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| 2. |
- Danielsson, Frida, et al.
(författare)
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Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia
- 2018
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Ingår i: Oncotarget. - : Impact Journals LLC. - 1949-2553. ; 9:28, s. 19730-19744
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Tidskriftsartikel (refereegranskat)abstract
- In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing their surrounding vasculature network. Transformed cancer cells are known to exhibit phenotypic alterations, enabling continuous proliferation despite a limited oxygen supply. The four-step isogenic BJ cell model enables studies of defined steps of tumorigenesis: the normal, immortalized, transformed, and metastasizing stages. By transcriptome profiling under atmospheric and moderate hypoxic (3% O2) conditions, we observed that despite being highly similar, the four cell lines of the BJ model responded strikingly different to hypoxia. Besides corroborating many of the known responses to hypoxia, we demonstrate that the transcriptome adaptation to moderate hypoxia resembles the process of malignant transformation. The transformed cells displayed a distinct capability of metabolic switching, reflected in reversed gene expression patterns for several genes involved in oxidative phosphorylation and glycolytic pathways. By profiling the stage-specific responses to hypoxia, we identified ASS1 as a potential prognostic marker in hypoxic tumors. This study demonstrates the usefulness of the BJ cell model for highlighting the interconnection of pathways involved in malignant transformation and hypoxic response.
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| 3. |
- Furberg, Helena, et al.
(författare)
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Genome-wide meta-analyses identify multiple loci associated with smoking behavior
- 2010
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 42:5, s. 134-441
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Tidskriftsartikel (refereegranskat)abstract
- Consistent but indirect evidence has implicated genetic factors in smoking behavior1,2. We report meta-analyses of several smoking phenotypes within cohorts of the Tobacco and Genetics Consortium (n = 74,053). We also partnered with the European Network of Genetic and Genomic Epidemiology (ENGAGE) and Oxford-GlaxoSmithKline (Ox-GSK) consortia to follow up the 15 most significant regions (n > 140,000). We identified three loci associated with number of cigarettes smoked per day. The strongest association was a synonymous 15q25 SNP in the nicotinic receptor gene CHRNA3 (rs1051730[A], b = 1.03, standard error (s.e.) = 0.053, beta = 2.8 x 10(-73)). Two 10q25 SNPs (rs1329650[G], b = 0.367, s. e. = 0.059, beta = 5.7 x 10(-10); and rs1028936[A], b = 0.446, s. e. = 0.074, beta = 1.3 x 10(-9)) and one 9q13 SNP in EGLN2 (rs3733829[G], b = 0.333, s. e. = 0.058, P = 1.0 x 10(-8)) also exceeded genome-wide significance for cigarettes per day. For smoking initiation, eight SNPs exceeded genome-wide significance, with the strongest association at a nonsynonymous SNP in BDNF on chromosome 11 (rs6265[C], odds ratio (OR) = 1.06, 95% confidence interval (Cl) 1.04-1.08, P = 1.8 x 10(-8)). One SNP located near DBH on chromosome 9 (rs3025343[G], OR = 1.12, 95% Cl 1.08-1.18, P = 3.6 x 10(-8)) was significantly associated with smoking cessation.
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| 4. |
- Hertting, Olof, et al.
(författare)
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Vitamin D-deficient mice have more invasive urinary tract infection
- 2017
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Ingår i: PLOS ONE. - : Public Library Science. - 1932-6203. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- Vitamin D deficiency is a common health problem with consequences not limited to bone and calcium hemostasis. Low levels have also been linked to tuberculosis and other respiratory infections as well as autoimmune diseases. We have previously shown that supplementation with vitamin D can induce the antimicrobial peptide cathelicidin during ex vivo infection of human urinary bladder. In rodents, however, cathelicidin expression is not linked to vitamin D and therefore this vitamin D-related effect fighting bacterial invasion is not relevant. To determine if vitamin D had further protective mechanisms during urinary tract infections, we therefore used a mouse model. In vitamin D-deficient mice, we detected more intracellular bacterial communities in the urinary bladder, higher degree of bacterial spread to the upper urinary tract and a skewed cytokine response. Furthermore, we show that the vitamin D receptor was upregulated in the urinary bladder and translocated into the cell nucleus after E. coli infection. This study supports a more general role for vitamin D as a local immune response mediator in the urinary tract.
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| 5. |
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| 6. |
- Mahdessian, Diana, et al.
(författare)
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Profiling the human cytoplasmic proteome.
- 2016
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Ingår i: Molecular Biology of the Cell. - : AMER SOC CELL BIOLOGY. - 1059-1524 .- 1939-4586. ; 27
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Tidskriftsartikel (refereegranskat)
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| 7. |
- Mahdessian, Diana, et al.
(författare)
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Spatiotemporal characterization of the human proteome.
- 2017
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Ingår i: Molecular Biology of the Cell. - : The American Society for Cell Biology - ASCB. - 1059-1524 .- 1939-4586. ; 28
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 8. |
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| 9. |
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| 10. |
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| 11. |
- Petroff, E., et al.
(författare)
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A polarized fast radio burst at low Galactic latitude
- 2017
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford Academic. - 0035-8711 .- 1365-2966. ; 469:4, s. 4465-4482
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Tidskriftsartikel (refereegranskat)abstract
- We report on the discovery of a new fast radio burst (FRB), FRB 150215, with the Parkes radio telescope on 2015 February 15. The burst was detected in real time with a dispersion measure (DM) of 1105.6 +/- 0.8 pc cm(-3), a pulse duration of 2.8(-0.5)(+1.2) ms, and a measured peak flux density assuming that the burst was at beam centre of 0.7(-0.1)(+0.2) Jy. The FRB originated at a Galactic longitude and latitude of 24.66 degrees, 5.28 degrees and 25 degrees away from the Galactic Center. The burst was found to be 43 +/- 5 per cent linearly polarized with a rotation measure (RM) in the range -9 < RM < 12 rad m(-2) (95 per cent confidence level), consistent with zero. The burst was followed up with 11 telescopes to search for radio, optical, X-ray, gamma-ray and neutrino emission. Neither transient nor variable emission was found to be associated with the burst and no repeat pulses have been observed in 17.25 h of observing. The sightline to the burst is close to the Galactic plane and the observed physical properties of FRB 150215 demonstrate the existence of sight lines of anomalously low RM for a given electron column density. The Galactic RM foreground may approach a null value due to magnetic field reversals along the line of sight, a decreased total electron column density from the Milky Way, or some combination of these effects. A lower Galactic DM contribution might explain why this burst was detectable whereas previous searches at low latitude have had lower detection rates than those out of the plane.
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| 12. |
- Sullivan, Devin, et al.
(författare)
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Design automation for biological models : A pipeline that incorporates spatial and molecular complexity
- 2015
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Ingår i: Proceedings of the ACM Great Lakes Symposium on VLSI, GLSVLSI. - New York, NY, USA : ACM Press. - 9781450334747 ; , s. 321-323
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Konferensbidrag (refereegranskat)abstract
- Understanding the dynamics of biochemical networks is a major goal of systems biology. Due to the heterogeneity of cells and the low copy numbers of key molecules, spatially resolved approaches are required to fully understand and model these systems. Until recently, most spatial modeling was performed using geometries obtained either through manual segmentation or manual fabrication both of which are time-consuming and tedious. Similarly, the system of reactions associated with the model had to be manually defined, a process that is both tedious and error-prone for large networks. As a result, spatially resolved simulations have typically only been performed in a limited number of geometries, which are often highly simplified, and with small reaction networks.
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| 13. |
- Sullivan, Devin P., et al.
(författare)
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Deep learning is combined with massive-scale citizen science to improve large-scale image classification
- 2018
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Ingår i: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 36:9, s. 820-
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Tidskriftsartikel (refereegranskat)abstract
- Pattern recognition and classification of images are key challenges throughout the life sciences. We combined two approaches for large-scale classification of fluorescence microscopy images. First, using the publicly available data set from the Cell Atlas of the Human Protein Atlas (HPA), we integrated an image-classification task into a mainstream video game (EVE Online) as a mini-game, named Project Discovery. Participation by 322,006 gamers over 1 year provided nearly 33 million classifications of subcellular localization patterns, including patterns that were not previously annotated by the HPA. Second, we used deep learning to build an automated Localization Cellular Annotation Tool (Loc-CAT). This tool classifies proteins into 29 subcellular localization patterns and can deal efficiently with multi-localization proteins, performing robustly across different cell types. Combining the annotations of gamers and deep learning, we applied transfer learning to create a boosted learner that can characterize subcellular protein distribution with F1 score of 0.72. We found that engaging players of commercial computer games provided data that augmented deep learning and enabled scalable and readily improved image classification.
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| 14. |
- Sullivan, Devin P., et al.
(författare)
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Seeing More : A Future of Augmented Microscopy
- 2018
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Ingår i: Cell. - : Cell Press. - 0092-8674 .- 1097-4172. ; 173:3, s. 546-548
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Tidskriftsartikel (refereegranskat)abstract
- Microscope images are information rich. In this issue of Cell, Christiansen et al. show that label-free images of cells can be used to predict fluorescent labels representing cell type, state, and organelle distribution using a deep-learning framework. This paves the way for computationally multiplexed assays derived from inexpensive label-free microscopy. Microscope images are information rich. In this issue of Cell, Christiansen et al. show that label-free images of cells can be used to predict fluorescent labels representing cell type, state, and organelle distribution using a deep-learning framework. This paves the way for computationally multiplexed assays derived from inexpensive label-free microscopy.
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| 15. |
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| 16. |
- Thul, Peter, et al.
(författare)
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Exploring the Proteome of Multilocalizing Proteins
- 2017
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Ingår i: Molecular Biology of the Cell. - : American Society for Cell Biology. - 1059-1524 .- 1939-4586. ; 28
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 17. |
- Thul, Peter J., et al.
(författare)
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A subcellular map of the human proteome
- 2017
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 356:6340
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Tidskriftsartikel (refereegranskat)abstract
- Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.
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| 18. |
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| 19. |
- Uhlén, Mathias, et al.
(författare)
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The human secretome
- 2019
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Ingår i: Science Signaling. - : American Association for the Advancement of Science (AAAS). - 1945-0877 .- 1937-9145. ; 12:609
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Tidskriftsartikel (refereegranskat)abstract
- The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immuno-assays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.
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| 20. |
- Wiking, Mikaela, et al.
(författare)
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Drafting the intermediate filament proteome
- 2016
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Ingår i: Molecular Biology of the Cell. - : American society of cell biology. - 1059-1524 .- 1939-4586. ; 27
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Tidskriftsartikel (refereegranskat)
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