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- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are 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 monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Amgad, M, et al.
(författare)
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Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group
- 2020
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Ingår i: NPJ breast cancer. - : Springer Science and Business Media LLC. - 2374-4677. ; 6:1, s. 16-
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Tidskriftsartikel (refereegranskat)abstract
- Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.
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| 5. |
- Darakchieva, Vanya, et al.
(författare)
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Role of impurities and dislocations for the unintentional n-type conductivity in InN
- 2009
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Ingår i: PHYSICA B-CONDENSED MATTER. - : Elsevier BV. - 0921-4526. ; 404:22, s. 4476-4481
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Tidskriftsartikel (refereegranskat)abstract
- We present a study on the role of dislocations and impurities for the unintentional n-type conductivity in high-quality InN grown by molecular beam epitaxy. The dislocation densities and H profiles in films with free electron concentrations in the low 10(17) cm(-1) and mid 10(18) cm(-3) range are measured, and analyzed in a comparative manner. It is shown that dislocations alone could not account for the free electron behavior in the InN films. On the other hand, large concentrations of H sufficient to explain, but exceeding substantially, the observed free electron densities are found. Furthermore, enhanced concentrations of H are revealed at the film surfaces, resembling the free electron behavior with surface electron accumulation. The low-conductive film was found to contain C and it is suggested that C passivates the H donors or acts as an acceptor, producing compensated material in this case. Therefore, it is concluded that the unintentional impurities play an important role for the unintentional n-type conductivity in InN. We suggest a scenario of H incorporation in InN that may reconcile the previously reported observations for the different role of impurities and dislocations for the unintentional n-type conductivity in InN.
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| 7. |
- Junaid, Muhammad, et al.
(författare)
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Epitaxial Growth of GaN (0001)/Al2O3 (0001) by Reactive High Power Impulse Magnetron Sputter Deposition
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Epitaxial GaN (0001) thin films were grown on Al2O3 (0001) substrates by reactive high power impulse magnetron sputtering of liquid Ga targets in a mixed N2/Ar discharge. A combination of x-ray diffraction, electron microscopy, atomic force microscopy, μ-Raman mapping and spectroscopy, μ-photoluminescence, time of flight elastic recoil detection, and cathodoluminescence showed the formation of relaxed and strained domains in the same films. While the strained domains form due to ion bombardment during growth, the relaxed domains exhibit
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