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- Cahill, Nicola, et al.
(author)
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450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments
- 2013
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In: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 27:1, s. 150-158
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Journal article (peer-reviewed)abstract
- In chronic lymphocytic leukemia (CLL), the microenvironment influences gene expression patterns; however, knowledge is limited regarding the extent to which methylation changes with time and exposure to specific microenvironments. Using high-resolution 450K arrays, we provide the most comprehensive DNA methylation study of CLL to date, analyzing paired diagnostic/follow-up samples from IGHV-mutated/untreated and IGHV-unmutated/treated patients (n = 36) and patient-matched peripheral blood and lymph node samples (n = 20). On an unprecedented scale, we revealed 2239 differentially methylated CpG sites between IGHV-mutated and unmutated patients, with the majority of sites positioned outside annotated CpG islands. Intriguingly, CLL prognostic genes (for example, CLLU1, LPL, ZAP70 and NOTCH1), epigenetic regulator (for example, HDAC9, HDAC4 and DNMT3B), B-cell signaling (for example, IBTK) and numerous TGF-beta and NF-kappa B/TNF pathway genes were alternatively methylated between subgroups. Contrary, DNA methylation over time was deemed rather stable with few recurrent changes noted within subgroups. Although a larger number of non-recurrent changes were identified among IGHV-unmutated relative to mutated cases over time, these equated to a low global change. Similarly, few changes were identified between compartment cases. Altogether, we reveal CLL subgroups to display unique methylation profiles and unveil methylation as relatively stable over time and similar within different CLL compartments, implying aberrant methylation as an early leukemogenic event. Leukemia (2013) 27, 150-158; doi:10.1038/leu.2012.245
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- Ghasemi, Rohollah, 1983-
(author)
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Tribological and Mechanical Behaviour of Lamellar and Compacted Graphite Irons in Engine Applications
- 2015
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Licentiate thesis (other academic/artistic)abstract
- There has been much discussion about the beneficial uses of lamellar graphite iron in piston rings–cylinder liner systems, where a good combinations of both thermal and tribological properties are essential. The excellent tribological performance of lamellar iron under such sliding conditions is principally associated with lubrication behaviour of the graphite particles which are distributed as lamellas throughout the matrix. During sliding, graphite particles are extruded and smeared onto the counterfaces, act as solid lubricating agents and form a thin graphite film between the sliding surfaces. Although this process especially, during the running-in period significantly changes the sliding wear response of the components, the exact mechanism behind of this phenomenon has rarely been discussed in previous studies.It is tribologically beneficial to keep the graphite open, particularly in applications where the scuffing issues do matter. In this thesis, the main causes involved in closing the graphite lamellas are discussed, with a focus on matrix plastic deformation that occurs during sliding. In first step, the relationship between graphite lamellae orientation and plastic deformation was investigated. To do so, two piston rings, belonging to the same two-stroke marine engine operated for different periods of time, were selected and compared to the unworn sample. The worn piston rings displayed a substantial decrease in both frequency and area fraction of the graphite lamellas. Most of the lamellas were closed as a result of plastic deformation of matrix. This happening was caused mainly by the interaction between abrasive particles and metallic matrix. Additionally, it was found that graphite lamellas parallel or near-parallel to the sliding direction exhibited maximum closing tendency under sliding condition.In next step, to have a better understanding of the graphite film formation mechanism and matrix deformation role in closing the graphite lamellas, microindentation and microscratch testing were performed on typical lamellar iron. The qualitative results showed a similar mechanism involving in graphite contribution to lubricate the sliding surfaces. Moreover, microindentations made nearby the graphite lamellas demonstrated that the deformation of the matrix causes the formation of cracks in the centre of the graphite lamellas, compressing and then extruding the graphite from its natural position, irrespective of the lamellas′ size. Furthermore, it was found that subsurface graphite orientation had a large influence on the extrusion behaviour, in that, for graphite lamellas oriented towards the indenter, the effect was observed more pronounced.Furthermore, an improved fully ferritic solution strengthened compacted graphite iron was produced for future wear studies. The effects of different Si levels and section thicknesses on tensile properties and hardness were investigated as well. The influence of Si content and section thickness on mechanical properties was revealed by improving the materials strength and slightly enhancing the hardness through increasing Si content. Besides, Si addition up to 4.5 wt% significantly affected the strength and elongation to failure of cast samples.
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- Oscarsson, Nicklas, 1974, et al.
(author)
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Radiation-induced cystitis treated with hyperbaric oxygen therapy (RICH-ART): a randomised, controlled, phase 2–3 trial
- 2019
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In: The Lancet Oncology. - 1470-2045 .- 1474-5488. ; 20:11, s. 1602-1614
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Journal article (peer-reviewed)abstract
- © 2019 Elsevier Ltd Background: Late radiation cystitis is an adverse effect of cancer treatment with radiotherapy in the pelvic region. Symptoms of late radiation cystitis can be assessed with the Expanded Prostate Index Composite Score (EPIC). Previous reports indicate that hyperbaric oxygen therapy reduces symptoms from late radiation cystitis, but the evidence is predominantly based on non-randomised and retrospective studies. We aimed to assess whether hyperbaric oxygen therapy would mitigate symptoms of late radiation cystitis. Methods: We did a randomised, controlled, phase 2–3 trial (RICH-ART [Radiation Induced Cystitis treated with Hyperbaric oxygen—A Randomised controlled Trial]) at five Nordic university hospitals. All patients aged 18–80 years, with pelvic radiotherapy completed at least 6 months previously, a score of less than 80 in the urinary domain of the Expanded Prostate Index Composite Score (EPIC), and referred to participating hyperbaric clinics due to symptoms of late radiation cystitis, were eligible for inclusion. Exclusion criteria were ongoing bleeding requiring blood transfusion exceeding 500 mL in the past 4 weeks, permanent urinary catheter, bladder capacity less than 100 mL, fistula in the urinary bladder, previous treatment with hyperbaric oxygen therapy for late radiation injuries, and contraindications to hyperbaric oxygen therapy. After computer-generated 1:1 randomisation with block sizes of four for each stratification group (sex, time from radiotherapy to inclusion, and previous invasive surgery in the pelvic area), patients received hyperbaric oxygen therapy (30–40 sessions, 100% oxygen, breathed at a pressure of 240–250 kPa, for 80–90 min daily) or standard care with no restrictions for other medications or interventions. No masking was applied. The primary outcome was change in patient-perceived urinary symptoms assessed with EPIC from inclusion to follow-up at visit 4 (6–8 months later), measured as absolute change in EPIC urinary total score. RICH-ART closed enrolment on Dec 31, 2017; the last follow-up data will be compiled in 2023. RICH-ART is registered with ClinicalTrials.gov, number NCT01659723, and with the European Medicines Agency, number EudraCT 2012-001381-15. Findings: Of 223 patients screened between May 9, 2012, and Dec 20, 2017, 87 patients were enrolled and randomly assigned to either hyperbaric oxygen therapy (n=42) or standard care (n=45). After excluding eight patients who withdrew consent directly after randomisation (one in the hyperbaric oxygen therapy group and seven in the standard care group), 79 were included in the intention-to-treat analyses (n=41 in the hyperbaric oxygen therapy group, n=38 in the standard care group). Median time from randomisation to visit 4 was 234 days (IQR 210–262) in the hyperbaric oxygen therapy group and 217 days (195–237) in the standard care group. The difference between change in group mean of EPIC urinary total score at visit 4 was 10·1 points (95% CI 2·2–18·1; p=0·013; 17·8 points [SD 18·4] in the hyperbaric oxygen therapy group vs 7·7 points [15·5] in the standard care group). 17 (41%) of 41 patients in the hyperbaric oxygen therapy group experienced transient grade 1–2 adverse events, related to sight and hearing, during the period of hyperbaric oxygen therapy. Interpretation: Our results suggest that hyperbaric oxygen therapy relieves symptoms of late radiation cystitis. We conclude that hyperbaric oxygen therapy is a safe and well tolerated treatment. Funding: The regional research fund of Region Västra Götaland, Sweden, the regional Health Technology Assessment Centre at Sahlgrenska University Hospital, Sweden, and Lions Cancer Research Fund of Western Sweden.
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- Rosén, Josefin, 1978-, et al.
(author)
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ChemGPS-NPweb : chemical space navigation online
- 2009
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In: Journal of Computer-Aided Molecular Design. - : Springer Science and Business Media LLC. - 0920-654X .- 1573-4951. ; 23:4, s. 253-259
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Journal article (peer-reviewed)abstract
- Internet has become a central source for information, tools, and services facilitating the work for medicinal chemists and drug discoverers worldwide. In this paper we introduce a web-based public tool, ChemGPS-NPWeb (http://chemgps.bmc.uu.se), for comprehensive chemical space navigation and exploration in terms of global mapping onto a consistent, eight dimensional map over structure derived physico-chemical characteristics. ChemGPS-NPWeb can assist in compound selection and prioritization; property description and interpretation; cluster analysis and neighbourhood mapping; as well as comparison and characterization of large compound datasets. By using ChemGPS-NPWeb, researchers can analyze and compare chemical libraries in a consistent manner. In this study it is demonstrated how ChemGPS-NPWeb can assist in interpreting results from two large datasets tested for activity in biological assays for pyruvate kinase and Bcl-2 family related protein interactions, respectively. Furthermore, a more than 30-year-old suggestion of “chemical similarity” between the natural pigments betalains and muscaflavins is tested.
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| 10. |
- Rosén, Stefan, et al.
(author)
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A multispecific saline-soluble lectin from the parasitic fungus Arthrobotrys oligospora. Similarities in the binding specificities compared with a lectin from the mushroom agaricus bisporus.
- 1996
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In: European journal of biochemistry / FEBS. - : Wiley. - 0014-2956 .- 1432-1033. ; 238:3, s. 830-7
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Journal article (peer-reviewed)abstract
- Several fungi can express high levels of saline-soluble and low-molecular-mass lectins that bind to glycoproteins such as fetuin and different mucins but not bind to any monosaccharides. In this paper, we report the binding specificities of such a lectin (designated AOL) isolated from the nematophagous fungus Arthrobotrys oligospora. The results show that AOL is a multispecific lectin that interacts with the following ligands: (a) Several sulfated glycoconjugates including sulfatide, dextran sulfate, and fucoidan. The specificity of this binding was indicated by experiments showing that none of the tested neutral- and sialic-acid-containing glycolipids, chondroitin sulfates B and C, heparin, and polyvinyl sulfate bound to AOL; (b) Phosphatidic acid and phospatidylglycerol, two out of several tested phospholipids. (c) N-linked and O-linked sugar chains bound to intact fetuin. The involvement of such sugar structures was demonstrated by analyzing the binding of AOL to chemically deglycosylated (trifluoromethanesulfonic acid) fetuin. Treating fetuin with O-glycosidase and N-glycosidase indicated that AOL bound to Gal beta GaLNAc alpha-Ser/Thr and to some N-linked complex sugars, respectively. Further assays demonstrated that AOL could interact with several other glycoproteins containing O-linked and/or N-linked sugar chains. The observations that AOL did not bind to free N-linked sugars isolated from fetuin, or to fetuin treated with trypsin or pronase, or to any of the tested neoglycoproteins and glycolipids with neutral- or sialic acid-containing sugars, indicated that the sugar chains need to be bound to an intact peptide backbone to interact with AOL. We have recently shown that the deduced primary structure of AOL has a high similarity to the sequence of a saline-soluble lectin isolated from the mushroom Agaricus bisporus (ABL) (Rosén, S., Kata, M., Persson, Y., Lipniunas, P. H., Wikström, M., van den Hondel, C. A. M. J. J., van den Brink, J. M., Rask, L., Hedén L.-O. and Tunlid, A., see companion paper). It is well known that ABL binds to Gal beta 3GaLNAc alpha-Ser/Thr, and in this paper we demonstrate that ABL binds to sulfatide, phosphatidic acid, phospatidylglycerol, and possibly also to the same N-linked complex sugars as AOL. The above data indicate that AOL and ABL are members of a novel family of fungal lectins sharing similar primary structure and binding properties.
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