Airway basal cells are crucial for regeneration of the human lung airway epithelium, and are thought to be important contributors to Chronic Obstructive Pulmonary Disease (COPD) and other lung disorders. In order to reveal how basal cells contribute to disease, and to discover novel therapeutic targets, these basal cells need to be further characterized. In this study, we optimized a flow cytometry-based cell sorting protocol for primary human airway basal cells dependent on cell size and Nerve-Growth Factor Receptor (NGFR) expression. The basal cell population was found to be molecularly and functionally heterogeneous in contrast to cultured basal cells. In addition, significant differences were found such as KRT14 expression exclusively existing in cultured cells. Also, colony-forming capacity was significantly increased in cultured cells showing a clonal enrichment in vitro. Next, by single cell RNA sequencing on primary basal cells from healthy donors and GOLD stage IV COPD patients, the gene expression revealed a continuum ranging from healthy basal cell signatures to diseased basal cell phenotypes. We identified several upregulated genes that may indicate COPD, such as stress response related genes GADD45B and AHSA1, along with genes involved in the response to hypoxia such as CITED2 and SOD1. Taken together, the presence of healthy basal cells in stage IV COPD demonstrates the potential for regeneration through the discovery of novel therapeutic targets. In addition, we show the importance of studying primary basal cells when investigating disease mechanisms as well as for developing future cell-based therapies in the human lung.
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