| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 2. |
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| 3. |
- Andersen, Torben, et al.
(author)
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A parallel integrated model of the Euro50
- 2004
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In: Proceedings of the SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. ; 5497:1, s. 251-265
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Conference paper (peer-reviewed)abstract
- The Euro50 is an astronomical extremely large telescope for optical and infrared wavelength with a 50 m primary mirror. The telescope will have an elaborate control system ("live optics") to correct for atmospheric and telescope aberrations. To study and predict performance of the complete telescope system, an integrated model combining the structural model of the telescope, optics models, the control systems, and the adaptive optics has been established. Wind is taken into account on the basis of wind tunnel measurements and computer fluid dynamics calculations. Atmospheric aberrations are included using a seven-layer atmosphere model. The integrated model is written in Matlab and is run on a cluster computer to achieve acceptable execution times. Dedicated ordinary differential equation solvers have been written and a special toolkit for communication between Matlab processes on different nodes of the cluster computer has been set up. Preliminary results from the complete integrated model, including adaptive optics, are shown
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| 4. |
- Andersen, Torben, et al.
(author)
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Status of the Euro50 project
- 2004
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In: Proceedings of the SPIE - The International Society for Optical Engineering. - : SPIE. - 0277-786X .- 1996-756X. ; 5489:1, s. 407-416
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Conference paper (peer-reviewed)abstract
- The Euro50 is an extremely large telescope for optical and infrared wavelength with a 50 m primary mirror. It has a segmented, aspherical primary mirror and an aspherical, deformable secondary in a Gregorian layout. A tentative conceptual design exists and has been documented in a study report. Recent activities have concentrated on the science case for extremely large telescopes in the 50 m class and on identification of potential technical "show stoppers". The science case investigation has identified four fields of particular interest. The studies of critical technical issues have concentrated on atmospheric dispersion effects for high-resolution adaptive optics for extremely large telescopes, and on the influence of wind and other disturbances on wavefront control. Wind load on the telescope, the primary mirror and the enclosure has been studied using wind tunnel measurements and computational fluid dynamics. The impact of wind on the total system has been investigated using an integrated model that includes the telescope structure, the primary mirror segment alignment system, the secondary mirror alignment system, and single conjugate adaptive optics using the deformable secondary mirror. The first, tentative results show that wind disturbances may be significant and that the task of correcting for wind residuals may be at least as large for the adaptive optics system as that of correcting for atmospheric aberrations. The results suggest that use of extremely large telescopes for observations of earth-like planets around nearby stars may imply a considerable challenge
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| 5. |
- Fan, Chengyu, et al.
(author)
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High-order laser guide star performance for the Euro50 telescope
- 2005
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In: Optics Express. - 1094-4087. ; 13:5, s. 1377-1383
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Journal article (peer-reviewed)abstract
- High-order laser guide star performance for the Euro50 telescope is analyzed. Focus anisoplanatism residual errors using multiple LGSs are obtained by numerical simulations. Results calculated for annual mean conditions at the La Palma site show that, considering only focus anisoplanatism, it will be possible to obtain a Strehl ratio of 0.72 similar to 0.82 at 2.2 mum using 13 LGSs. A Strehl ratio of 0.60 similar to 0.70 can be obtained at 1.25 mum using 21 LGSs. The dependence of wavefront measurement error on pulsed laser power is also investigated. The variance of the measurement error is lower than 0.2 rad(2) when the laser power is larger than 14 W.
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| 6. |
- Su, Fan-Chi, et al.
(author)
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A graphic user interface toolkit for specification, report and comparison of dose-response relations and treatment plans using the biologically effective uniform dose
- 2010
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In: Computer Methods and Programs in Biomedicine. - : Elsevier BV. - 0169-2607 .- 1872-7565. ; 100:1, s. 69-78
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Journal article (peer-reviewed)abstract
- A toolkit (BEUDcal) has been developed for evaluating the effectiveness and for predicting the outcome of treatment plans by calculating the biologically effective uniform dose (BEUD) and complication-free tumor control probability. The input for the BEUDcal is the differential dose-volume histograms of organs exported from the treatment planning system. A clinical database is built for the dose-response parameters of different tumors and normal tissues. Dose-response probabilities of all the examined organs are illustrated together with the corresponding BEUDs and the P+ values. Furthermore, BEUDcal is able to generate a report that simultaneously presents the radiobiological evaluation together with the physical dose indices, showing the complementary relation between the physical and radiobiological treatment plan analysis performed by BEUDcal. Comparisons between treatment plans for helical tomotherapy and multileaf collimator-based intensity modulated radiotherapy of a lung patient were demonstrated to show the versatility of BEUDcal in the assessment and report of dose-response relations.
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