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Sökning: WFRF:(Grund S)

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1.
  • Waszak, S. M., et al. (författare)
  • Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort
  • 2018
  • Ingår i: Lancet Oncology. - : Elsevier BV. - 1470-2045. ; 19:6, s. 785-798
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Medulloblastoma is associated with rare hereditary cancer predisposition syndromes; however, consensus medulloblastoma predisposition genes have not been defined and screening guidelines for genetic counselling and testing for paediatric patients are not available. We aimed to assess and define these genes to provide evidence for future screening guidelines. Methods In this international, multicentre study, we analysed patients with medulloblastoma from retrospective cohorts (International Cancer Genome Consortium [ICGC] PedBrain, Medulloblastoma Advanced Genomics International Consortium [MAGIC], and the CEFALO series) and from prospective cohorts from four clinical studies (SJMB03, SJMB12, SJYC07, and I-HIT-MED). Whole-genome sequences and exome sequences from blood and tumour samples were analysed for rare damaging germline mutations in cancer predisposition genes. DNA methylation profiling was done to determine consensus molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGroup3), and group 4 (MBGroup4). Medulloblastoma predisposition genes were predicted on the basis of rare variant burden tests against controls without a cancer diagnosis from the Exome Aggregation Consortium (ExAC). Previously defined somatic mutational signatures were used to further classify medulloblastoma genomes into two groups, a clock-like group (signatures 1 and 5) and a homologous recombination repair deficiency-like group (signatures 3 and 8), and chromothripsis was investigated using previously established criteria. Progression-free survival and overall survival were modelled for patients with a genetic predisposition to medulloblastoma. Findings We included a total of 1022 patients with medulloblastoma from the retrospective cohorts (n=673) and the four prospective studies (n=349), from whom blood samples (n=1022) and tumour samples (n=800) were analysed for germline mutations in 110 cancer predisposition genes. In our rare variant burden analysis, we compared these against 53 105 sequenced controls from ExAC and identified APC, BRCA2, PALB2, PTCH1, SUFU, and TP53 as consensus medulloblastoma predisposition genes according to our rare variant burden analysis and estimated that germline mutations accounted for 6% of medulloblastoma diagnoses in the retrospective cohort. The prevalence of genetic predispositions differed between molecular subgroups in the retrospective cohort and was highest for patients in the MBSHH subgroup (20% in the retrospective cohort). These estimates were replicated in the prospective clinical cohort (germline mutations accounted for 5% of medulloblastoma diagnoses, with the highest prevalence [14%] in the MBSHH subgroup). Patients with germline APC mutations developed MBWNT and accounted for most (five [71%] of seven) cases of MBWNT that had no somatic CTNNB1 exon 3 mutations. Patients with germline mutations in SUFU and PTCH1 mostly developed infant MBSHH. Germline TP53 mutations presented only in childhood patients in the MBSHH subgroup and explained more than half (eight [57%] of 14) of all chromothripsis events in this subgroup. Germline mutations in PALB2 and BRCA2 were observed across the MBSHH, MBGroup3, and MBGroup4 molecular subgroups and were associated with mutational signatures typical of homologous recombination repair deficiency. In patients with a genetic predisposition to medulloblastoma, 5-year progression-free survival was 52% (95% CI 4069) and 5-year overall survival was 65% (95% CI 5281); these survival estimates differed significantly across patients with germline mutations in different medulloblastoma predisposition genes. Interpretation Genetic counselling and testing should be used as a standard-of-care procedure in patients with MBWNT and MBSHH because these patients have the highest prevalence of damaging germline mutations in known cancer predisposition genes. We propose criteria for routine genetic screening for patients with medulloblastoma based on clinical and molecular tumour characteristics. Copyright (c) 2018 The Author(s). Published by Elsevier Ltd.
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  • Demichev, Vadim, et al. (författare)
  • A time-resolved proteomic and prognostic map of COVID-19
  • 2021
  • Ingår i: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7
  • Tidskriftsartikel (refereegranskat)abstract
    • COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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6.
  • Emminger, Carola, et al. (författare)
  • Analysis of temperature-dependent and time-resolved ellipsometry spectra of Ge
  • 2021
  • Konferensbidrag (refereegranskat)abstract
    • The dielectric function of Ge measured with static and time-resolved spectroscopic ellipsometry is analyzed using linear filtering techniques to investigate the temperature dependence of the direct band gap, as well as the temporal evolvement of critical points obtained from femtosecond pump-probe ellipsometry measurements.
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  • Grund, Sofia, et al. (författare)
  • The autocrine motility factor receptor is overexpressed on the surface of B cells in Binet C chronic lymphocytic leukemia.
  • 2011
  • Ingår i: Medical Oncology. - : Springer Science and Business Media LLC. - 1559-131X .- 1357-0560. ; 28:4, s. 1542-8
  • Tidskriftsartikel (refereegranskat)abstract
    • Chronic lymphocytic leukemia (CLL) is a heterogeneous disease with a clinical spectrum reaching from discrete lymphocytosis to extensive enlargement of lymph nodes, spleen and liver, and bone marrow failure. The aim of this study was to identify genes that differentiate between patients with disease stage A vs. C according to Binet in order to better understand the disease. To achieve this, we performed DNA microarray analysis on B cells from CLL patients with stage A and C according to Binet and matched controls. Between CLL patients and controls, there were 1,528 differentially expressed genes and 360 genes were differentially expressed between Binet A and C patients. Due to the sheer number of regulated genes, we focused on the autocrine motility factor receptor (AMFR). AMFR has not previously been investigated in hematological disorders, but high expression of AMFR correlates with a more advanced stage and invasive potential in several human tumors. AMFR mRNA expression was higher in Binet A compared with Binet C patients (P=0.0053) and healthy controls (P=0.0051). Total AMFR protein was higher in Binet A patients compared to Binet C as analyzed by intracellular flow cytometry. However, AMFR exist both in the ER involved in protein degradation and on the cell surface involved in metastasis and cell motility. Cell surface AMFR was increased in Binet C compared with Binet A+B (P=0.016). In conclusion, the mRNA levels reflect the total amount of AMFR, whereas cell surface expression is associated with progression in CLL.
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  • Herrfurth, O., et al. (författare)
  • Transient birefringence and dichroism in ZnO studied with fs-time-resolved spectroscopic ellipsometry
  • 2021
  • Ingår i: Physical Review Research. - : American Physical Society. - 2643-1564. ; 3:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The full transient dielectric-function (DF) tensor of ZnO after UV-laser excitation in the spectral range 1.4–3.6 eV is obtained by measuring an m-plane-oriented ZnO thin film with femtosecond (fs)-time-resolved spectroscopic ellipsometry. From the merits of the method, we can distinguish between changes in the real and the imaginary part of the DF as well as changes in birefringence and dichroism, respectively. We find pump-induced switching from positive to negative birefringence in almost the entire measured spectral range for about 1 ps. Simultaneously, weak dichroism in the spectral range below 3.0 eV hints at contributions of inter-valence-band transitions. Line-shape analysis of the DF above the band gap based on discrete exciton, exciton-continuum, and exciton-phonon-complex contributions shows a maximal dynamic increase in the transient exciton energy by 80 meV. The absorption coefficient below the band gap reveals an exponential line shape attributed to Urbach-rule absorption mediated by exciton–longitudinal-optic-phonon interaction. The transient DF is supported by first-principles calculations for 1020cm−3 excited electron-hole pairs in ideal bulk ZnO.
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  • Karlsson, Stefan, 1984-, et al. (författare)
  • Non-destructive testing of the glass strength in flat glass with indentationinduced cracks by Nonlinear Acoustic Wave method
  • 2022
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • Glass is a unique but unfortunately brittle material whose strength is primarily limited by the presenceof cracks on the surface [1]. The strength of glass is limited by the fact that very high stresses arise atthe crack tips when subjected to tensile load. In principle, without the presence of surface cracks, glasswould have a strength far exceeding many other structural materials, e.g., steel. The size and thedistribution of surface cracks vary greatly, which results in the strength of glass exhibit a great variationand thus requires that large safety margins must be applied for glass in practical applications, e.g., whenused as a load bearing building material.Today, there are no methods to determine the strength of flat glass non-destructively. Instead, thestrength is determined by different experimental methods requiring >10 samples for sufficient statistics.This procedure requires both lots of glassy materials and time. The future aim is to investigate if the useof nonlinear acoustic waves (NAW) could be an alternative for developing a standardized designstrength value. Developing a non-destructive inspection method for determining the glass strength is ascientific breakthrough that will have a great industrial impact for the sustainable development of glassmanufacturing.With the use of NAW it is possible to detect and quantify the defects in materials [2,3]. The nonlinearwaves are transmitted through the object and the nonlinear effects, caused by the defects in thematerial, corresponds to the level of damage in the material. This work present result from samplescontaining relatively precise defects. The defects were created using a microindenter with a sufficientload to cause indentation induced cracking in the glass. The indentations were created using a Vickersdiamond tip in the middle of commercial 4 mm float glass samples of the dimensions 10x10 cm2. Theapplied loads were 0.5N, 1N, 2N, 5N and 10N. The “damage value” of the sample series was thenquantified using the NAW technique. The fracture strength of the samples was correlated destructivelyusing a conventional ring-on-ring setup.The results show that there is a clear correlation between the indenter load, the damage value from theNAW inspection and the fracture strength. We noted that the standard deviation for the ring-on-ringtests for the 1N, 2N, 5N and 10N was low while the 0.5N and the reference samples presented a highstandard deviation. A possible explanation for this observation is that for 0.5N not all indents give radialcracks but in some cases the indentation produces only plastic deformation. The main conclusion fromthe research is that is possible to detect realistically large defects in glass using the non-destructive NAWmethod and these defects cannot be seen with the naked eye. Moreover, the results can be directlycorrelated with the strength of glass [4].References[1] Veer, F.A. and Y.M. Rodichev, The structural strength of glass: hidden damage. Strength of Materials, 2011.43(3): p. 302-315. DOI: 10.1007/s11223-011-9298-5.[2] Persson, K., K. Haller, S. Karlsson, and M. Kozłowski, Non-destructive testing of the strength of glass by a nonlinearultrasonic method. Challenging Glass Conference Proceedings, 2020. 7. DOI: 10.7480/cgc.7.4498.[3] Haller, K., Doctoral Thesis: Acoustical measurements of material nonlinearity and nonequilibrium recovery.2008: Department of Mechanical Engineering, Blekinge Institute of Technology.[4] Karlsson, S., L. Grund Bäck, S. Andersson, K. Haller, M. Kozłowski, and K. Persson, Strength classification of flatglass for better quality – validation of method by well-defined surface defects and strength testing, in ÅForskReport,19-479. 2021: http://dx.doi.org/10.13140/RG.2.2.32992.40962.
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