| 1. |
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| 2. |
- 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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| 3. |
- Richards, Stephen, et al.
(författare)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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Ingår i: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Tidskriftsartikel (refereegranskat)abstract
- Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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| 4. |
- Breznau, Nate, et al.
(författare)
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Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:44
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Tidskriftsartikel (refereegranskat)abstract
- This study explores how researchers analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each teams workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
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| 5. |
- Ruess, H., et al.
(författare)
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HPPMS deposition from composite targets : Effect of two orders of magnitude target power density changes on the composition of sputtered Cr-Al-C thin films
- 2017
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Ingår i: Vacuum. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0042-207X .- 1879-2715. ; 145, s. 285-289
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Tidskriftsartikel (refereegranskat)abstract
- The effect of target power density, substrate bias potential and substrate temperature on the thin film composition was studied. A Cr-Al-C composite target was sputtered utilizing direct current (DCMS: 2.3 W/cm(2)) and high power pulsed magnetron sputtering (HPPMS: 373 W/cm(2)) generators. At floating potential, all Cr-Al-C thin films showed similar compositions, independently of the applied target power density. However, as substrate bias potential was increased to -400 V, aluminum deficiencies by a factor of up to 1.6 for DCMS and 4.1 for HPPMS were obtained. Based on the measured ion currents at the substrate, preferential re-sputtering of Al is suggested to cause the dramatic Al depletion. As the substrate temperature was increased to 560 degrees C, the Al concentration was reduced by a factor of up to 1.9 compared to the room temperature deposition. This additional reduction may be rationalized by thermally induced desorption being active in addition to re-sputtering.
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| 6. |
- Achenbach, Jan-Ole, et al.
(författare)
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Low temperature oxidation behavior of Mo2BC coatings
- 2020
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Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : A V S AMER INST PHYSICS. - 0734-2101 .- 1520-8559. ; 38:2
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Tidskriftsartikel (refereegranskat)abstract
- Mo2BC exhibits a unique combination of high stiffness and moderate ductility, enabling the application as a protective and wear resistant coating. As the low temperature oxidation behavior of Mo2BC coatings is unexplored, direct current magnetron sputtered Mo2BC coatings were oxidized at temperatures ranging from 500 to 100 degrees C for up to 28 days. Time-of-flight elastic recoil detection analysis reveals that the onset of oxidation takes place at approximately 300 degrees C as a significant increase in the O content was observed. Crystalline oxide scales containing orthorhombic MoO3 were identified after oxidation for 15 min at 500 degrees C and 10 days at 200 degrees C. Isothermal oxidation at 200 and 100 degrees C exhibits oxide scale thicknesses of 401 +/- 33 and 22 +/- 10 nm after 14 days. Oxidation for 28 days at 100 degrees C exhibits an oxide scale thickness of 13 +/- 3 nm, which is comparable to the aforementioned oxide scale thickness after oxidation for 14 days at 100 degrees C. Based on the combination of mechanical properties and the here reported low temperature oxidation behavior, Mo2BC coatings qualify for applications in solid wood machining and low temperature forming processes at temperatures close to 100 degrees C or below.
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| 7. |
- Aghda, Soheil Karimi, et al.
(författare)
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Ion kinetic energy- and ion flux-dependent mechanical properties and thermal stability of (Ti,Al)N thin films
- 2023
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Ingår i: Acta Materialia. - : Elsevier. - 1359-6454 .- 1873-2453. ; 250
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Tidskriftsartikel (refereegranskat)abstract
- Ion-irradiation-induced changes in structure, elastic properties, and thermal stability of metastable c-(Ti,Al)N thin films synthesized by high-power pulsed magnetron sputtering (HPPMS) and cathodic arc deposition (CAD) are systematically investigated by experiments and density functional theory (DFT) simulations. While films deposited by HPPMS show a random orientation at ion kinetic energies (Ek)>105 eV, an evolution towards (111) orientation is observed in CAD films for Ek>144 eV. The measured ion energy flux at the growing film surface is 3.3 times larger for CAD compared to HPPMS. Hence, it is inferred that formation of the strong (111) texture in CAD films is caused by the ion flux-and ion energy-induced strain energy minimization in defective c-(Ti,Al)N. The ion energy-dependent elastic modulus can be rationalized by considering the ion energy-and orientation -dependent formation of point defects from DFT predictions: The balancing effects of bombardment-induced Frenkel defects formation and the concurrent evolution of compressive intrinsic stress result in the apparent independence of the elastic modulus from Ek for HPPMS films without preferential orientation. However, an ion energy-dependent elastic modulus reduction of similar to 18% for the CAD films can be understood by considering the 34% higher Frenkel pair concentration formed at Ek=182 eV upon irradiation of the experimentally observed (111)-oriented (Ti,Al)N in comparison to the (200)-configuration at similar Ek. Moreover, the effect of Frenkel pair concentration on the thermal stability of metastable c-(Ti,Al)N is investigated by differential scanning calorimetry: Ion-irradiation-induced increase in Frenkel pairs concentration retards the wurtzite formation temperature by up to 206 degrees C.
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| 8. |
- Aghda, Soheil Karimi, et al.
(författare)
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Valence electron concentration- and N vacancy-induced elasticity in cubic early transition metal nitrides
- 2023
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Ingår i: Acta Materialia. - : Elsevier. - 1359-6454 .- 1873-2453. ; 255
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Tidskriftsartikel (refereegranskat)abstract
- Motivated by frequently reported deviations from stoichiometry in cubic transition metal nitride (TMNx) thin films, the effect of N-vacancy concentration on the elastic properties of cubic TiNx, ZrNx, VNx, NbNx, and MoNx (0.72 & LE; x & LE; 1.00) is systematically studied by density functional theory (DFT) calculations. The predictions are validated experimentally for VNx (0.77 & LE; x & LE; 0.97). The DFT results indicate that the elastic behavior of the TMNx depends on both the N-vacancy concentration and the valence electron concentration (VEC) of the transition metal: While TiNx and ZrNx exhibit vacancy-induced reductions in elastic modulus, VNx and NbNx show an increase. These trends can be rationalized by considering vacancy-induced changes in elastic anisotropy and bonding. While introduction of N-vacancies in TiNx results in a significant reduction of elastic modulus along all directions and a lower average bond strength of Ti-N, the vacancy-induced reduction in [001] direction of VNx is overcompensated by the higher stiffness along [011] and [111] directions, resulting in a higher average bond strength of V-N. To validate the predicted vacancy-induced changes in elasticity experimentally, close-to-singlecrystal VNx (0.77 & LE; x & LE; 0.97) are grown on MgO(001) substrates. As the N-content is reduced, the relaxed lattice parameter a0, as probed by X-ray diffraction, decreases from 4.128 & ANGS; to 4.096 & ANGS;. This reduction in lattice parameter is accompanied by an anomalous 11% increase in elastic modulus, as determined by nanoindentation. As the experimental data agree with the predictions, the elasticity enhancement in VNx upon N-vacancy formation can be understood based on the concomitant changes in elastic anisotropy and bonding.
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| 9. |
- Azina, Clio, et al.
(författare)
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Yttrium incorporation in Cr2AlC : On the metastable phase formation and decomposition of (Cr,Y)(2)AlC MAX phase thin films
- 2023
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Ingår i: Journal of The American Ceramic Society. - : John Wiley & Sons. - 0002-7820 .- 1551-2916. ; 106:4, s. 2652-2665
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Tidskriftsartikel (refereegranskat)abstract
- Herein we report on the synthesis of a metastable (Cr,Y)(2)AlC MAX phase solid solution by co-sputtering from a composite Cr-Al-C and elemental Y target, at room temperature, followed by annealing. However, direct high-temperature synthesis resulted in multiphase films, as evidenced by X-ray diffraction analyses, room-temperature depositions, followed by annealing to 760 degrees C led to the formation of phase pure (Cr,Y)(2)AlC by diffusion. Higher annealing temperatures caused a decomposition of the metastable phase into Cr2AlC, Y5Al3, and Cr-carbides. In contrast to pure Cr2AlC, the Y-containing phase crystallizes directly in the MAX phase structure instead of first forming a disordered solid solution. Furthermore, the crystallization temperature was shown to be Y-content dependent and was increased by similar to 200 degrees C for 5 at.% Y compared to Cr2AlC. Calculations predicting the metastable phase formation of (Cr,Y)(2)AlC and its decomposition are in excellent agreement with the experimental findings.
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| 10. |
- Evertz, Simon, et al.
(författare)
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Boron Concentration Induced Co-Ta-B Composite Formation Observed in the Transition from Metallic to Covalent Glasses
- 2020
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Ingår i: Condensed Matter. - : MDPI. - 2410-3896. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Due to their unique property combination of high strength and toughness, metallic glasses are promising materials for structural applications. As the behaviour of metallic glasses depends on the electronic structure which in turn is defined by chemical composition, we systematically investigate the influence of B concentration on glass transition, topology, magnetism, and bonding for B concentrations x = 2 to 92 at.% in the (Co6.8 +/- 3.9Ta)(100-x)B-x system. From an electronic structure and coordination point of view, the B concentration range is divided into three regions: Below 39 +/- 5 at.% B, the material is a metallic glass due to the dominance of metallic bonds. Above 69 +/- 6 at.%, the presence of an icosahedra-like B network is observed. As the B concentration is increased above 39 +/- 5 at.%, the B network evolves while the metallic coordination of the material decreases until the B concentration of 67 +/- 5 at.% is reached. Hence, a composite is formed. It is evident that, based on the B concentration, the ratio of metallic bonding to icosahedral bonding in the composite can be controlled. It is proposed that, by tuning the coordination in the composite region, glassy materials with defined plasticity and processability can be designed.
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