| 1. |
- Winzell, Filip, et al.
(författare)
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Systematic Augmentation in HSV Space for Semantic Segmentation of Prostate Biopsies
- 2023
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Ingår i: Image Analysis : 23rd Scandinavian Conference, SCIA 2023, Proceedings, Part II - 23rd Scandinavian Conference, SCIA 2023, Proceedings, Part II. - 1611-3349 .- 0302-9743. - 9783031314377 - 9783031314384 ; 13886, s. 293-308
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Konferensbidrag (refereegranskat)abstract
- In recent years, the combination of the digitization of the field of pathology and increased computational power has led to a big increase in research of computer-aided diagnostics using systems based on artificial intelligence (AI). This includes detection and classification of prostate cancer, where several studies have shown great promise in automated prostate cancer grading using deep learning based AI systems. However, there is still work to be done to ensure that these algorithms are invariant to possible variations of the digitized microscopy images they are applied to. A standard method in deep learning to increase the variation of the training data is dataset augmentation. All of these studies apply some augmentation of their data, however, there is a lack of evaluation of different methods and their impact on this crucial part of the AI systems. In this study, we look into different color augmentation methods for the task of segmentation of prostate biopsies. Furthermore, we introduce a novel color augmentation method based on stereographic projection. Our results affirm the importance of studying different augmentation methods and indicate a gain in performance using our method.
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| 2. |
- Abels, Mia, et al.
(författare)
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CART is overexpressed in human type 2 diabetic islets and inhibits glucagon secretion and increases insulin secretion
- 2016
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Ingår i: Diabetologia. - : Springer Science and Business Media LLC. - 0012-186X .- 1432-0428. ; 59:9, s. 1928-1937
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Tidskriftsartikel (refereegranskat)abstract
- Aims/hypothesis Insufficient insulin release and hyperglucagonaemia are culprits in type 2 diabetes. Cocaine- and amphetamine-regulated transcript (CART, encoded by Cartpt) affects islet hormone secretion and beta cell survival in vitro in rats, and Cart(-/-) mice have diminished insulin secretion. We aimed to test if CART is differentially regulated in human type 2 diabetic islets and if CART affects insulin and glucagon secretion in vitro in humans and in vivo in mice. Methods CART expression was assessed in human type 2 diabetic and non-diabetic control pancreases and rodent models of diabetes. Insulin and glucagon secretion was examined in isolated islets and in vivo in mice. Ca2+ oscillation patterns and exocytosis were studied in mouse islets. Results We report an important role of CART in human islet function and glucose homeostasis in mice. CART was found to be expressed in human alpha and beta cells and in a subpopulation of mouse beta cells. Notably, CART expression was several fold higher in islets of type 2 diabetic humans and rodents. CART increased insulin secretion in vivo in mice and in human and mouse islets. Furthermore, CART increased beta cell exocytosis, altered the glucose-induced Ca2+ signalling pattern in mouse islets from fast to slow oscillations and improved synchronisation of the oscillations between different islet regions. Finally, CART reduced glucagon secretion in human and mouse islets, as well as in vivo in mice via diminished alpha cell exocytosis. Conclusions/interpretation We conclude that CART is a regulator of glucose homeostasis and could play an important role in the pathophysiology of type 2 diabetes. Based on the ability of CART to increase insulin secretion and reduce glucagon secretion, CART-based agents could be a therapeutic modality in type 2 diabetes.
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| 3. |
- Derba-Maceluch, Marta, et al.
(författare)
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Suppression of xylan endotransglycosylase PtxtXyn10A affects cellulose microfibril angle in secondary wall in aspen wood
- 2015
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Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 205:2, s. 666-681
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Tidskriftsartikel (refereegranskat)abstract
- Certain xylanases from family GH10 are highly expressed during secondary wall deposition, but their function is unknown. We carried out functional analyses of the secondary-wall specific PtxtXyn10A in hybrid aspen (Populus tremulaxtremuloides).PtxtXyn10A function was analysed by expression studies, overexpression in Arabidopsis protoplasts and by downregulation in aspen.PtxtXyn10A overexpression in Arabidopsis protoplasts resulted in increased xylan endotransglycosylation rather than hydrolysis. In aspen, the enzyme was found to be proteolytically processed to a 68kDa peptide and residing in cell walls. Its downregulation resulted in a corresponding decrease in xylan endotransglycosylase activity and no change in xylanase activity. This did not alter xylan molecular weight or its branching pattern but affected the cellulose-microfibril angle in wood fibres, increased primary growth (stem elongation, leaf formation and enlargement) and reduced the tendency to form tension wood. Transcriptomes of transgenic plants showed downregulation of tension wood related genes and changes in stress-responsive genes. The data indicate that PtxtXyn10A acts as a xylan endotransglycosylase and its main function is to release tensional stresses arising during secondary wall deposition. Furthermore, they suggest that regulation of stresses in secondary walls plays a vital role in plant development.
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| 4. |
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| 5. |
- Gray-Mitsumune, Madoka, et al.
(författare)
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Expansins abundant in secondary xylem belong to subgroup a of the alpha-expansin gene family (1 w )
- 2004
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 135:3, s. 1552-1564
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Tidskriftsartikel (refereegranskat)abstract
- Differentiation of xylem cells in dicotyledonous plants involves expansion of the radial primary cell walls and intrusive tip growth of cambial derivative cells prior to the deposition of a thick secondary wall essential for xylem function. Expansins are cell wall-residing proteins that have an ability to plasticize the cellulose-hemicellulose network of primary walls. We found expansin activity in proteins extracted from the cambial region of mature stems in a model tree species hybrid aspen (Populus tremula X Populus tremuloides Michx). We identified three a-expansin genes (PttEXP1, PttEXP2, and PttEXP8) and one beta-expansin gene (PttEXPB1) in a cambial region expressed sequence tag library, among which PttEXP1 was most abundantly represented. Northern-blot analyses in aspen vegetative organs and tissues showed that PttEXP1 was specifically expressed in mature stems exhibiting secondary growth, where it was present in the cambium and in the radial expansion zone. By contrast, PttEXP2 was mostly expressed in developing leaves. In situ reverse transcription-PCR provided evidence for accumulation of mRNA of PttEXP1 along with ribosomal rRNA at the tips of intrusively growing xylem fibers, suggesting that PttEXP1 protein has a role in intrusive tip growth. An examination of tension wood and leaf cDNA libraries identified another expansin, PttEXP5, very similar to PttEXP1, as the major expansin in developing tension wood, while PttEXP3 was the major expansin expressed in developing leaves. Comparative analysis of expansins expressed in woody stems in aspen, Arabidopsis, and pine showed that the most abundantly expressed expansins share sequence similarities, belonging to the subfamily A of alpha-expansins and having two conserved motifs at the beginning and end of the mature protein, RIPVG and KNFRV, respectively. This conservation suggests that these genes may share a specialized, not yet identified function.
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| 6. |
- Ohlsson, Anna B., et al.
(författare)
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Cell suspension cultures of Populus tremula x P. tremuloides exhibit a high level of cellulose synthase gene expression that coincides with increased in vitro cellulose synthase activity.
- 2006
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Ingår i: Protoplasma. - : Springer Science and Business Media LLC. - 0033-183X .- 1615-6102. ; 228:4, s. 221-9
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Tidskriftsartikel (refereegranskat)abstract
- Compared to wood, cell suspension cultures provide convenient model systems to study many different cellular processes in plants. Here we have established cell suspension cultures of Populus tremula L. x P. tremuloides Michx. and characterized them by determining the enzymatic activities and/or mRNA expression levels of selected cell wall-specific proteins at the different stages of growth. While enzymes and proteins typically associated with primary cell wall synthesis and expansion were detected in the exponential growth phase of the cultures, the late stationary phase showed high expression of the secondary-cell-wall-associated cellulose synthase genes. Interestingly, detergent extracts of membranes from aging cell suspension cultures exhibited high levels of in vitro cellulose synthesis. The estimated ratio of cellulose to callose was as high as 50 : 50, as opposed to the ratio of 30 : 70 so far achieved with membrane preparations extracted from other systems. The increased cellulose synthase activity was also evidenced by higher levels of Calcofluor white binding in the cell material from the stationary-phase cultures. The ease of handling cell suspension cultures and the improved capacity for in vitro cellulose synthesis suggest that these cultures offer a new basis for studying the mechanism of cellulose biosynthesis.
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| 7. |
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| 8. |
- Winzell, Anders, 1978-
(författare)
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Analysis of Genes and Proteins Involved in Wood Formation
- 2007
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- SAMMANFATTNING Vedbildning är en underliggande mekanism för så skilda områden som industri, boende och en hållbar miljö. Vedbildning sker i det vaskulära kambiet där organiserade celldelningar åtföljs av differentiering till specialiserade vedceller. Ved består av sekundärt xylem som är starka, stora celler med tjocka cellväggar som är lignifierade. Dessa celler transporterar vatten och näringsämnen samt ger trädet dess styrka. Grunden för de starka cellerna är en avancerad komposit bestående av cellulosafibrer tvärbundna av hemicellulosa och slutligen ingjutet i lignin. Denna fiberkomposit är den sekundära cellväggen i vedartade växter. Celldelning och differentiering regleras genom att sätta igång och stänga av gener. Proteiner som kodas av dessa gener utför de viktigaste funktionerna i cellerna. De styr hela maskineriet som upprätthåller cellernas struktur och funktion, underhåller tillväxt samt tillverkar nödvändiga produkter såsom cellväggskolhydraterna. Träbioteknologiforskningsgruppen har varit en del av ett kraftfullt åtagande att identifiera de proteiner som är ansvariga för nyckelprocesser i vedbildning. Detta har utförts genom att övervaka genexpressionen vid olika tidpunkter av vedcellsmognad i Populus tremula x tremuloides. Här beskriver vi undersökningen av proteiner som är inblandade i cellexpansion och bildandet av sekundär cellvägg liksom utvecklandet av ett modellsystem som kommer vara en hjälp i den funktionella analysen av cellulosabiosyntes. Expansin är ett protein som verkar i cellexpansionen i alla växtens vävnader. Vi har studerat ett expansin, PttEXPA1, som visat sig vara särskilt närvarande i celler som genomgår vedbildning. Dessutom har vi undersökt glykosyltransferaser som tycks spela en viktig roll i bildandet av sekundär cellvägg. En av dessa, PttGT43A har uttryckts i jästen Pichia pastoris och i baculovirusinfekterade insektsceller. Dessvärre var proteinnivåerna för låga för biokemisk karakterisering. Dessutom har vi demonstrerat att flytande cellkulturer av hybridasp kan användas som ett modellsystem för cellulosabiosyntes. Genom att bemästra proteinerna som är ansvariga för vedbildning får vi verktyg att utveckla skogsproduktsmarknaden. En vision är nya produkter som till exempel träd som växer snabbare, ändrade fiberegenskaper, produktion av vedkolhydrater såväl som utvecklandet av intelligenta material genom biomimetisk ingenjörskonst.
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| 9. |
- Winzell, Anders, et al.
(författare)
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Biochemical characterization of family 43 glycosyltransferases in the Populus xylem : challenges and prospects
- 2010
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Ingår i: Plant Biotechnology. - : Japanese Society for Plant Cell and Molecular Biology. - 1342-4580 .- 1347-6114. ; 27:3, s. 283-288
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Tidskriftsartikel (refereegranskat)abstract
- Wood formation is a biological process of great economical importance. Genes active during the secondary cellwall formation of wood fibers from Populus tremulatremuloides were previously identified by expression profilingthrough microarray analyses. A number of these genes encode glycosyltransferases (GTs) with unknown substratespecificities. Here we report heterologous expression of one of these enzymes, PttGT43A, a putative IRREGULARXYLEM9 (IRX9) homologue. Expression trials in Pichia pastoris and insect cells revealed very low levels of accumulationof immunoreactive PttGT43A, whereas transient expression in Nicotiana benthamiana leaves by Agrobacterium infiltration(agroinfiltration) using a viral vector produced substantial amounts of protein that mostly precipitated in the crude pellet.Agroinfiltration induced weak endogenous xylosyltransferase activity in microsomal extracts, and transient PttGT43Aexpression further increased this activity, albeit only to low levels. PttGT43A may be inactive as an individual subunit,requiring complex formation with unknown partners to display enzymatic activity. Our results suggest that transient coexpressionin leaves of candidate subunit GTs may provide a viable approach for formation of an active xylanxylosyltransferase enzymatic complex.
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| 10. |
- Winzell, Anders, et al.
(författare)
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Conserved CA-rich motifs in gene promoters of Pt x tMYB021-responsive secondary cell wall carbohydrate-active enzymes in Populus
- 2010
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Ingår i: Biochemical and Biophysical Research Communications - BBRC. - : Elsevier BV. - 0006-291X .- 1090-2104. ; 394:3, s. 848-853
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Tidskriftsartikel (refereegranskat)abstract
- In order to understand gene regulation during wood formation, we cloned a MYB46-like gene in hybrid aspen. Populus tremula x tremuloides, called PtxtMYB021 Phylogenetic and paired identity analysis of MYB46-like genes in Populus and Arabidopsis reveals relationships between paralogous pairs of Populus MYB46-like proteins and their Arabidopsis counterparts MYB46 and MYB83, and suggest that PtxtMYB021 is the ortholog of MYB46 Ptxt-MYB021 is expressed mainly in xylem tissues, and transiently expressed PtxtMYB46 transactivates gene promoters of xylan-active CAZymes GT43A, GT43B and Xyn10A Analysis of conserved motifs within these promoters identify the sequence CCACCAAC, called ACTYP, which is similar to the AC elements mediating transactivation by MYB transcription factors during lignin biosynthesis Further analysis by Motif Finder identifies four 6 bp CA-rich motifs overlapping ACTYP, and we show that these motifs are enriched in xylem-specific promoters We propose that AC-type regulatory elements mediate xylem-specific MYB46-dependent expression of secondary cell wall carbohydrate-active enzymes (CAZymes), besides activating gene expression of lignin biosynthesis enzymes.
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| 11. |
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| 12. |
- Winzell, Anders, 1978-
(författare)
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Investigation of genes and proteins involved in xylan biosynthesis
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Wood formation or xylogenesis is a fundamental process for so diverse issues as industry, shelter and a sustainable environment. Wood is comprised of secondary xylem, rigid large cells with thick cell walls that are lignified. The basis for the sturdy cells is an advanced composite made up of cellulose fibers cross-linked by hemicelluloses and finally embedded in lignin. This fiber-composite is the secondary cell walls of woody plants. Cell division and differentiation is regulated by switching on and off genes. Proteins encoded by these genes execute the major functions in the cells. They steer the entire machinery operating the structure and function of the cells, maintaining growth and synthesising essential products such as the cell wall carbohydrates. Here we describe the investigation of genes and proteins involved in xylan formation as well as the development of a model system that will aid the functional analysis of wood formation. Xylan is the main hemicellulose or cross linking glycan in dicot wood and thereby one of the most abundant carbohydrates on earth. We demonstrate that hybrid aspen cell suspension cultures can be used as a model system for secondary cell wall formation. We have also examined glycosyltransferases from CAZy family 43 that play a part in secondary cell wall formation. We have focused on one of these, Pt×tGT43A, a likely ortholog of Arabidopsis IRX9, which plays a crucial role in xylan formation. The protein was transiently expressed in Nicotiana benthamiana and its function and localization is described. Also, we investigate a glycoside hydrolase, Pt×tXyn10A, involved in wood formation. Its role is not clear but it most likely modifies xylan as it gets incorporated into the secondary cell wall after secretion from the Golgi. This influences the interaction between cellulose, xylan and lignin in the finished wood cell. We have also cloned a transcription factor, Pt×tMYB021, a likely ortholog of Arabidopsis MYB46 and we show that it activates GT43A, GT43B and Xyn10A. By analysis of the promoter sequences we identify a CA-rich motif putatively important for xylem-specific genes. By mastering proteins involved in xylogenesis we will acquire the tools to improve and develop the wood product market. Xylan is an immense unexploited source of renewable carbohydrate. New products envisioned include e.g. faster growing trees, changed fiber characteristics, optimised utilization of wood carbohydrates for biofuels and biomaterials as well as invention of intelligent materials by biomimetic engineering.
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| 14. |
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