| 1. |
- Machiela, Mitchell J., et al.
(författare)
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Genetically predicted longer telomere length is associated with increased risk of B-cell lymphoma subtypes
- 2016
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 25:8, s. 1663-1676
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Tidskriftsartikel (refereegranskat)abstract
- Evidence from a small number of studies suggests that longer telomere length measured in peripheral leukocytes is associated with an increased risk of non-Hodgkin lymphoma (NHL). However, these studies may be biased by reverse causation, confounded by unmeasured environmental exposures and might miss time points for which prospective telomere measurement would best reveal a relationship between telomere length and NHL risk. We performed an analysis of genetically inferred telomere length and NHL risk in a study of 10 102 NHL cases of the four most common B-cell histologic types and 9562 controls using a genetic risk score (GRS) comprising nine telomere length-associated single-nucleotide polymorphisms. This approach uses existing genotype data and estimates telomere length by weighing the number of telomere length-associated variant alleles an individual carries with the published change in kb of telomere length. The analysis of the telomere length GRS resulted in an association between longer telomere length and increased NHL risk [four B-cell histologic types combined; odds ratio (OR) = 1.49, 95% CI 1.22-1.82, P-value = 8.5 x 10(-5)]. Subtype-specific analyses indicated that chronic lymphocytic leukemia or small lymphocytic lymphoma (CLL/SLL) was the principal NHL subtype contributing to this association (OR = 2.60, 95% CI 1.93-3.51, P-value = 4.0 x 10(-10)). Significant interactions were observed across strata of sex for CLL/SLL and marginal zone lymphoma subtypes as well as age for the follicular lymphoma subtype. Our results indicate that a genetic background that favors longer telomere length may increase NHL risk, particularly risk of CLL/SLL, and are consistent with earlier studies relating longer telomere length with increased NHL risk.
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| 2. |
- Aad, G., et al.
(författare)
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Commissioning of the ATLAS Muon Spectrometer with cosmic rays
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 875-916
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS detector at the Large Hadron Collider has collected several hundred million cosmic ray events during 2008 and 2009. These data were used to commission the Muon Spectrometer and to study the performance of the trigger and tracking chambers, their alignment, the detector control system, the data acquisition and the analysis programs. We present the performance in the relevant parameters that determine the quality of the muon measurement. We discuss the single element efficiency, resolution and noise rates, the calibration method of the detector response and of the alignment system, the track reconstruction efficiency and the momentum measurement. The results show that the detector is close to the design performance and that the Muon Spectrometer is ready to detect muons produced in high energy proton-proton collisions.
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| 3. |
- Aad, G., et al.
(författare)
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The ATLAS Inner Detector commissioning and calibration
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 787-821
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS Inner Detector is a composite tracking system consisting of silicon pixels, silicon strips and straw tubes in a 2 T magnetic field. Its installation was completed in August 2008 and the detector took part in data-taking with single LHC beams and cosmic rays. The initial detector operation, hardware commissioning and in-situ calibrations are described. Tracking performance has been measured with 7.6 million cosmic-ray events, collected using a tracking trigger and reconstructed with modular pattern-recognition and fitting software. The intrinsic hit efficiency and tracking trigger efficiencies are close to 100%. Lorentz angle measurements for both electrons and holes, specific energy-loss calibration and transition radiation turn-on measurements have been performed. Different alignment techniques have been used to reconstruct the detector geometry. After the initial alignment, a transverse impact parameter resolution of 22.1 +/- 0.9 mu m and a relative momentum resolution sigma (p) /p=(4.83 +/- 0.16)x10(-4) GeV(-1)xp (T) have been measured for high momentum tracks.
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| 4. |
- Aad, G., et al.
(författare)
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The ATLAS Simulation Infrastructure
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 823-874
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Tidskriftsartikel (refereegranskat)abstract
- The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.
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| 5. |
- Haider, Zahra, 1988-
(författare)
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DNA methylation signatures in precursor lymphoid neoplasms : with focus on clinical implications & the biology behind
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Precursor lymphoid neoplasms, namely acute lymphoblastic leukemias (ALL) and lymphoblastic lymphomas (LBL), are characterized by an aggressive proliferation of malignant progenitor B- or T-cells. To improve risk classification at diagnosis, better prognostic and treatment stratifying biomarkers are needed. Altered DNA methylation pattern is a hallmark of neoplastic transformation, and has been employed as a molecular prognostic and predictive marker in various cancers, including hematological malignancies. Our research group previously identified a CpG island methylator phenotype (CIMP) panel that classified pediatric T-ALL patients into prognostic subgroups.The aim of this thesis was to evaluate distinct DNA methylation signatures in precursor lymphoid neoplasms, and to validate the prognostic value of CIMP classification in separate patient cohorts. Additionally, the biological mechanisms underlying the distinct CIMP methylation signatures in these malignancies were investigated.The prognostic relevance of CIMP classification was validated in an independent Nordic cohort of pediatric T-ALL patients. Combination of CIMP status with minimal residual disease (MRD) status, could further dissect the high-risk MRD positive T-ALL patients into two CIMP subgroups with significantly distinct outcomes. Furthermore, CIMP classification at diagnosis was shown to predict overall survival in relapsed BCP-ALL patients. CIMP methylation signatures were also identified in T-LBL patients, indicating a broader relevance of CIMP based classification in lymphoid malignancies. Investigating the biology behind CIMP methylation signatures showed the association of CIMP status with the proliferative history of the leukemic cells. A differential transcriptomic analysis revealed a correlation of CIMP subgroups with known T-ALL drivers, as well as with novel genes in T-ALL biology. Finally, we identified distinct DNA methylation patterns and genetic aberrations in T-ALL and T-LBL that might contribute to the different clinical presentation of these two diseases. In conclusion, we validated the prognostic significance of CIMP methylation signature in precursor lymphoid malignancies and identified transcriptomic profiles that associated with the subgroups. DNA methylation is a strong candidate for further risk classification in lymphoid neoplasms and our findings can contribute to the identification of new potential targets for treatment.
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| 6. |
- Hansen, Violeta, et al.
(författare)
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Iodide and iodate ((129)I and (127)I) in surface water of the Baltic Sea, Kattegat and Skagerrak
- 2011
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 412, s. 296-303
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Tidskriftsartikel (refereegranskat)abstract
- Despite the common incorporation of iodine in the biological cycle and occurrence of huge contamination of the radioactive isotope (129)I in the Baltic Proper, Skagerrak and Kattegat, there is no data on chemical speciation of iodine in these waters. We here present first time data on iodine isotopes (129)I and (127)I species as iodide and iodate in surface seawater samples collected from 16 locations in August 2006 and 19 locations in April 2007 in the Baltic Proper, Skagerrak and Kattegat. After extensive separation methods, the isotopes concentrations were determined using accelerator mass spectrometry (AMS) technique for the (129)I and inductively coupled plasma mass spectroscopy (ICP-MS) for (127)I. High concentrations of both isotopes species were found in the Skagerrak-Kattegat basins, whereas the values in the Baltic Proper are low for both species. The ratios of (129)I(-)/(129)IO(3)(-) and (127)I-/(127)IO(3)(-) significantly increase from south to central Baltic Sea, and iodide (both isotopes) appears as the predominant inorganic iodine species along the Baltic Sea. The results show insignificant change in (129)I and (127)I speciation and suggest that reduction of iodate and oxidation of iodide in Skagerrak and Kattegat may be a slow process. Additionally, the positive correlation between salinity and iodide and iodate (both isotopes) may reflect effective control of Skagerrak water mass on iodine distribution in surface water of the Baltic Sea.
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| 7. |
- Hansen, Violeta, et al.
(författare)
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Partition of iodine ((129)I and (127)I) isotopes in soils and marine sediments
- 2011
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Ingår i: Journal of Environmental Radioactivity. - : Elsevier BV. - 0265-931X .- 1879-1700. ; 102:12, s. 1096-1104
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Tidskriftsartikel (refereegranskat)abstract
- Natural organic matter, such as humic and fulvic acids and humin, plays a key role in determining the fate and mobility of radioiodine in soil and sediments. The radioisotope (129)I is continuously produced and released from nuclear fuel reprocessing plants, and as a biophilic element, its environmental mobility is strongly linked to organic matter. Due to its long half-life (15.7 million years), (129)I builds up in the environment and can be traced since the beginning of the nuclear era in reservoirs such as soils and marine sediments. Nevertheless, partition of the isotope between the different types of organic matter in soil and sediment is rarely explored. Here we present a sequential extraction of (129)I and (127)I chemical forms encountered in a Danish soil, a soil reference material (IAEA-375), an anoxic marine sediment from Southern Norway and an oxic sediment from the Barents Sea. The different forms of iodine are related to water soluble, exchangeable, carbonates, oxides as well as iodine bound to humic acid, fulvic acid and to humin and minerals. This is the first study to identify (129)I in humic and fulvic acid and humin. The results show that 30-56% of the total (127)I and 42-60% of the total (129)I are associated with organic matter in soil and sediment samples. At a soil/sediment pH below 5.0-5.5, (127)I and (129)I in the organic fraction associate primarily with the humic acid while at soil/sediment pH > 6 (129)I was mostly found to be bound to fulvic acid. Anoxic conditions seem to increase the mobility and availability of iodine compared to oxic, while subaerial conditions (soils) reduces the availability of water soluble fraction compared to subaqueous (marine) conditions.
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| 8. |
- Lansåker, Pia C., et al.
(författare)
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Au-Based Transparent Conductors for Window Applications : Effect of Substrate Material
- 2010
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Ingår i: Advances in Science and Technology. - 1662-0356. ; 75, s. 25-30
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Tidskriftsartikel (refereegranskat)abstract
- Thin films of Au were made by sputter deposition onto glass substrates with and without transparent and electrically conducting layers of SnO2:In. The Au films were up to ~11 nm in thickness and covered the range for thin film growth from discrete islands, via large scale coalescence and formation of a meandering conducting network, to the formation of a more or less “holey” film. Scanning electron microscopy and atomic force microscopy showed that the SnO2:In films were considerably rougher than the glass itself. This roughness influenced the Au film formation so that large scale coalescence set in at a somewhat larger thickness for films on SnO2:In than on glass. Measurements of spectral optical transmittance and electrical resistance could be reconciled with impeded Au film formation on the SnO2:In layer, leading to pronounced “plateaus” in the near infrared optical properties for Au films on SnO2:In and an accompanying change from such two-layer films having a lower resistance than the single gold film at thicknesses below large scale coalescence to the opposite behavior for larger film thicknesses.
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| 9. |
- Lindh, Roland, 1958-, et al.
(författare)
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A MCSCF study of homoaromaticity and the role of ion pairing in the stabilization of carbanions
- 1986
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 108:21, s. 6554-6561
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Tidskriftsartikel (refereegranskat)abstract
- The bicyclo[3.2.1]octa-3,6-dien-2-yl anion (I), the anion I lithium cation complex, the allyl anion (X), the allylradical, the allyl anion lithium cation complex, the ethene molecule, and the ethene lithium cation complex have been studiedby means of multiconfigurational SCF (MCSCF) and analytical gradients. The calculations have been confined to minimaland split-valence basis sets. The large distance between the C2 olefinic bridge and the C3 carbanionic bridge of anion I andthe short C6-C7 bond distance imply bishomoaromaticity to be negligible. According to these results, homoaromaticity isnot responsible for the observed stability in many potentially homoaromatic carbanions. The stability of anion I in the gasphase is instead explained in terms of a simple electrostatic model, where the quadrupole moment in the C2 olefinic bridgestabilizes the charge in the C, carbanionic bridge. This model agrees quantitatively with experiment. Calculations on theanion I lithium cation complex showed that in solution an additional attractive interaction between the C2 olefinic bridge andthe lithium cation can contribute. This additional interaction is estimated to stabilize the carbanion-lithium ion pair in thegas phase by about 16 kcal/mol. However, the stabilizing interactions of anion I in solution (quadrupole-charge andcounterion-anion interactions) will be reduced by solvent shielding. The relative ratios of the different stabilizing interactionsare therefore difficult to estimate. The geometrical findings of this paper have been verified by a recent X-ray experiment.
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| 10. |
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