| 1. |
- Hudson, Thomas J., et al.
(författare)
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International network of cancer genome projects
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
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Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 2. |
- Micke, Patrick, et al.
(författare)
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The prognostic impact of the tumour stroma fraction : A machine learning-based analysis in 16 human solid tumour types
- 2021
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Ingår i: EBioMedicine. - : Elsevier. - 2352-3964. ; 65
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Tidskriftsartikel (refereegranskat)abstract
- Background: The development of a reactive tumour stroma is a hallmark of tumour progression and pronounced tumour stroma is generally considered to be associated with clinical aggressiveness. The variability between tumour types regarding stroma fraction, and its prognosis associations, have not been systematically analysed.Methods: Using an objective machine-learning method we quantified the tumour stroma in 16 solid cancer types from 2732 patients, representing retrospective tissue collections of surgically resected primary tumours. Image analysis performed tissue segmentation into stromal and epithelial compartment based on pan-cytokeratin staining and autofluorescence patterns.Findings: The stroma fraction was highly variable within and across the tumour types, with kidney cancer showing the lowest and pancreato-biliary type periampullary cancer showing the highest stroma proportion (median 19% and 73% respectively). Adjusted Cox regression models revealed both positive (pancreato-biliary type periampullary cancer and oestrogen negative breast cancer, HR(95%CI)=0.56(0.34-0.92) and HR (95%CI)=0.41(0.17-0.98) respectively) and negative (intestinal type periampullary cancer, HR(95%CI)=3.59 (1.49-8.62)) associations of the tumour stroma fraction with survival.Interpretation: Our study provides an objective quantification of the tumour stroma fraction across major types of solid cancer. Findings strongly argue against the commonly promoted view of a general associations between high stroma abundance and poor prognosis. The results also suggest that full exploitation of the prognostic potential of tumour stroma requires analyses that go beyond determination of stroma abundance.
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| 3. |
- Ståhl, Patrik, Dr., et al.
(författare)
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Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
- 2016
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Ingår i: Science. - : AMER ASSOC ADVANCEMENT SCIENCE. - 0036-8075 .- 1095-9203. ; 353:6294, s. 78-82
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics. This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.
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| 4. |
- Andersen Borg, Marc, 1967-
(författare)
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Non-indigenous zooplankton : the role of predatory cladocerans and of copepods in trophic dynamics
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Human-mediated introductions of non-indigenous species now threaten to homogenize the biota of the Globe, causing huge economic and ecological damage. This thesis studies the ecological role of 3 invasive planktonic crustaceans, the omnivorous copepod Acartia tonsa (western Atlantic and Indo-Pacific) and the predatory cladocerans, Cercopagis pengoi (Ponto-Caspian) and Bythotrephes longimanus (Eurasian). B. longimanus invaded the North American Great Lakes in 1982, C. pengoi the Baltic in 1992 and the Great Lakes in 1999, while A. tonsa has an extensive invasion history that includes the Baltic.We review current knowledge on feeding biology of the predatory cladocerans. A study of stable C and N isotope ratios indicated mesozooplankton as the main food source of C. pengoi in the northern Baltic Sea proper, with young C. pengoi also eating microzooplankton, such as rotifers. Young-of-the-year herring did eat C. pengoi and herring trophic position shifted from 2.6 before the invasion to 3.4 after, indicating that C. pengoi had been “sandwiched” into the modified food web between mesozooplankton and fish.Salinity tolerance experiments on Acartia tonsa and co-occurring Acartia clausi showed the formers euryhaline character and high grazing potential. Energy partitioning between ingestion, production and respiration was rather constant over the tested salinity range of 2 to 33, with small differences in gross growth efficiency and cost of growth, but maximum ingestion at 10-20. Egg hatching in A. tonsa was only reduced at the lowest salinity. Extreme changes in salinity were needed to cause significant mortality of A. tonsa in the field, but its feeding activity could be severely reduced by salinity changes likely to occur in estuaries. A study of a hypertrophic estuary showed that A. tonsa can sustain a population despite very high mortality rates, caused by predation, high pH and low oxygen, helping explain the success of A. tonsa as an invader of estuaries.
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| 5. |
- Andersson, Alma, et al.
(författare)
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Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases. While transcriptomics have enhanced our understanding for cancer, spatial transcriptomics enable the characterisation of cellular interactions. Here, the authors integrate single cell data with spatial information for HER2 + tumours and develop tools for the prediction of interactions between tumour-infiltrating cells.
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| 6. |
- Andersson, Alma, et al.
(författare)
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Spatial Deconvolution of HER2-positive Breast Tumors Reveals Novel Intercellular Relationships
- 2020
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra-and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. We integrate and spatially map tumor-associated types from single cell data to find: segregated epithelial cells, interactions between B and T-cells and myeloid cells, co-localization of macrophage and T-cell subsets. A model is constructed to infer presence of tertiary lymphoid structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define novel interactions between tumor-infiltrating cells in breast cancer and provide tools generalizing across tissues and diseases.
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| 7. |
- Ansari, Daniel, et al.
(författare)
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Pancreatic cancer : Yesterday, today and tomorrow
- 2016
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Ingår i: Future Oncology. - : Future Medicine Ltd. - 1479-6694 .- 1744-8301. ; 12:16, s. 1929-1946
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Tidskriftsartikel (refereegranskat)abstract
- Pancreatic cancer is one of our most lethal malignancies. Despite substantial improvements in the survival rates for other major cancer forms, pancreatic cancer survival rates have remained relatively unchanged since the 1960s. Pancreatic cancer is usually detected at an advanced stage and most treatment regimens are ineffective, contributing to the poor overall prognosis. Herein, we review the current understanding of pancreatic cancer, focusing on central aspects of disease management from radiology, surgery and pathology to oncology.
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| 8. |
- Ashitani, Tatsuya, et al.
(författare)
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Activity studies of sesquiterpene oxides and sulfides from the plant Hyptis suaveolens (Lamiaceae) and its repellency on Ixodes ricinus (Acari:Ixodidae)
- 2015
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Ingår i: Experimental & applied acarology. - : Springer Science and Business Media LLC. - 0168-8162 .- 1572-9702. ; 67:4, s. 595-606
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Tidskriftsartikel (refereegranskat)abstract
- Hyptis suaveolens (Lamiaceae), a plant traditionally used as a mosquito repellent, has been investigated for repellent properties against nymphs of the tick Ixodes ricinus. Essential oils and volatile compounds of fresh and dried leaves, from plants originating from Laos and Guinea-Bissau, were identified by GC-MS and tested in a tick repellency bioassay. All the essential oils were strongly repellent against the ticks, even though the main volatile constituents differed in their proportions of potentially tick repellent chemicals. (+)/(-)-sabinene were present in high amounts in all preparations, and dominated the emission from dry and fresh leaves together with 1,8-cineol and alpha-phellandrene. 1,8-Cineol and sabinene were major compounds in the essential oils from H. suaveolens from Laos. Main compounds in H. suaveolens from Guinea-Bissau were (-)-sabinene, limonene and terpinolene. Among the sesquiterpene hydrocarbons identified, alpha-humulene exhibited strong tick repellency (96.8 %). Structure activity studies of oxidation or sulfidation products of germacrene D, alpha-humulene and beta-caryophyllene, showed increased tick repellent activity: of mint sulfide (59.4 %), humulene-6,7-oxide (94.5 %) and caryophyllene-6,7-oxide (96.9 %). The substitution of oxygen with sulfur slightly lowered the repellency. The effects of the constituents in the oils can then be regarded as a trade off between the subsequently lower volatility of the sesquiterpene derivatives compared to the monoterpenes and may thus increase their potential usefulness as tick repellents.
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| 9. |
- Bijnens, Johan, et al.
(författare)
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Isospin breaking in K -> 3 pi decays I: strong isospin breaking
- 2004
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Ingår i: Nuclear Physics, Section B. - : Elsevier BV. - 0550-3213. ; 697:1-2, s. 319-342
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Tidskriftsartikel (refereegranskat)abstract
- The CP conserving amplitudes for the decays K --> 3pi are calculated in Chiral Perturbation Theory. The calculation is made at the next-to-leading order including strong and local electromagnetic isospin breaking. A comparison is made between the squared amplitudes with and without isospin violation to estimate the size of the effect. We find corrections of order five percent in the amplitudes.
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| 10. |
- Bijnens, Johan, et al.
(författare)
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Isospin breaking in K -> 3 pi decays II: radiative corrections
- 2005
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 39:3, s. 347-357
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Tidskriftsartikel (refereegranskat)abstract
- The five different CP conserving amplitudes for the decays K --> 3pi are calculated using Chiral Perturbation Theory. The calculation is made to next-to-leading order and includes full isospin breaking. The squared amplitudes are compared with the corresponding ones in the isospin limit to estimate the size of the isospin breaking effects. In this paper we add the radiative corrections to the earlier calculated m(u) - m(d) and local electromagnetic effects. We find corrections of order 5 - 10 percent.
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