| 1. |
- Osorio, A., et al.
(author)
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Evaluation of a candidate breast cancer associated SNP in ERCC4 as a risk modifier in BRCA1 and BRCA2 mutation carriers. Results from the consortium of investigators of modifiers of BRCA1/BRCA2 (CIMBA)
- 2009
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In: British Journal of Cancer. - : Nature Publishing Group. - 0007-0920 .- 1532-1827. ; 101:12, s. 2048-2054
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Journal article (peer-reviewed)abstract
- Background: In this study we aimed to evaluate the role of a SNP in intron 1 of the ERCC4 gene (rs744154), previously reported to be associated with a reduced risk of breast cancer in the general population, as a breast cancer risk modifier in BRCA1 and BRCA2 mutation carriers. Methods: We have genotyped rs744154 in 9408 BRCA1 and 5632 BRCA2 mutation carriers from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) and assessed its association with breast cancer risk using a retrospective weighted cohort approach. Results: We found no evidence of association with breast cancer risk for BRCA1 (per-allele HR: 0.98, 95% CI: 0.93-1.04, P0.5) or BRCA2 (per-allele HR: 0.97, 95% CI: 0.89-1.06, P0.5) mutation carriers. Conclusion: This SNP is not a significant modifier of breast cancer risk for mutation carriers, though weak associations cannot be ruled out.
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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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In: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Research review (peer-reviewed)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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| 3. |
- Schaap, M., et al.
(author)
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Standardized evaluation methodology and reference database for evaluating coronary artery centerline extraction algorithms
- 2009
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In: Medical Image Analysis. - : Elsevier. - 1361-8415 .- 1361-8423. ; 13:5, s. 701-714
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Journal article (peer-reviewed)abstract
- Efficiently obtaining a reliable coronary artery centerline from computed tomography angiography data is relevant in clinical practice. Whereas numerous methods have been presented for this purpose, up to now no standardized evaluation methodology has been published to reliably evaluate and compare the performance of the existing or newly developed coronary artery centerline extraction algorithms. This paper describes a standardized evaluation methodology and reference database for the quantitative evaluation of coronary artery centerline extraction algorithms. The contribution of this work is fourfold: (1) a method is described to create a consensus centerline with multiple observers, (2) well-defined measures are presented for the evaluation of coronary artery centerline extraction algorithms, (3) a database containing 32 cardiac CTA datasets with corresponding reference standard is described and made available, and (4) 13 coronary artery centerline extraction algorithms, implemented by different research groups, are quantitatively evaluated and compared. The presented evaluation framework is made available to the medical imaging community for benchmarking existing or newly developed coronary centerline extraction algorithms.
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| 4. |
- Lim, W., et al.
(author)
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Migration and Luminescence Enhancement Effects of Deuterium in ZnO/ZnCdO Quantum Wells
- 2008
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In: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 92, s. 032103-
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Journal article (peer-reviewed)abstract
- ZnO/ZnCdO/ZnO multiple quantum well samples grown on sapphire substrates by molecular beam epitaxy and annealed in situ were exposed to D2 plasmas at 150 °C. The deuterium showed migration depths of ~0.8 µm for 30 min plasma exposures, with accumulation of 2H in the ZnCdO wells. The photoluminescence (PL) intensity from the samples was increased by factors of 5 at 5 K and ~20 at 300 K as a result of the deuteration, most likely due to passivation of competing nonradiative centers. Annealing up to 300 °C led to increased migration of 2H toward the substrate but no loss of deuterium from the sample and little change in the PL intensity. The initial PL intensities were restored by annealing at >=400 °C as 2H was evolved from the sample (~90% loss by 500 °C). By contrast, samples without in situ annealing showed a decrease in PL intensity with deuteration. This suggests that even moderate annealing temperatures lead to degradation of ZnCdO quantum wells.
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| 5. |
- Wang, L.-L., et al.
(author)
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Origin of bulklike structure and bond length disorder of Pt37 and Pt6Ru31 clusters on carbon : Comparison of theory and experiment
- 2006
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 128:1, s. 131-142
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Journal article (peer-reviewed)abstract
- We describe a theoretical analysis of the structures of self-organizing nanoparticles formed by Pt and Ru-Pt on carbon support. The calculations provide insights into the nature of these metal particle systems-ones of current interest for use as the electrocatalytic materials of direct oxidation fuel cells- and clarify complex behaviors noted in earlier experimental studies. With clusters deposited via metalloorganic Pt or PtRu5 complexes, previous experiments [Nashner et al. J. Am. Chem. Soc. 1997, 119, 7760, Nashner et al. J. Am. Chem. Soc. 1998, 120, 8093, Frenkel et al. J. Phys. Chem. B 2001, 105, 12689] showed that the Pt and Pt-Ru based clusters are formed with fcc(111)-stacked cuboctahedral geometry and essentially bulklike metal-metal bond lengths, even for the smallest (few atom) nanoparticles for which the average coordination number is much smaller than that in the bulk, and that Pt in bimetallic [PtRu5] clusters segregates to the ambient surface of the supported nanoparticles. We explain these observations and characterize the cluster structures and bond length distributions using density functional theory calculations with graphite as a model for the support. The present study reveals the origin of the observed metal-metal bond length disorder, distinctively different for each system, and demonstrates the profound consequences that result from the cluster/carbon-support interactions and their key role in the structure and electronic properties of supported metallic nanoparticles. © 2006 American Chemical Society.
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| 6. |
- Buyanova, Irina A, et al.
(author)
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Effects of Ga doping on optical and structural properties of ZnO epilayers
- 2009
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In: Superlattices and Microstructures. - : Elsevier BV. - 0749-6036 .- 1096-3677. ; 45:4-5, s. 413-420
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Journal article (peer-reviewed)abstract
- Effects of Ga incorporation on electrical, structural and optical properties of ZnO epilayers are systematically studied by employing structural and optical characterization techniques combined with electrical and secondary ion mass spectrometry measurements. A non-monotonous dependence of free electron concentrations on Ga content is observed and is attributed to defect formation and phase separation. The former process is found to dominate for Ga concentrations of around 2-3x1020 cm-3. corresponding defects are suggested to be responsible for a broad red emission, which peaks at around 1.8 eV at K. Characteristic properties of this emission are well accounted for by assuming intracenter transitions at a deep center, of which the associated Huang-Rhys factor and mean phonon energy are determined. For higher Ga doping levels, the phase separation is found to be significant. It is that under these conditions only a minor fraction of incorporated Ga atoms form shallow donors, which leads to the observed dramatic decrease of carrier concentration.
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| 7. |
- Buyanova, Irina, 1960-, et al.
(author)
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Optical characterization of Zn(1-x)Cd(x)O alloys grown by molecular-beam epitaxy
- 2006
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In: 210th ECS Meeting Volume 3, Issue 5. - : The Electrochemical Society. ; , s. 391-398
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Conference paper (other academic/artistic)abstract
- We have carried out comprehensive optical studies to evaluate structural and bandgap properties of Zn1-xCdxO alloys with x{less than or equalto}0.17 grown by molecular beam epitaxy. High crystalline quality ofthe alloys was concluded from cathodoluminescence measurements. Based on absorptionand reflectance measurements, the compositional dependence of the bandgap energyof ZnCdO, estimated without taking into account excitonic effects, wasfound to follow the trend Eg(x)=3.28-2.23x+0.45x2. Degradation in the alloyquality due to possible phase separation was found to causedeviations from this trend, evident from a more rapid redshift of the absorption edge. Effects of Cd incorporation onthe variation of the bandgap energies with temperature are alsodiscussed.
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| 8. |
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| 9. |
- Dagnelund, Daniel, 1980-, et al.
(author)
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Effect of growth conditions on grown-in defect formation and luminescence efficiency in GaInNP epilayers grown by molecular-beam epitaxy.
- 2008
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In: Physica status solidi (c)Special Issue: E-MRS 2007 Spring Meeting – Symposium F and Conference on Photonic Materials. - Weinheim : Wiley-VCH Verlagsgesellschaft. ; , s. 460-463
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Conference paper (peer-reviewed)abstract
- A detailed study of the impact of different growth conditions (i.e. ion bombardment, nitrogen flow and In content) on the defect formation in Ga(In)NP epilayers grown on GaP substrates by solid-source molecular beam epitaxy is performed. Reduced nitrogen ion bombardment during the growth is shown to significantly reduce formation of defects acting as competing recombination centers, such as a Ga interstitial defect and other unidentified defects revealed by optically detected magnetic resonance. Further, high nitrogen flow is found to be even more effective than the ion bombardment in introducing the defects. The incorporation of In by 5.1% is, on the other hand, found not to affect the introduction of defects. The results provide a useful insight into the formation mechanism of the defects that will hopefully shed light on a control of the defect introduction in the alloys by optimizing growth conditions.
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| 10. |
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