| 1. |
- 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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| 2. |
- Faatz, B., et al.
(författare)
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Simultaneous operation of two soft x-ray free-electron lasers driven by one linear accelerator
- 2016
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Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- Extreme-ultraviolet to x-ray free-electron lasers (FELs) in operation for scientific applications are up to now single-user facilities. While most FELs generate around 100 photon pulses per second, FLASH at DESY can deliver almost two orders of magnitude more pulses in this time span due to its superconducting accelerator technology. This makes the facility a prime candidate to realize the next step in FELs-dividing the electron pulse trains into several FEL lines and delivering photon pulses to several users at the same time. Hence, FLASH has been extended with a second undulator line and self-amplified spontaneous emission (SASE) is demonstrated in both FELs simultaneously. FLASH can now deliver MHz pulse trains to two user experiments in parallel with individually selected photon beam characteristics. First results of the capabilities of this extension are shown with emphasis on independent variation of wavelength, repetition rate, and photon pulse length.
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| 3. |
- Bowman, L. R., et al.
(författare)
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Alarm Variables for Dengue Outbreaks: A Multi-Centre Study in Asia and Latin America
- 2016
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Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 11:6
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Tidskriftsartikel (refereegranskat)abstract
- Background Worldwide, dengue is an unrelenting economic and health burden. Dengue outbreaks have become increasingly common, which place great strain on health infrastructure and services. Early warning models could allow health systems and vector control programmes to respond more cost-effectively and efficiently. The Shewhart method and Endemic Channel were used to identify alarm variables that may predict dengue outbreaks. Five country datasets were compiled by epidemiological week over the years 2007-2013. These data were split between the years 2007-2011 (historic period) and 2012-2013 (evaluation period). Associations between alarm/outbreak variables were analysed using logistic regression during the historic period while alarm and outbreak signals were captured during the evaluation period. These signals were combined to form alarm/outbreak periods, where 2 signals were equal to 1 period. Alarm periods were quantified and used to predict subsequent outbreak periods. Across Mexico and Dominican Republic, an increase in probable cases predicted outbreaks of hospitalised cases with sensitivities and positive predictive values (PPV) of 93%/83% and 97%/86% respectively, at a lag of 1-12 weeks. An increase in mean temperature ably predicted outbreaks of hospitalised cases in Mexico and Brazil, with sensitivities and PPVs of 79%/73% and 81%/46% respectively, also at a lag of 1-12 weeks. Mean age was predictive of hospitalised cases at sensitivities and PPVs of 72%/74% and 96%/45% in Mexico and Malaysia respectively, at a lag of 4-16 weeks. An increase in probable cases was predictive of outbreaks, while meteorological variables, particularly mean temperature, demonstrated predictive potential in some countries, but not all. While it is difficult to define uniform variables applicable in every country context, the use of probable cases and meteorological variables in tailored early warning systems could be used to highlight the occurrence of dengue outbreaks or indicate increased risk of dengue transmission.
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| 4. |
- de Winter, J M, et al.
(författare)
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KBTBD13 is an actin-binding protein that modulates muscle kinetics
- 2020
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Ingår i: Journal of Clinical Investigation. - : Stanford University Press. - 0021-9738 .- 1558-8238. ; 130:2, s. 754-767
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Tidskriftsartikel (refereegranskat)abstract
- The mechanisms that modulate the kinetics of muscle relaxation are critically important for muscle function. A prime example of the impact of impaired relaxation kinetics is nemaline myopathy caused by mutations in KBTBD13 (NEM6). In addition to weakness, NEM6 patients have slow muscle relaxation, compromising contractility and daily life activities. The role of KBTBD13 in muscle is unknown, and the pathomechanism underlying NEM6 is undetermined. A combination of transcranial magnetic stimulation-induced muscle relaxation, muscle fiber- and sarcomere-contractility assays, low-angle x-ray diffraction, and superresolution microscopy revealed that the impaired muscle-relaxation kinetics in NEM6 patients are caused by structural changes in the thin filament, a sarcomeric microstructure. Using homology modeling and binding and contractility assays with recombinant KBTBD13, Kbtbd13-knockout and Kbtbd13(R408c)-knockin mouse models, and a GFP-labeled Kbtbd13-transgenic zebrafish model, we discovered that KBTBD13 binds to actin - a major constituent of the thin filament - and that mutations in KBTBD13 cause structural changes impairing muscle-relaxation kinetics. We propose that this actin-based impaired relaxation is central to NEM6 pathology.
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| 5. |
- Allum, F., et al.
(författare)
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A localized view on molecular dissociation via electron-ion partial covariance
- 2022
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Ingår i: Communications Chemistry. - : Springer Science and Business Media LLC. - 2399-3669. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Inner-shell photoelectron spectroscopy provides an element-specific probe of molecular structure, as core-electron binding energies are sensitive to the chemical environment. Short-wavelength femtosecond light sources, such as Free-Electron Lasers (FELs), even enable time-resolved site-specific investigations of molecular photochemistry. Here, we study the ultraviolet photodissociation of the prototypical chiral molecule 1-iodo-2-methylbutane, probed by extreme-ultraviolet (XUV) pulses from the Free-electron LASer in Hamburg (FLASH) through the ultrafast evolution of the iodine 4d binding energy. Methodologically, we employ electron-ion partial covariance imaging as a technique to isolate otherwise elusive features in a two-dimensional photoelectron spectrum arising from different photofragmentation pathways. The experimental and theoretical results for the time-resolved electron spectra of the 4d(3/2) and 4d(5/2) atomic and molecular levels that are disentangled by this method provide a key step towards studying structural and chemical changes from a specific spectator site. Coincidence experiments at free-electron lasers enable time resolved site-specific investigations of molecular photochemistry at high signal rates, but isolating individual dissociation processes still poses a considerable technical challenge. Here, the authors use electron-ion partial covariance imaging to isolate otherwise elusive chemical shifts in UV-induced photofragmentation pathways of the prototypical chiral molecule 1-iodo-2-methylbutane.
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| 9. |
- Gonschorek, M., et al.
(författare)
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Two-dimensional electron gas density in Al1-x InMx N/AlN/GaN heterostructures (0.03=x=0.23)
- 2008
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 103:9, s. 093714-
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Tidskriftsartikel (refereegranskat)abstract
- Compared to the AlGaN alloy, which can only be grown under tensile strain on GaN, the AlInN alloy is predicted by Vegard's law to be lattice-matched (LM) on fully relaxed GaN templates for an indium content of ~17.5%, i.e., it can be grown either tensely or compressively on GaN. The effect of strain on the polarization induced sheet charge density at the Al1-x Inx N/AlN/GaN heterointerfaces is carefully investigated for 6 and 14 nm thick AlInN barriers including a 1 nm thick AlN interlayer. The barrier indium content ranges at 0.03=x=0.23 for 6 nm thick barriers and 0.07=x=0.21 for 14 nm thick barriers. It is found that the two-dimensional electron gas (2DEG) density varies between (3.5±0.1) × 1013 cm-2 and (2.2±0.1) × 1013 cm-2 for 14 nm thick barriers. Finally, a 2DEG density up to (1.7±0.1) × 1013 cm-2 is obtained for a nearly LM AlInN barrier with ~14.5% indium on GaN as thin as 6 nm. © 2008 American Institute of Physics.
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| 10. |
- Hans, Marcus, et al.
(författare)
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Substrate rotation-induced chemical modulation in Ti-Al-O-N coatings synthesized by cathodic arc in an industrial deposition plant
- 2016
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Ingår i: Surface & Coatings Technology. - : Elsevier BV. - 0257-8972 .- 1879-3347. ; 305, s. 249-253
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Tidskriftsartikel (refereegranskat)abstract
- Reactive cathodic arc evaporation of Ti-Al-O-N was carried out in an industrial deposition system with two-fold substrate rotation. The structural and compositional evolution of the coatings was studied by combining scanning transmission electron microscopy and 3D atom probe tomography (APT). The formation of alternating O- and N-rich sublayers was identified by APT and can be understood by considering the substrate rotation induced variation in plasma density and fluxes of film-forming species. The effect of plasma density and fluxes on the incorporation of reactive species was studied in stationary deposition experiments and preferred N incorporation occurs, when the growing coating surface is facing the arc source. Thus, the growing surface is positioned in a region of high plasma density characterized by large fluxes of film forming-species. Preferred O incorporation takes place in a region of low plasma density where small fluxes are present, when the growing surface is blocked from the arc source by the substrate holder. Hence, compositional modulations are caused by substrate rotation as the growing coating surface is periodically exposed to regions of high plasma density and large fluxes of film-forming species and regions of low plasma density and small fluxes. These findings are highly relevant for all reactive industrial plasma assisted physical vapor deposition processes utilizing substrate rotation.
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