| 1. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 2. |
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| 3. |
- Bruzzi, M, et al.
(författare)
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Radiation-hard semiconductor detectors for SuperLHC
- 2005
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002. ; 541:1-2, s. 189-201
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Tidskriftsartikel (refereegranskat)abstract
- An option of increasing the luminosity of the Large Hadron Collider (LHC) at CERN to 1035 cm-2 s-1 has been envisaged to extend the physics reach of the machine. An efficient tracking down to a few centimetres from the interaction point will be required to exploit the physics potential of the upgraded LHC. As a consequence, the semiconductor detectors close to the interaction region will receive severe doses of fast hadron irradiation and the inner tracker detectors will need to survive fast hadron fluences of up to above 1016cm-2. The CERN-RD50 project "Development of Radiation Hard Semiconductor Devices for Very High Luminosity Colliders" has been established in 2002 to explore detector materials and technologies that will allow to operate devices up to, or beyond, this limit. The strategies followed by RD50 to enhance the radiation tolerance include the development of new or defect engineered detector materials (SiC, GaN, Czochralski and epitaxial silicon, oxygen enriched Float Zone silicon), the improvement of present detector designs and the understanding of the microscopic defects causing the degradation of the irradiated detectors. The latest advancements within the RD50 collaboration on radiation hard semiconductor detectors will be reviewed and discussed in this work.
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| 4. |
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| 5. |
- Jokipii-Lukkari, Soile, et al.
(författare)
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NorWood : a gene expression resource for evo-devo studies of conifer wood development
- 2017
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 216:2, s. 482-494
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Tidskriftsartikel (refereegranskat)abstract
- The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development.RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks.Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in A. thaliana and P. tremula, but not in P. abies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies.The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.
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| 6. |
- Kuzmin, M., et al.
(författare)
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Surface core-level shifts on Ge(111)c(2 x 8) : Experiment and theory
- 2011
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 83:24, s. 245319-
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Tidskriftsartikel (refereegranskat)abstract
- Combining high-resolution photoelectron spectroscopy and density functional theory (DFT) calculations, 3d photoemission line shape and surface core-level shifts have been reinvestigated on the Ge(111)c(2 x 8) surface. It is found that 3d spectra include, in addition to the bulk and three surface-shifted components reported in literature, a component that was not identified in earlier measurements with a lower resolution. The detailed interpretation of these spectra and their line shape is made on the basis of DFT calculations. It is shown that the lowest binding energy component is due to the rest atoms. The higher binding energy emission is caused by the adatoms and the third-layer atoms that are below the adatoms. Finally, the two other surface components originate from the first- and second-layer atoms. The screening effects in the Ge(111)c(2 x 8) are discussed.
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| 7. |
- Lang, J. J. K., et al.
(författare)
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Tin-stabilized (1 x 2) and (1 x 4) reconstructions on GaAs(100) and InAs(100) studied by scanning tunneling microscopy, photoelectron spectroscopy, and ab initio calculations
- 2011
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Ingår i: Surface Science. - : Elsevier BV. - 0039-6028 .- 1879-2758. ; 605:9-10, s. 883-888
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Tidskriftsartikel (refereegranskat)abstract
- Tin (Sn) induced (1 x 2) reconstructions on GaAs(100) and InAs(100) substrates have been studied by low energy electron diffraction (LEED), photoelectron spectroscopy, scanning tunneling microscopy/spectroscopy (STM/STS) and ab initio calculations. The comparison of measured and calculated STM images and surface core-level shifts shows that these surfaces can be well described with the energetically stable building blocks that consist of Sn-III dimers. Furthermore, a new Sn-induced (1 x 4) reconstruction was found. In this reconstruction the occupied dangling bonds are closer to each other than in the more symmetric (1 x 2) reconstruction, and it is shown that the (1 x 4) reconstruction is stabilized as the adatom size increases.
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| 8. |
- Sundell, David, et al.
(författare)
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AspWood : High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula
- 2017
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Ingår i: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 29:7, s. 1585-1604
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Tidskriftsartikel (refereegranskat)abstract
- Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula. The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies. The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.
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| 9. |
- Sundell, David, et al.
(författare)
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High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
- 2016
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, however, efforts to engineer new, elite varieties are constrained by the lack of a comprehensive understanding of the transcriptional network underlying cambial growth and wood formation. We generated RNA Sequencing transcriptome data for four mature, wild-growing aspens (Populus tremula) from high-spatial-resolution tangential cryosection series spanning the secondary phloem, vascular cambium, expanding and secondary cell wall forming xylem cells, cell death zone and the previous years annual ring. The transcriptome comprised 28,294 expressed, previously annotated protein-coding genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication had diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. We performed co-expression network analysis to identify central transcriptional modules and associated several of these with known biological processes. This revealed previously uncharacterized complexity underlying the regulation of cambial growth and wood formation, with modules forming a continuum of activated processes across the tissues. The high spatial resolution suggested novel roles for known genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and components of lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the co-expression network of cambial growth and wood formation.
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| 10. |
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| 11. |
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| 12. |
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| 13. |
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| 14. |
- Azimi, A, et al.
(författare)
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Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells
- 2017
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Ingår i: Cell death & disease. - : Springer Science and Business Media LLC. - 2041-4889. ; 8:8, s. e3029-
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Tidskriftsartikel (refereegranskat)abstract
- A majority of patients with BRAF-mutated metastatic melanoma respond to therapy with BRAF inhibitors (BRAFi), but relapses are common owing to acquired resistance. To unravel BRAFi resistance mechanisms we have performed gene expression and mass spectrometry based proteome profiling of the sensitive parental A375 BRAF V600E-mutated human melanoma cell line and of daughter cell lines with induced BRAFi resistance. Increased expression of two novel resistance candidates, aminopeptidase-N (CD13/ANPEP) and ETS transcription factor FLI1 was observed in the BRAFi-resistant daughter cell lines. In addition, increased levels of the previously reported resistance mediators, receptor tyrosine kinase ephrine receptor A2 (EPHA2) and the hepatocyte growth factor receptor MET were also identified. The expression of these proteins was assessed in matched tumor samples from melanoma patients obtained before BRAFi and after disease progression. MET was overexpressed in all progression samples while the expression of the other candidates varied between the individual patients. Targeting CD13/ANPEP by a blocking antibody induced apoptosis in both parental A375- and BRAFi-resistant daughter cells as well as in melanoma cells with intrinsic BRAFi resistance and led to dephosphorylation of EPHA2 on S897, previously demonstrated to cause inhibition of the migratory capacity. AKT and RSK, both reported to induce EPHA2 S897 phosphorylation, were also dephosphorylated after inhibition of CD13/ANPEP. FLI1 silencing also caused decreases in EPHA2 S897 phosphorylation and in total MET protein expression. In addition, silencing of FLI1 sensitized the resistant cells to BRAFi. Furthermore, we show that BRAFi in combination with the multi kinase inhibitor dasatinib can abrogate BRAFi resistance and decrease both EPHA2 S897 phosphorylation and total FLI1 protein expression. This is the first report presenting CD13/ANPEP and FLI1 as important mediators of resistance to BRAF inhibition with potential as drug targets in BRAFi refractory melanoma.
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| 15. |
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| 16. |
- Das, I, et al.
(författare)
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AXL and CAV-1 play a role for MTH1 inhibitor TH1579 sensitivity in cutaneous malignant melanoma
- 2020
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Ingår i: Cell death and differentiation. - : Springer Science and Business Media LLC. - 1476-5403 .- 1350-9047. ; 27:7, s. 2081-2098
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Tidskriftsartikel (refereegranskat)abstract
- Cutaneous malignant melanoma (CMM) is the deadliest form of skin cancer and clinically challenging due to its propensity to develop therapy resistance. Reactive oxygen species (ROS) can induce DNA damage and play a significant role in CMM. MTH1 protein protects from ROS damage and is often overexpressed in different cancer types including CMM. Herein, we report that MTH1 inhibitor TH1579 induced ROS levels, increased DNA damage responses, caused mitotic arrest and suppressed CMM proliferation leading to cell death both in vitro and in an in vivo xenograft CMM zebrafish disease model. TH1579 was more potent in abrogating cell proliferation and inducing cell death in a heterogeneous co-culture setting when compared with CMM standard treatments, vemurafenib or trametinib, showing its broad anticancer activity. Silencing MTH1 alone exhibited similar cytotoxic effects with concomitant induction of mitotic arrest and ROS induction culminating in cell death in most CMM cell lines tested, further emphasizing the importance of MTH1 in CMM cells. Furthermore, overexpression of receptor tyrosine kinase AXL, previously demonstrated to contribute to BRAF inhibitor resistance, sensitized BRAF mutant and BRAF/NRAS wildtype CMM cells to TH1579. AXL overexpression culminated in increased ROS levels in CMM cells. Moreover, silencing of a protein that has shown opposing effects on cell proliferation, CAV-1, decreased sensitivity to TH1579 in a BRAF inhibitor resistant cell line. AXL-MTH1 and CAV-1-MTH1 mRNA expressions were correlated as seen in CMM clinical samples. Finally, TH1579 in combination with BRAF inhibitor exhibited a more potent cell killing effect in BRAF mutant cells both in vitro and in vivo. In summary, we show that TH1579-mediated efficacy is independent of BRAF/NRAS mutational status but dependent on the expression of AXL and CAV-1.
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| 17. |
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| 18. |
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| 19. |
- Das, I, et al.
(författare)
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Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status
- 2019
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Ingår i: Cell death & disease. - : Springer Science and Business Media LLC. - 2041-4889. ; 10:9, s. 663-
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Tidskriftsartikel (refereegranskat)abstract
- Current treatment modalities for disseminated cutaneous malignant melanoma (CMM) improve survival; however, relapses are common. A number of receptor tyrosine kinases (RTKs) including EGFR and MET have been reported to be involved in CMM metastasis and in the development of resistance to therapy, targeting the mitogen-activated protein kinase (MAPK pathway). IHC analysis showed that patients with higher MET protein expression had a significantly shorter overall survival. In addition, silencing of MET caused an upregulation of EGFR and p-AKT, which was abrogated by concomitant silencing of MET and EGFR in CMM cells resistant to MAPK-targeting drugs. We therefore explored novel treatment strategies using clinically approved drugs afatinib (ERBB family inhibitor) and crizotinib (MET inhibitor), to simultaneously block MET and ERBB family RTKs. The effects of the combination were assessed in cell culture and spheroid models using established CMM and patient-derived short-term cell lines, and an in vivo xenograft mouse model. The combination had a synergistic effect, promoting cell death, concomitant with a potent downregulation of migratory and invasive capacity independent of their BRAF/NRAS mutational status. Furthermore, the combination attenuated tumor growth rate, as ascertained by the significant reduction of Ki67 expression and induced DNA damage in vivo. Importantly, this combination therapy had minimal therapy-related toxicity in mice. Lastly, the cell cycle G2 checkpoint kinase WEE1 and the RTK IGF1R, non-canonical targets, were altered upon exposure to the combination. Knockdown of WEE1 abrogated the combination-mediated effects on cell migration and proliferation in BRAF mutant BRAF inhibitor-sensitive cells, whereas WEE1 silencing alone inhibited cell migration in NRAS mutant cells. In summary, our results show that afatinib and crizotinib in combination is a promising alternative targeted therapy option for CMM patients, irrespective of BRAF/NRAS mutational status, as well as for cases where resistance has developed towards BRAF inhibitors.
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| 20. |
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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Ferreira, Ana R. V., et al.
(författare)
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Comparison of different coating techniques on the properties of FucoPol films
- 2017
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Ingår i: International Journal of Biological Macromolecules. - : Elsevier BV. - 0141-8130 .- 1879-0003. ; 103, s. 268-274
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Tidskriftsartikel (refereegranskat)abstract
- Plasma deposition, liquid flame spray (LFS) and atomic layer deposition (ALD) were used to form inorganic coatings in new exopolysaccharide (FucoPol) biodegradable films. Coated films were characterised in terms of surface, optical and barrier properties in order to evaluate their potential use in food packaging. FucoPol films presented dense and homogeneous surface with instant water contact angle of 95̊. Plasma deposition of perfluorohexane (PFH) on FucoPol surface has not shown significant improvement in the hydrophobic behaviour over the time. The FucoPol coating of SiO2 nanoparticles deposited by LFS and plasma deposition of PFH have shown higher instant water contact angle (135°) caused by coating surface roughness, but this hydrophobic behaviour was not stable over time. FucoPol films coated only with TiO2 deposited by ALD and combination of that with plasma deposition of PFH have shown stable water contact angle during time (90̊ and 115̊, respectively), transparency in the same order of magnitude and significantly lower permeability to water vapour (3.45 × 10−11 mol/m s Pa and 3.45 × 10−11 mol/m s Pa when compared to uncoated films with 5.32 × 10−11 mol/m s Pa). Moreover, films coated with TiO2-PFH have also shown a permeability to oxygen of 1.70 × 10−16 molm/m2s Pa which is 67% lower than uncoated films.
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| 25. |
- Gandla, Madhavi Latha, et al.
(författare)
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Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
- 2021
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Ingår i: Biotechnology for Biofuels. - : Springer Science and Business Media LLC. - 1754-6834. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth. Results In this study, we report on transgenic hybrid aspen (Populus tremula x tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula x tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20-44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26-50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control. Conclusions The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.
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| 26. |
- Giacomello, Stefania, et al.
(författare)
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High spatial resolution profiling in tree species
- 2019
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Ingår i: Annual Plant Reviews Online. - : Wiley. - 2639-3832. ; 2:1, s. 329-359
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Tidskriftsartikel (refereegranskat)abstract
- Until recently, the majority of genomics assays have been performed on bulk tissue samples containing multiple cell types. Tissues such as the wood formation zone in trees contain a complex mix of cell types organised in three-dimensional space. Moreover, cells within the wood formation zone represent a continual developmental progression from meristematic cambial initials through to cell death. This spatiotemporal developmental gradient and cell type information are not assayed by bulk samples. New and improved sampling methods coupled to next-generation sequencing assays are enabling the generation of high spatial resolution and single-cell transcriptomics data, offering unprecedented insight into the biology of unique cell types and cell developmental programs.We overview the application of these approaches to the study of wood development, in particular, and highlight challenges associated with the analysis of such data.
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| 27. |
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| 28. |
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| 29. |
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| 30. |
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| 31. |
- Iles, Mark M., et al.
(författare)
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A variant in FTO shows association with melanoma risk not due to BMI
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:4, s. 428-432
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Tidskriftsartikel (refereegranskat)abstract
- We report the results of an association study of melanoma that is based on the genome-wide imputation of the genotypes of 1,353 cases and 3,566 controls of European origin conducted by the GenoMEL consortium. This revealed an association between several SNPs in intron 8 of the FTO gene, including rs16953002, which replicated using 12,313 cases and 55,667 controls of European ancestry from Europe, the USA and Australia (combined P = 3.6 x 10(-12), per-allele odds ratio for allele A = 1.16). In addition to identifying a new melanomasusceptibility locus, this is to our knowledge the first study to identify and replicate an association with SNPs in FTO not related to body mass index (BMI). These SNPs are not in intron 1 (the BMI-related region) and exhibit no association with BMI. This suggests FTO's function may be broader than the existing paradigm that FTO variants influence multiple traits only through their associations with BMI and obesity.
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| 32. |
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| 33. |
- Kuzmin, M., et al.
(författare)
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Atomic structure of Yb/Si(100)(2X6) : Interrelation between the silicon dimer arrangement and Si 2p photoemission line shape
- 2010
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 82:11, s. 113302-
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Tidskriftsartikel (refereegranskat)abstract
- Combining photoelectron spectroscopy and density-functional theory calculations, we have studied the atomic geometry of Yb/Si(100)(2 X 6) reconstruction and the mechanisms responsible for its stabilization as well as the influence of this reconstruction on Si 2p core-level photoemission. The analysis of measured and calculated surface core-level shifts supports the recently proposed model of the Yb/Si(100)(2 X 6). It involves, in agreement with valence-band measurements, unbuckled (symmetrical) silicon dimers, leading to unusually narrowed Si 2p line shape as compared to those of related systems. The origin of the symmetrical dimers in the (2 X 6) structure is discussed in the context of previous results in literature.
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| 34. |
- Lang, J. J. K., et al.
(författare)
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Unveiling and controlling the electronic structure of oxidized semiconductor surfaces: Crystalline oxidized InSb(100)(1 x 2)-O
- 2014
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 90:4
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Tidskriftsartikel (refereegranskat)abstract
- The exothermic nature of oxidation causes nearly all semiconductor applications in various fields like electronics, medicine, photonics, and sensor technology to acquire an oxidized semiconductor surface part during the application manufacturing. The significance of understanding and controlling the atomic scale properties of oxidized semiconductor surfaces is expected to increase even further with the development of nanoscale semiconductor crystals. The nature of oxidized semiconductor layers is, however, hard to predict and characterize as they are usually buried and amorphous. To shed light on these issues, we pursue a different approach based on oxidized III-V semiconductor layers that are crystalline. We present a comprehensive characterization of oxidized crystalline InSb(100)(1 x 2)-O layers by ab initio calculations, photoelectron spectroscopy, scanning tunneling microscopy, and spectroscopy, and demonstrate the electronic band structures of different oxidized phases of the semiconductor, which elucidate the previous contradictory semiconductor-oxidation effects. At 0.5 monolayer (ML) oxidation, oxygen atoms tend to occupy subsurface Sb sites, leading to metallic states in the semiconductor band gap, which arise from top dimers. When the oxidation is increased to the 1.0-2.0 ML concentration, oxygen occupies also interstitial sites, and the insulating band structure without gap states is stabilized with unusual occupied In dangling bonds. In contrast, the 2.5-3.0 ML oxide phases undergo significant changes toward a less ordered structure. The findings suggest a methodology for manipulating the electronic structure of oxidized semiconductor layers.
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| 35. |
- Laukkanen, P, et al.
(författare)
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Local variation in Bi crystal sites of epitaxial GaAsBi studied by photoelectron spectroscopy and first-principles calculations
- 2017
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Ingår i: Applied Surface Science. - : Elsevier BV. - 0169-4332. ; 396, s. 688-694
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Tidskriftsartikel (refereegranskat)abstract
- Epitaxial Bi-containing III–V crystals (III-V1-xBix) have attracted increasing interest due to their potential in infrared applications. Atomic-scale characterization and engineering of bulk-like III-V1-xBix properties (e.g., Bi incorporation and defect formation) are challenging but relevant to develop applications. Toward that target, we report here that the traditional surface-science measurement of photoelectron spectroscopy (PES) is a potential, non-destructive method to be combined in the studies of bulk-like properties, when surface effects are properly removed. We have investigated epitaxial GaAs1-xBix films, capped by epitaxial AlAs layers, with high-resolution photoelectron spectroscopy. The Bi5d core-level spectra of GaAs1-xBix together with ab-initio calculations give direct evidence of variation of Bi bonding environment in the lattice sites. The result agrees with photoluminescence (PL) measurement which shows that the studied GaAs1-xBix films include local areas with higher Bi content, which contribute to PL but do not readily appear in x-ray diffraction (XRD). The measured and calculated Bi core-level shifts show also that Ga vacancies and Bi clusters are dominant defects.
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| 36. |
- Makela, J., et al.
(författare)
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Line shape and composition of the In 3d(5/2) core-level photoemission for the interface analysis of In-containing III-V semiconductors
- 2015
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Ingår i: Applied Surface Science. - : Elsevier BV. - 1873-5584 .- 0169-4332. ; 329, s. 371-375
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Tidskriftsartikel (refereegranskat)abstract
- The In 3d(5/2) photoelectron spectroscopy peak has been widely used to determine the interface structures of In-containing III-V device materials (e.g., oxidation states). However, an unclear parameter affecting the determination of the energy shifts and number of the core-level components, and therefore, the interpreted interface structure and composition, is still the intrinsic In 3d(5/2) peak line shape. It is undecided whether the line shape is naturally symmetric or asymmetric for pure In-containing III-V compounds. By using high-resolution photoelectron spectroscopy, we show that the In 3d(5/2) asymmetry arising from the emission at high binding-energy tail is not an intrinsic property of InAs, InP, InSb and InGaAs. Furthermore, it is shown that asymmetry of In 3d(5/2) peaks of pure III-V's originates from the natural surface reconstructions which cause the coexistence of slightly shifted In 3d(5/2) components with the symmetric peak shape and dominant Lorentzian broadening. (C) 2015 Elsevier B.V. All rights reserved.
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| 37. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 38. |
- Obudulu, Ogonna, et al.
(författare)
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A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees
- 2018
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Ingår i: BMC Genomics. - : Springer Publishing Company. - 1471-2164. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3;Potri.019G104000).Results: The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis.Conclusions: Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.
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| 39. |
- Perkins, CE, et al.
(författare)
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Internet connectivity for mobile ad hoc networks
- 2002
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Ingår i: Wireless Communications & Mobile Computing. - : Wiley. - 1530-8677 .- 1530-8669. ; 2:5, s. 465-482
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Tidskriftsartikel (refereegranskat)abstract
- The need for ad hoc networks arises when a number of mobile nodes gather in one particular location and form autonomous networks. Ad hoc networks can be adjoined to the Internet, introducing routing and addressing issues that require new features from ad hoc networking protocols. The Internet Gateway can offer global addressability and bidirectional Internet connectivity to every node in the ad hoc network. This can be done in such a way that mobile wireless nodes can migrate between wireless access points that have direct access to the wired Internet and the wireless ad hoc networks that do not have any such local access point infrastructure. Mobile IP can be employed to make such movement seamless (whenever physically possible), even though it occurs between domains with previously incompatible routing models. We believe that IPv6 and Mobile IPv6 afford important advantages for making such attachments, especially regarding router advertisement and address autoconfiguration. In this paper, we show how general ad hoc networks can be connected to the Internet by Internet Gateways, and then describe our specific experiments with Ad hoc On-Demand Distance Vector Routing (AODV) for IPv6 (AODV6). After demonstrating the basic principles allowing access to the Internet, we then detail our further experiments using Mobile IPv6. Copyright (C) 2002 John Wiley Sons, Ltd.
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| 43. |
- Seyfferth, Carolin, et al.
(författare)
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PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen
- 2021
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Ingår i: Cells. - : MDPI. - 2073-4409. ; 10:8
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Tidskriftsartikel (refereegranskat)abstract
- Secondary growth relies on precise and specialized transcriptional networks that determine cell division, differentiation, and maturation of xylem cells. We identified a novel role for the ethylene-induced Populus Ethylene Response Factor PtERF85 (Potri.015G023200) in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen (Populus tremula x tremuloides). Expression of PtERF85 is high in phloem and cambium cells and during the expansion of xylem cells, while it is low in maturing xylem tissue. Extending PtERF85 expression into SCW forming zones of woody tissues through ectopic expression reduced wood density and SCW thickness of xylem fibers but increased fiber diameter. Xylem transcriptomes from the transgenic trees revealed transcriptional induction of genes involved in cell expansion, translation, and growth. The expression of genes associated with plant vascular development and the biosynthesis of SCW chemical components such as xylan and lignin, was down-regulated in the transgenic trees. Our results suggest that PtERF85 activates genes related to xylem cell expansion, while preventing transcriptional activation of genes related to SCW formation. The importance of precise spatial expression of PtERF85 during wood development together with the observed phenotypes in response to ectopic PtERF85 expression suggests that PtERF85 contributes to the transition of fiber cells from elongation to secondary cell wall deposition.
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- Svedman, FC, et al.
(författare)
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Proliferation and Immune Response Gene Signatures Associated with Clinical Outcome to Immunotherapy and Targeted Therapy in Metastatic Cutaneous Malignant Melanoma
- 2022
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 14:15
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Tidskriftsartikel (refereegranskat)abstract
- Targeted therapy (TT), together with immune checkpoint inhibitors (ICI), has significantly improved clinical outcomes for patients with advanced cutaneous malignant melanoma (CMM) during the last decade. However, the magnitude and the duration of response vary considerably. There is still a paucity of predictive biomarkers to identify patients who benefit most from treatment. To address this, we performed targeted transcriptomics of CMM tumors to identify biomarkers associated with clinical outcomes. Pre-treatment tumor samples from 28 patients with advanced CMM receiving TT (n = 13) or ICI (n = 15) were included in the study. Targeted RNA sequencing was performed using Ion AmpliSeq ™, followed by gene set enrichment analysis (GSEA) using MSigDB’s Hallmark Gene Set Collection to identify gene expression signatures correlating with treatment outcome. The GSEA demonstrated that up-regulation of allograft rejection genes, together with down-regulation of E2F and MYC targets as well as G2M checkpoint genes, significantly correlated with longer progression-free survival on ICI while IFNγ and inflammatory response genes were associated with a better clinical outcome on TT. In conclusion, we identify novel genes and their expression signatures as potential predictive biomarkers for TT and ICI in patients with metastatic CMM, paving the way for clinical use following larger validation studies.
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- Tuominen, R, et al.
(författare)
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Susceptibility factors and DNA adducts in peripheral blood mononuclear cells of aluminium smelter workers exposed to polycyclic aromatic hydrocarbons
- 2002
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Ingår i: Archives of Toxicology. - : Springer Science and Business Media LLC. - 0340-5761 .- 1432-0738. ; 76:3, s. 178-186
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Tidskriftsartikel (refereegranskat)abstract
- Formation of DNA adducts as a result of exposure to polycyclic aromatic hydrocarbons (PAH) was studied in 98 potroom workers from an aluminium smelting plant and in 55 blue-collar workers without occupational PAH exposure. DNA from peripheral blood mononuclear cells (PBMC) was used for quantitation of individual PAH-DNA adducts by P-32-postlabelling/high performance liquid chromatography (HPLC) analysis. Four individual DNA adducts (denoted A, B, C and D) were quantified in 141 of a total of 153 subjects. Genetic polymorphisms for cytochrome P-4501A1 (CYP1A1), Microsomal epoxide hydrolase, N-acetyltransferase 2, glutathione transferases M1, P1 and T1 (GSTM1, GSTP1 and GSTT1, respectively) and NAD(P)H: quinone oxidoreductase I (NQ01) were analysed. For 52 subjects, analysis of mRNA inducibility of CYP1A1 was performed. No statistically significant differences in the levels of total or individual DNA adducts A, C and D were found between potroom workers and control subjects. All potroom workers and the subgroup of potroom workers who reported to never/sometimes use personal respiratory protection (n = 72) were found to have a significantly higher likelihood of having high levels of adduct B than control subjects [odds ratio (OR) = 3.4 with 95% confidence interval (CI) of 1.3-9.2, and OR=4.2 with 95% CI 1.6-11.5, respectively]. In the subgroup, levels of adducts A and B were found to be significantly higher among workers with employment time of less than 6 months (n = 5). Also, the levels of the individual DNA adducts were to some extent modified by genetic polymorphisms in CYP1A1, GSTM1, GSTP1 and NQO1 and by CYP1A1 inducibility. In conclusion, levels of adduct B, identified by P-32-postlabelling/HPLC methodology as an indicator of PAH exposure in aluminium production, were modified by the use of respiratory protection, length of employment and genetic polymorphisms.
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