| 1. |
- Bergner, Adam, et al.
(författare)
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Influences of forest type and habitat structure on bird assemblagesof oak (Quercus spp.) and pine (Pinus spp.) stands in southwesternTurkey
- 2015
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Ingår i: Forest Ecology and Management. - : Elsevier. - 0378-1127 .- 1872-7042. ; 336, s. 137-147
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Tidskriftsartikel (refereegranskat)abstract
- The Mediterranean basin exhibits a multitude of forest habitats affected by former and current exploitation and management. Recent afforestation programs have resulted in an increase in the proportion of coniferous trees, while oak stands, formerly utilized for coppicing and grazing, are abandoned or converted into coniferous plantations. The loss of oak stands might negatively affect birds dependent upon broadleaved forests. Studies confirming or rejecting that statement are scarce, particularly in the eastern part of the region. Using a study area in southwestern Turkey we applied a guild-based approach to investigate how pine and oak stands across a chronosequence differ in their capacity to support forest bird assemblages. Variables describing the vegetation were sampled to characterize the stands and relate bird assemblages to stand structure. Bird abundance and species richness was positively associated with age for both stand types. Richness and diversity was highest in oak stands, while there were no differences in bird abundance between the two forest types. Pine stands supported a different bird species composition compared to oak stands of the same age. Stand age and structure, rather than forest type, held the highest explanatory powers for bird assembly structure. Primary cavity-nesters and ground-nesters were more abundant in oak stands, possibly reflecting differences in stand structure and resource distribution. To support these birds with suitable habitats, oaks stands need conservation. Management practices in pine stands should strive for increasing the amount of old trees and retain vegetation in the understory to benefit breeding birds.
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| 2. |
- Chantzi, Efthymia, et al.
(författare)
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COMBImage : a modular parallel processing framework for pairwise drug combination analysis that quantifies temporal changes in label-free video microscopy movies
- 2018
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Large-scale pairwise drug combination analysis has lately gained momentum in drug discovery and development projects, mainly due to the employment of advanced experimental-computational pipelines. This is fortunate as drug combinations are often required for successful treatment of complex diseases. Furthermore, most new drugs cannot totally replace the current standard-of-care medication, but rather have to enter clinical use as add-on treatment. However, there is a clear deficiency of computational tools for label-free and temporal image-based drug combination analysis that go beyond the conventional but relatively uninformative end point measurements.Results: COMBImage is a fast, modular and instrument independent computational framework for in vitro pairwise drug combination analysis that quantifies temporal changes in label-free video microscopy movies. Jointly with automated analyses of temporal changes in cell morphology and confluence, it performs and displays conventional cell viability and synergy end point analyses. The image processing algorithms are parallelized using Google's MapReduce programming model and optimized with respect to method-specific tuning parameters. COMBImage is shown to process time-lapse microscopy movies from 384-well plates within minutes on a single quad core personal computer.This framework was employed in the context of an ongoing drug discovery and development project focused on glioblastoma multiforme; the most deadly form of brain cancer. Interesting add-on effects of two investigational cytotoxic compounds when combined with vorinostat were revealed on recently established clonal cultures of glioma-initiating cells from patient tumor samples. Therapeutic synergies, when normal astrocytes were used as a toxicity cell model, reinforced the pharmacological interest regarding their potential clinical use.Conclusions: COMBImage enables, for the first time, fast and optimized pairwise drug combination analyses of temporal changes in label-free video microscopy movies. Providing this jointly with conventional cell viability based end point analyses, it could help accelerating and guiding any drug discovery and development project, without use of cell labeling and the need to employ a particular live cell imaging instrument.
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| 3. |
- Chantzi, Efthymia, et al.
(författare)
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COMBImage2 : a parallel computational framework for higher-order drug combination analysis that includes automated plate design, matched filter based object counting and temporal data mining
- 2019
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Ingår i: BMC Bioinformatics. - : BMC. - 1471-2105. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Background: Pharmacological treatment of complex diseases using more than two drugs is commonplace in the clinic due to better efficacy, decreased toxicity and reduced risk for developing resistance. However, many of these higher-order treatments have not undergone any detailed preceding in vitro evaluation that could support their therapeutic potential and reveal disease related insights. Despite the increased medical need for discovery and development of higher-order drug combinations, very few reports from systematic large-scale studies along this direction exist. A major reason is lack of computational tools that enable automated design and analysis of exhaustive drug combination experiments, where all possible subsets among a panel of pre-selected drugs have to be evaluated.Results: Motivated by this, we developed COMBImage2, a parallel computational framework for higher-order drug combination analysis. COMBImage2 goes far beyond its predecessor COMBImage in many different ways. In particular, it offers automated 384-well plate design, as well as quality control that involves resampling statistics and inter-plate analyses. Moreover, it is equipped with a generic matched filter based object counting method that is currently designed for apoptotic-like cells. Furthermore, apart from higher-order synergy analyses, COMBImage2 introduces a novel data mining approach for identifying interesting temporal response patterns and disentangling higher- from lower- and single-drug effects.COMBImage2 was employed in the context of a small pilot study focused on the CUSP9v4 protocol, which is currently used in the clinic for treatment of recurrent glioblastoma. For the first time, all 246 possible combinations of order 4 or lower of the 9 single drugs consisting the CUSP9v4 cocktail, were evaluated on an in vitro clonal culture of glioma initiating cells.Conclusions: COMBImage2 is able to automatically design and robustly analyze exhaustive and in general higher-order drug combination experiments. Such a versatile video microscopy oriented framework is likely to enable, guide and accelerate systematic large-scale drug combination studies not only for cancer but also other diseases.
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| 4. |
- Drobyshev, Igor, et al.
(författare)
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A 700-year record of large fire years in northern Scandinavia shows large variability and increased frequency during the 1800s
- 2015
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Ingår i: Journal of Quaternary Science. - : Wiley. - 1099-1417 .- 0267-8179. ; 30:3, s. 211-221
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Tidskriftsartikel (refereegranskat)abstract
- Years with climatically mediated increases in boreal forest fire activity, referred to as large fire years (LFYs), contribute to a disproportionally large portion of the burned area over centuries, and are important drivers of ecosystem processes by affecting forest structure, biodiversity, and carbon balance at regional and continental scales. We analysed changes in LFY return intervals in northern Sweden (the area above 60°N) over 1273-1960 using a network of 29 sites with dendrochronologically reconstructed fires, complemented by documentary records of fires available from forestry statistics. We observed large variability in return intervals of LFYs, an increase in LFY frequency during the 1800s, and consistent associations between LFY occurrence and 500-hPa pressure anomalies over the European sub-continent over 1800xps2#1960. An increase in LFY frequency during the 1800s might be climatically driven, and would thus long precede the period of likely human-induced climatic changes of the 1900s. Long-term variability in climatically driven LFYs may present a challenge in partitioning the effects of human-related and human-independent components of climatic forcing upon forest fire activity. © 2015 John Wiley & Sons, Ltd.
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| 5. |
- Drobyshev, Igor, et al.
(författare)
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A mixture of human and climatic effects shapes the 250-year long fire history of a semi-natural pine dominated landscape of Northern Latvia
- 2019
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 441, s. 192-201
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Tidskriftsartikel (refereegranskat)abstract
- Fire has been shown to shape successional pathways and dynamics of forest vegetation. However, its role in European hemiboreal forests remains poorly understood. Here we provide the first annually resolved reconstruction of fire history from the Eastern Baltic Sea region, developed in the pine-dominated landscape of Slitere National Park (SNP), northwestern Latvia, over the last 250 years. Our results suggest that forest fires have been a common disturbance factor in the studied landscape. In total, we dated 62 single fire years, with the mean-point scale fire return interval of 46 years and the length of the fire cycle ranging from 45 to 80 years. We identified periods of high (1750-1950) and low (1960-2000) fire activity, with the corresponding lengths of fire cycles being 45-68 and 58-80 years, respectively. Although both long-term (century and decade-long) and annual dynamics of fire activity in SNP was closely linked to socio-political changes in Latvia, fire activity in SNP was also affected by climate, as indicated by the close positive association of years with increased area burned and positive SST anomalies in the Baltic and North Seas. Future management of SNP should make fire an important element of natural forest dynamics and consider using prescribed fires of various spatial extent and severity.
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| 6. |
- Drobyshev, Igor, et al.
(författare)
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Atlantic SSTs control regime shifts in forest fire activity of Northern Scandinavia
- 2016
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the drivers of the boreal forest fire activity is challenging due to the complexity of the interactions driving fire regimes. We analyzed drivers of forest fire activity in Northern Scandinavia (above 60 N) by combining modern and proxy data over the Holocene. The results suggest that the cold climate in northern Scandinavia was generally characterized by dry conditions favourable to periods of regionally increased fire activity. We propose that the cold conditions over the northern North Atlantic, associated with low SSTs, expansion of sea ice cover, and the southward shift in the position of the subpolar gyre, redirect southward the precipitation over Scandinavia, associated with the westerlies. This dynamics strengthens high pressure systems over Scandinavia and results in increased regional fire activity. Our study reveals a previously undocumented teleconnection between large scale climate and ocean dynamics over the North Atlantic and regional boreal forest fire activity in Northern Scandinavia. Consistency of the pattern observed annually through millennium scales suggests that a strong link between Atlantic SST and fire activity on multiple temporal scales over the entire Holocene is relevant for understanding future fire activity across the European boreal zone.
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| 7. |
- Felton, Adam, et al.
(författare)
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Replacing monocultures with mixed-species : Ecosystem service implications of two production forest alternatives in Sweden
- 2016
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 45:Suppl. 2, s. 124-139
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Tidskriftsartikel (refereegranskat)abstract
- Whereas there is evidence that mixed-species approaches to production forestry in general can provide positive outcomes relative to monocultures, it is less clear to what extent multiple benefits can be derived from specific mixed-species alternatives. To provide such insights requires evaluations of an encompassing suite of ecosystem services, biodiversity, and forest management considerations provided by specific mixtures and monocultures within a region. Here, we conduct such an assessment in Sweden by contrasting even-aged Norway spruce (Picea abies)-dominated stands, with mixed-species stands of spruce and birch (Betula pendula or B. pubescens), or spruce and Scots pine (Pinus sylvestris). By synthesizing the available evidence, we identify positive outcomes from mixtures including increased biodiversity, water quality, esthetic and recreational values, as well as reduced stand vulnerability to pest and pathogen damage. However, some uncertainties and risks were projected to increase, highlighting the importance of conducting comprehensive interdisciplinary evaluations when assessing the pros and cons of mixtures.
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| 8. |
- Felton, Adam, et al.
(författare)
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Replacing monocultures with mixed-species stands : Ecosystem service implications of two production forest alternatives in Sweden
- 2016
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 45, s. 124-139
-
Tidskriftsartikel (refereegranskat)abstract
- Whereas there is evidence that mixed-species approaches to production forestry in general can provide positive outcomes relative to monocultures, it is less clear to what extent multiple benefits can be derived from specific mixed-species alternatives. To provide such insights requires evaluations of an encompassing suite of ecosystem services, biodiversity, and forest management considerations provided by specific mixtures and monocultures within a region. Here, we conduct such an assessment in Sweden by contrasting even-aged Norway spruce (Picea abies)-dominated stands, with mixed-species stands of spruce and birch (Betula pendula or B. pubescens), or spruce and Scots pine (Pinus sylvestris). By synthesizing the available evidence, we identify positive outcomes from mixtures including increased biodiversity, water quality, esthetic and recreational values, as well as reduced stand vulnerability to pest and pathogen damage. However, some uncertainties and risks were projected to increase, highlighting the importance of conducting comprehensive interdisciplinary evaluations when assessing the pros and cons of mixtures.
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| 9. |
- Ji, Yu-Xia, et al.
(författare)
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Thermochromic VO2 films by thermal oxidation of vanadium in SO2
- 2016
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Ingår i: Solar Energy Materials and Solar Cells. - : Elsevier BV. - 0927-0248 .- 1879-3398. ; 144, s. 713-716
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Tidskriftsartikel (refereegranskat)abstract
- Thermochromic films of VO2 were prepared by a two-step procedure: Sputtering was first used to deposit metallic vanadium, and such layers were subsequently oxidized in SO2 at a temperature in the 600-650 degrees C range. X-ray diffraction, Raman spectroscopy, measurements of temperature-dependent electrical resistance, and spectrophotometric transmittance data at different temperatures were employed to demonstrate that the films consisted of polycrystalline VO2 with good thermochromism, especially when oxidized at the highest temperature. Oxidation in SO2 is able to produce VO2 without the stringent process control that can be an obstacle for making VO2 by oxidation in O-2.
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| 10. |
- Johansson, Malin B, 1972-, et al.
(författare)
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Porous Fractals of MAPbI3 Perovskite : Characterization of Crystal Grain Formation by Irreversible Diffusion-Limited Aggregation
- 2018
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Konferensbidrag (refereegranskat)abstract
- Isopropanol solution based methylammonium lead triiodide (MAPbI3) is studied during the crystallization process. The crystal growth starts in an unstable suspension far from equilibrium by forming different dendritic patterns and terminates with aggregation of stable cubic crystalline grains into fractal clusters. Using transmission electron microscopy (TEM), the time evolution of a newly mixed suspension was studied over a period of two weeks at room temperature and a sequence of the morphological changes was observed. The crystallization process started with single dendritic growth exhibiting branches at 90 degrees angles to one another. After 4 hours, a multi-dendritic growth pattern and a transformation into small crystalline quantum dots were observed. After a week, clusters of crystal grains were formed into a fractal pattern and these patterns appear to be stable also during the second week. Electron and x-ray diffraction revealed the crystallinity of the quantum dots and the clusters of micrometer-sized crystals. Scanning transmission electron microscope (STEM) together with energy dispersive X-ray spectroscopy (EDS) showed that newly formed large grains, from a one hour old solution, displayed a core-shell structure with higher percentage of Pb atoms as compared to iodine at the surface. In the inner core of the grains the percentage of iodine was slightly higher. The electron diffraction (ED) scan over the newly formed grains revealed a polycrystalline surface whereas the inner part had a single crystal pattern. The same solution, now one-week-old, contained grains with only single crystal patterns in the ED scan and showed no core-shell character or polycrystalline surface. The measured percentage of iodine atoms compared to lead was 2:1 throughout the cross section, which is a quantitative value within the measurement. It can be concluded from these measurements that the suspension approaches higher crystallinity of the perovskite grains in an irreversible process, where the perovskite grains are insoluble in isopropanol. The perovskite material has also been characterized with scanning electron microscopy (SEM) and photoluminescence (PL) mapping where both techniques showed a very porous crystalline material. The PL mapping revealed two peaks at 730 and 760 nm for a thin film spin coated from a newly mixed solution, while a film deposited from a one week old solution showed three peaks, the last one at 830 nm. Because of the high crystallinity, it is suggested that all three peaks are due to band-to-band transitions and not due to localized states. These data will be analyzed further; however, the results contain information of the content of quantum dots versus larger crystals, as well as displaying emission intensity variations at different positions of the grains. The purpose with this project is to understand these phenomena of crystal growth. A new mesoporous perovskite material has been designed for optoelectronic purposes.
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