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1.
  • Heumann, Benjamin, et al. (författare)
  • AVHRR Derived Phenological Change in the Sahel and Soudan, Africa, 1982 - 2005
  • 2007
  • Ingår i: Remote Sensing of Environment. - Elsevier Science Inc.. - 0034-4257. ; 108:4, s. 385-392
  • Tidskriftsartikel (refereegranskat)abstract
    • The Sahel region of Africa has experienced a decrease in rainfall from the early 1960s to mid 1990s. Recent studies have detected an increased in NDVI amplitude and growing season integrated NDVI for the region since 1982. However, these studies have not examined how plant phenology has changed. Phenology examines life cycle events such as bud burst and leaf senescence. Using the software TIMESAT to estimate phenological parameters from the GlMMS AVHRR NDVI dataset, we have found significant positive trends for the length of the growing and end of the growing season for the Soudan and Guinean regions, but significant trends in the Sahel could not be detected. The geographical extent of these trends contrasts with the more northern extent of positive trends of NDVI amplitude and growing season integrated NDVI. Results suggest two types of "greening" trends associated with rainfall change since the drought in the early 1980s. (c) 2006 Elsevier Inc. All rights reserved.
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3.
  • Staaf, Johan, et al. (författare)
  • Relation between smoking history and gene expression profiles in lung adenocarcinomas
  • 2012
  • Ingår i: BMC Medical Genomics. - BioMed Central. - 1755-8794. ; 5
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Lung cancer is the worldwide leading cause of death from cancer. Tobacco usage is the major pathogenic factor, but all lung cancers are not attributable to smoking. Specifically, lung cancer in never-smokers has been suggested to represent a distinct disease entity compared to lung cancer arising in smokers due to differences in etiology, natural history and response to specific treatment regimes. However, the genetic aberrations that differ between smokers and never-smokers' lung carcinomas remain to a large extent unclear. Methods: Unsupervised gene expression analysis of 39 primary lung adenocarcinomas was performed using Illumina HT-12 microarrays. Results from unsupervised analysis were validated in six external adenocarcinoma data sets (n=687), and six data sets comprising normal airway epithelial or normal lung tissue specimens (n=467). Supervised gene expression analysis between smokers and never-smokers were performed in seven adenocarcinoma data sets, and results validated in the six normal data sets. Results: Initial unsupervised analysis of 39 adenocarcinomas identified two subgroups of which one harbored all never-smokers. A generated gene expression signature could subsequently identify never-smokers with 79-100% sensitivity in external adenocarcinoma data sets and with 76-88% sensitivity in the normal materials. A notable fraction of current/former smokers were grouped with never-smokers. Intriguingly, supervised analysis of never-smokers versus smokers in seven adenocarcinoma data sets generated similar results. Overlap in classification between the two approaches was high, indicating that both approaches identify a common set of samples from current/former smokers as potential never-smokers. The gene signature from unsupervised analysis included several genes implicated in lung tumorigenesis, immune-response associated pathways, genes previously associated with smoking, as well as marker genes for alveolar type II pneumocytes, while the best classifier from supervised analysis comprised genes strongly associated with proliferation, but also genes previously associated with smoking. Conclusions: Based on gene expression profiling, we demonstrate that never-smokers can be identified with high sensitivity in both tumor material and normal airway epithelial specimens. Our results indicate that tumors arising in never-smokers, together with a subset of tumors from smokers, represent a distinct entity of lung adenocarcinomas. Taken together, these analyses provide further insight into the transcriptional patterns occurring in lung adenocarcinoma stratified by smoking history.
4.
  • Aronsson, Per, et al. (författare)
  • An operational decision support tool for stump harvest
  • 2011
  • Konferensbidrag (övrigt vetenskapligt)abstract
    • A multi-criteria decision support tool was developed to optimise stump harvesting for energy in Sweden. The decision tool takes account of multiple, sometimes conflicting, criteria relating to stump harvest; energy and climate, economics, biodiversity, and soil and water. Data on harvested stems are used as primary input data in the tool. Such data are routinely collected in harvester computers. The tool effectively deals with mixed sets of data; quantitative harvest data are re-calculated to metric (e.g. stump biomass), and qualitative data (e.g. biodiversity implications) are incorporated. A digital terrain map derived from air-borne laser scanning provides basic data for estimating soil wetness, while digital maps of water courses, key habitats and protected areas, or other sensitive habitats, are used to identify potentially and practically harvestable stumps.In four sub-models, an index from 0 to 10 is calculated for each stump, with 0 representing ‘Not at all suitable’ and 10 ‘Highly suitable for extraction’. Through this, a stump of high value for wood-living species is assigned a low index in the biodiversity sub-model and a large, easily accessible stump is assigned a high index in the economic sub-model. When calculating the net index, the sub-indices can be weighted according to the preferences of the end-user.An energy and climate sub-model incorporates greenhouse gas (GHG) emissions from forest operations and the effect of advancing GHG emissions when stump biomass is incinerated instead of being left to decompose. In the economic sub-model the potential monetary return from each stump is calculated based on estimated revenue from harvested stump biomass and the costs of stump harvesting and forwarding operations (based on cost functions and GIS calculations of transport distances).The biodiversity sub-model considers four types of wood-dependent organisms (lichens, mosses, insects and fungi) in terms of their habitat requirements, vulnerability, sun exposure preferences, locality, etc. A panel of external experts has drawn up a grading scale of stump values for the different taxonomic groups. The proximity to key habitats and exposure to sunlight are derived from a spatial model.Soil and water issues are handled within a sub-model estimating the consequences for long-term soil fertility (nutrient cycling and soil compaction) and water (leaching of plant nutrients and mercury, and particle transport due to soil damage by heavy machinery).The tool offers the end-user possibilities to prioritise and plan for cost-effective stump harvesting, while minimising negative environmental impacts.
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5.
  • Blom, Kristin, et al. (författare)
  • Eosinophil associated genes in the inflammatory bowel disease 4 region : Correlation to inflammatory bowel disease revealed
  • 2012
  • Ingår i: World Journal of Gastroenterology. - 1007-9327. ; 18:44, s. 6409-6419
  • Tidskriftsartikel (refereegranskat)abstract
    • AIM: To study the association between inflammatory bowel disease (IBD) and genetic variations in eosinophil protein X (EPX) and eosinophil cationic protein (ECP). METHODS: DNA was extracted from ethylene diamine tetraacetic acid blood of 587 patients with Crohn's disease (CD), 592 with ulcerative colitis (UC) and 300 healthy subjects. The EPX405 (G > C, rs2013109), ECP434 (G > C, rs2073342) and ECP562 (G > C, rs2233860) gene polymorphisms were analysed, by the 5'-nuclease allelic discrimination assay. For determination of intracellular content of EPX and ECP in granulocytes, 39 blood samples was collected and extracted with a buffer containing cetyltrimethylammonium bromide. The intracellular content of EPX was analysed using an enzyme-linked immunosorbent assay. The intracellular content of ECP was analysed with the UniCAP (R) system as described by the manufacturer. Statistical tests for calculations of results were chi(2) test, Fisher's exact test, ANOVA, Student-Newman-Keuls test, and Kaplan-Meier survival curve with Log-rank test for trend, the probability values of P < 0.05 were considered statistically significant. RESULTS: The genotype frequency for males with UC and with an age of disease onset of >= 45 years (n = 57) was for ECP434 and ECP562, GG = 37%, GC = 60%, CC = 4% and GG = 51%, GC = 49%, CC = 0% respectively. This was significantly different from the healthy subject's genotype frequencies of ECP434 (GG = 57%, GC = 38%, CC = 5%; P = 0.010) and ECP562 (GG = 68%, GC = 29 /0,CC = 3%; P = 0.009). The genotype frequencies for females, with an age of disease onset of >= 45 years with CD (n = 62), was for the ECP434 and ECP562 genotypes GG = 37%, GC = 52%, CC = 11% and GG = 48%, GC = 47% and CC = 5% respectively. This was also statistically different from healthy controls for both ECP434 (P = 0.010) and ECP562 (P = 0.013). The intracellular protein concentration of EPX and ECP was calculated in mu g/10(6) eosinophils and then correlated to the EPX 405 genotypes. The protein content of EPX was highest in the patients with the CC genotype of EPX405 (GG = 4.65, GC = 5.93, and CC = 6.57) and for ECP in the patients with the GG genotype of EPX405 (GG = 2.70, GC = 2.47 and CC = 1.90). ANOVA test demonstrated a difference in intracellular protein content for EPX (P = 0.009) and ECP (P = 0.022). The age of disease onset was linked to haplotypes of the EPX405, ECP434 and ECP562 genotypes. Kaplan Maier curve showed a difference between haplotype distributions for the females with CD (P = 0.003). The highest age of disease onset was seen in females with the EPX405CC, ECP434GC, ECP562CC haplotype (34 years) and the lowest in females with the EPX405GC, ECP434GC, ECP562GG haplotype (21 years). For males with UC there was also a difference between the highest and lowest age of the disease onset (EPX405CC, ECP434CC, ECP562CC, mean 24 years vs EPX405GC, ECP434GC, ECP562GG, mean 34 years, P = 0.0009). The relative risk for UC patients with ECP434 or ECP562-GC/CC genotypes to develop dysplasia/cancer was 2.5 (95%CI: 1.2-5.4, P = 0.01) and 2.5 (95%CI: 1.1-5.4, P = 0.02) respectively, compared to patients carrying the GG-genotypes. CONCLUSION: Polymorphisms of EPX and ECP are associated to IBD in an age and gender dependent manner, suggesting an essential role of eosinophils in the pathophysiology of IBD.
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6.
  • Brunnström, Hans, et al. (författare)
  • Immunohistochemistry in the differential diagnostics of primary lung cancer: an investigation within the southern Swedish lung cancer study.
  • 2013
  • Ingår i: American journal of clinical pathology. - AMER SOC CLINICAL PATHOLOGY. - 0002-9173 .- 1943-7722. ; 140:1, s. 37-46
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives: To assess immunohistochemical (IHC) stains differentially expressed between different types of lung cancer. Methods: We evaluated 16 different IHC stains in 209 prospectively included, surgically treated primary lung cancers, including 121 adenocarcinomas, 65 squamous cell carcinomas, 15 large-cell carcinomas, 5 adenosquamous carcinomas, 2 sarcomatoid carcinomas, and 1 small-cell carcinoma, using the tissue microarray technique. Results: Cytokeratin 5 (CK5) and P63 were both positive in 10% or more of the cells in 97% of the squamous cell carcinomas, with the former being positive (<10% of the cells) in only 2 non-squamous cell carcinomas. Thyroid transcription factor 1 (TTF1) and napsin A were positive in 10% or more of the cells in 88% and 87% of the adenocarcinomas, respectively, with 94% of the adenocarcinomas being positive in at least 1 marker. Fifteen percent of the adenocarcinomas were positive for estrogen receptor. Conclusions: CK5, TTF1, and napsin A are sensitive markers for squamous cell carcinoma and adenocarcinoma of the lung.
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8.
  • Isaksson, Sofi, et al. (författare)
  • Detecting EGFR alterations in clinical specimens-pitfalls and necessities.
  • 2013
  • Ingår i: Virchows Archiv : an international journal of pathology. - Springer. - 0945-6317 .- 1432-2307. ; 463:6, s. 755-764
  • Tidskriftsartikel (refereegranskat)abstract
    • We investigated the epidermal growth factor receptor (EGFR) status in early stage lung cancer in Southern Sweden, a population for which there are no previous reports on the EGFR mutation frequency. Three hundred fifty small cell lung cancers, adenocarcinomas (AC), squamous cell carcinomas (SqCC), and large cell carcinomas were analyzed using a combination of techniques for the analysis of protein expression, gene copy numbers, and mutations. Immunohistochemical (IHC) staining with antibodies for the EGFR mutations L858R and del E746-A750 revealed intratumoral heterogeneity and several discrepant cases when compared to mutation-specific polymerase chain reaction (PCR)-based analysis. The frequencies of these two mutations, when considering IHC staining with mutation-specific antibodies in a cohort of 298 cases and subsequent confirmation by PCR, were 10 % in AC and <2 % in SqCC. Furthermore, screening by sequencing of EGFR in a cohort of 52 lung AC and squamous carcinomas demonstrated a more diverse mutation spectrum, not covered by the mutation-specific antibodies. High expression of total EGFR protein was correlated to high gene copy numbers but did not reflect the mutational status of the tumors. We believe that the mutation spectra in a Southern Swedish population is too diverse to be covered by the mutation-specific antibodies, and we also raise some other issues regarding the use of the mutation-specific antibodies, for example concerning heterogeneous expression of the mutated protein, optimal antibody dilution, and discrepancies between staining results and PCR.
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9.
  • Jonsson, Ingemar, et al. (författare)
  • Sexual patterns of prebreeding energy reserves in the common frog Rana temporaria along a latitudinal gradient
  • 2009
  • Ingår i: Ecography. - 0906-7590. ; 32:5, s. 831-839
  • Tidskriftsartikel (refereegranskat)abstract
    • The ability to store energy is an important life history trait for organisms facing long periods without energy income, and in particular for capital breeders such as temperate zone amphibians, which rely on stored energy during reproduction. However, large scale comparative studies of energy stores in populations with different environmental constraints on energy allocation are scarce. We investigated energy storage patterns in spring (after hibernation and before reproduction) in eight common frog (Rana temporaria) populations exposed to different environmental conditions along a 1600 km latitudinal gradient across Scandinavia (range of annual activity period 3-7 months). Analyses of lean body weight (eviscerated body mass), weight of fat bodies, liver weight, and liver fat content, showed that (i) post-hibernation/pre-breeding energy stores increased with increasing latitude in both sexes, (ii) males generally had larger energy reserves than females and (iii) the difference in energy stores between sexes decreased towards the north. Larger energy reserves towards the north can serve as a buffer against less predictable and/or less benign weather conditions during the short activity period, and may also represent a risk-averse tactic connected with a more pronounced iteroparous life history. In females, the continuous and overlapping vitellogenic activity in the north may also demand more reserves in early spring. The general sexual difference could be a consequence of the fact that, at the time of our sampling, females had already invested their energy into reproduction in the given year (i.e. their eggs were already ovulated), while the males' main reproductive activities (e.g. calling, mate searching, sexual competition) occurred later in the season.
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10.
  • Jönsson, Anna Maria, et al. (författare)
  • Annual changes in MODIS vegetation indices of Swedish coniferous forests in relation to snow dynamics and tree phenology
  • 2010
  • Ingår i: Remote Sensing of the Environment;11. - Elsevier. - 0034-4257. ; :11
  • Tidskriftsartikel (refereegranskat)abstract
    • Remote sensing provides spatially and temporally continuous measures of forest reflectance, and vegetation indices calculated from satellite data can be useful for monitoring climate change impacts on forest tree phenology. Monitoring of evergreen coniferous forest is more difficult than monitoring of deciduous forest, as the new buds only account for a small proportion of the green biomass, and the shoot elongation process is relatively slow. In this study, we have analyzed data from 186 coniferous monitoring sites in Sweden covering boreal, southern-boreal, and boreo-nemoral conditions. Our objective was to examine the possibility to track seasonal changes in coniferous forests by time-series of MODIS eight-day vegetation indices, testing the coherence between satellite monitored vegetation indices (VI) and temperature dependent phenology. The relationships between two vegetation indices (NDVI and WDRVI) and four phenological indicators (length of snow season, modeled onset of vegetation period, tree cold hardiness level and timing of budburst) were analyzed. The annual curves produced by two curve fitting methods for smoothening of seasonal changes in NDVI and WDRVI were to a large extent characterized by the occurrence of snow, producing stable seasonal oscillations in the northern part and irregular curves with less pronounced annual amplitude in the southern part of the country. Measures based on threshold values of the VI-curves, commonly used for determining the timing of different phenological phases, were not applicable for Swedish coniferous forests. Evergreen vegetation does not have a sharp increase in greenness during spring, and the melting of snow can influence the vegetation indices at the timing of budburst in boreal forests. However, the interannual variation in VI-values for specific eight-day periods was correlated with the phenological indicators. This relation can be used for satellite monitoring of potential climate change impacts on northern coniferous spring phenology.
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