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| 3. |
- 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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| 5. |
- Maeda, Y., et al.
(författare)
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Differential cross section and analyzing power measurements for (n)over-right-arrowd elastic scattering at 248 MeV
- 2007
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 76:1, s. 014004-
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Tidskriftsartikel (refereegranskat)abstract
- The differential cross sections and vector analyzing powers for nd elastic scattering at E-n=248 MeV were measured for 10 degrees-180 degrees in the center-of-mass (c.m.) system. To cover the wide angular range, the experiments were performed separately by using two different setups for forward and backward angles. The data are compared with theoretical results based on Faddeev calculations with realistic nucleon-nucleon (NN) forces such as AV18, CD Bonn, and Nijmegen I and II, and their combinations with the three-nucleon forces (3NFs), such as Tucson-Melbourne 99 (TM99), Urbana IX, and the coupled-channel potential with Delta-isobar excitation. Large discrepancies are found between the experimental cross sections and theory with only 2N forces for theta(c.m.)>90 degrees. The inclusion of 3NFs brings the theoretical cross sections closer to the data but only partially explains this discrepancy. For the analyzing power, no significant improvement is found when 3NFs are included. Relativistic corrections are shown to be small for both the cross sections and the analyzing powers at this energy. For the cross sections, these effects are mostly seen in the very backward angles. Compared with the pd cross section data, quite significant differences are observed at all scattering angles that cannot be explained only by the Coulomb interaction, which is usually significant at small angles.
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| 6. |
- Raiteri, C. M., et al.
(författare)
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WEBT and XMM-Newton observations of 3C 454.3 during the post-outburst phase - Detection of the little and big blue bumps
- 2007
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 473:3, s. 819-827
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Tidskriftsartikel (refereegranskat)abstract
- Context. The quasar-type blazar 3C 454.3 was observed to undergo an unprecedented optical outburst in spring 2005, affecting the source brightness from the near-IR to the X-ray frequencies. This was first followed by a millimetric and then by a radio outburst, which peaked in February 2006. Aims. In this paper we report on follow-up observations to study the multiwavelength emission in the post-outburst phase. Methods. Radio, near-infrared, and optical monitoring was performed by the Whole Earth Blazar Telescope (WEBT) collaboration in the 2006-2007 observing season. XMM-Newton observations on July 2-3 and December 18-19, 2006 added information on the X-ray and UV states of the source. Results. The source was in a faint state. The radio flux at the higher frequencies showed a fast decreasing trend, which represents the tail of the big radio outburst. It was followed by a quiescent state, common at all radio frequencies. In contrast, moderate activity characterized the near-IR and optical light curves, with a progressive increase of the variability amplitude with increasing wavelength. We ascribe this redder-when-brighter behaviour to the presence of a ""little blue bump"" due to line emission from the broad line region, which is clearly visible in the source spectral energy distribution (SED) during faint states. Moreover, the data from the XMM- Newton Optical Monitor reveal a rise of the SED in the ultraviolet, suggesting the existence of a "" big blue bump"" due to thermal emission from the accretion disc. The X-ray spectra are well fitted with a power- law model with photoelectric absorption, possibly larger than the Galactic one. However, the comparison with previous X-ray observations would imply that the amount of absorbing matter is variable. Alternatively, the intrinsic X-ray spectrum presents a curvature, which may depend on the X-ray brightness. In this case, two scenarios are possible. i) There is no extra absorption, and the X-ray spectrum hardens at low energies, the hardening being more evident in bright states; ii) there is a constant amount of extra absorption, likely in the quasar environment, and the X-ray spectrum softens at low energies, at least in faint X-ray states. This softening might be the result of a flux contribution by the high-frequency tail of the big blue bump.
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| 7. |
- Khan, H. R., et al.
(författare)
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Cross-cultural prevalence of sleep quality and psychological distress in healthcare workers during COVID-19 pandemic
- 2021
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Ingår i: Brain and Behavior. - : John Wiley & Sons. - 2162-3279 .- 2162-3279. ; 11:11
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Tidskriftsartikel (refereegranskat)abstract
- Background: Poor quality sleep and emotional disturbances are expected in times of crisis. COVID-19 has severely impacted healthcare worldwide and with that comes the concern about its effects on healthcare workers. The purpose of the present study was to assess sleep quality and psychological distress in healthcare workers during the COVID-19 pandemic.Methods: The present work is a multi-centric cross-sectional study targeting healthcare workers from India, Pakistan, and Nepal. It used an online version of the Pittsburg Sleep Quality Index and the General Health Questionnaire, and data were analyzed using SPSS V.24.Results: A total of 1790 participants completed the questionnaire. Of the 1790 participants, 57% reported poor sleep quality, and 10% reported a high level of psychological distress. A cross-cultural comparison found some differences between the different groups of participants. The details of the differences were further explored in the article.Conclusion: The present study highlights that a significant proportion of healthcare workers are affected by poor sleep quality and psychological distress during the COVID-19 pandemic. It also emphasizes the imperative to provide them with psychosocial support to avoid potential short- and long-term psychological consequences of these troubling times.
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| 8. |
- Sawa, H, et al.
(författare)
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Spatiotemporal expression of C-CAM in the rat placenta
- 1997
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Ingår i: The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society. - : SAGE Publications. - 0022-1554. ; 45:7, s. 1021-1034
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the expression of the immunoglobulin superfamily cell adhesion molecule, C-CAM, in developing and mature rat placenta. By immunohistochemical staining at the light microscopic level, no C-CAM-expression was seen before Day 9 of gestation, when it appeared in the trophoblasts of ectoplacental cones. On Day 10.5, spongiotrophoblasts and invasive trophoblasts around the maternal vessels of the decidua basalis were stained positively. On Day 12.5, C-CAM was detected in the spongiotrophoblasts of the junctional layer, but labyrinth trophoblasts and secondary giant trophoblasts were not stained. On Day 17.5, C-CAM was found only in the labyrinth and lacunae of the junctional layer. At this stage, both the labyrinth cytotrophoblasts of the maternal blood vessels and the endothelial cells of the embryonic capillaries were strongly stained. Placental tissues from gestational Days 12.5 and 17.5 were analyzed by immunoelectron microscopy to determine the location of C-CAM at the subcellular level. On Day 12.5, positive staining of the spongiotrophoblasts was observed, mainly on surface membranes and microvilli between loosely associated cells. On Day 17.5, staining was found primarily on the microvilli of the maternal luminal surfaces of the labyrinth cytotrophoblasts, and both on the luminal surface and in the cytoplasm of endothelial cells of the embryonic vessels. RT-PCR analysis and Southern blotting of the PCR products revealed expression of mRNA species for both of the major isoforms, C-CAM1 and C-CAM2. Immunoblotting analysis of C-CAM isolated from 12.5-day and 14.5-day placentae showed that it appeared as a broad band with an apparent molecular mass of 110–170 kD. In summary, C-CAM was strongly expressed in a specific spatiotemporal pattern in trophoblasts actively involved in formation of the placental tissue, suggesting an important role in placental development. In the mature placenta, C-CAM expression was confined to the trophoblastic and endothelial cells lining the maternal and embryonic vessels, respectively, suggesting important functions in placental physiology.
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| 10. |
- Thörngren Engblom, Pia, et al.
(författare)
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Experimental search for evidence of the three-nucleon force and a new analysis method
- 2004
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Ingår i: FEW-BODY PROBLEMS IN PHYSICS. - : AIP. - 0735402531 ; , s. 65-68
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- A research program with the aim of investigating the spin dependence of the three-nucleon continuum in pd collisions at intermediate energies was carried out at IUCF using the Polarized INternal Target EXperiments (PINTEX) facility. In the elastic scattering experiment at 135 and 200 MeV proton beam energies a total of 15 independent spin observables were obtained. The breakup experiment was done with a vector and tensor polarized beam of 270 MeV and an internal polarized hydrogen gas target. We developed a novel technique for the analysis of the breakup observables, the sampling method. The new approach takes into account acceptance and non-uniformities of detection efficiencies and is suitable for any kinematically complete experiment with three particles in the final state.
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| 11. |
- Lonnroth, J. S., et al.
(författare)
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Effects of ripple-induced ion thermal transport on H-mode plasma performance
- 2007
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Ingår i: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 0741-3335 .- 1361-6587. ; 49:3, s. 273-295
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Tidskriftsartikel (refereegranskat)abstract
- A recent series of dimensionless pedestal identity experiments at JET and JT-60U failed to produce a match in the dimensional pedestal parameters and edge-localized mode (ELM) frequency despite a good match in the main dimensionless plasma parameters. This paper describes the progress made in understanding these experimental results. First, it is investigated whether differences in the magnetohydrodynamic stability of the pedestal, including those potentially arising from the 10% difference in the aspect ratio between the two tokamaks, can explain the results. The potential effects of differences in plasma rotation between the two machines are also examined. Given the result that these mechanisms fail to explain the experimental observations and the fact that JT-60U features considerably stronger toroidal magnetic field ripple than JET, the bulk of the paper, however, discusses the effects of ripple losses. The analysis shows that ripple losses of thermal ions can affect H-mode plasma performance very sensitively. Orbit-following simulations indicate that losses due to diffusive transport give rise to a wide radial distribution of enhanced ion thermal transport, whereas non-diffusive losses have a very edge-localized distribution. In predictive transport simulations with an energy sink term in the continuity equation for the ion pressure representing non-diffusive losses, reduced performance as well as an increase in the ELM
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| 13. |
- Nagao-Kitamoto, H., et al.
(författare)
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Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota
- 2020
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26, s. 608-617
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Tidskriftsartikel (refereegranskat)abstract
- In germ-free mice colonized with human microbiota, mucosal IL-22 signaling promotes the growth of succinate-consuming commensal bacteria via host mucus glycosylation, and transplantation of these bacteria limits Clostridioides difficile infection. The involvement of host immunity in the gut microbiota-mediated colonization resistance to Clostridioides difficile infection (CDI) is incompletely understood. Here, we show that interleukin (IL)-22, induced by colonization of the gut microbiota, is crucial for the prevention of CDI in human microbiota-associated (HMA) mice. IL-22 signaling in HMA mice regulated host glycosylation, which enabled the growth of succinate-consuming bacteria Phascolarctobacterium spp. within the gut microbiome. Phascolarctobacterium reduced the availability of luminal succinate, a crucial metabolite for the growth of C. difficile, and therefore prevented the growth of C. difficile. IL-22-mediated host N-glycosylation is likely impaired in patients with ulcerative colitis (UC) and renders UC-HMA mice more susceptible to CDI. Transplantation of healthy human-derived microbiota or Phascolarctobacterium reduced luminal succinate levels and restored colonization resistance in UC-HMA mice. IL-22-mediated host glycosylation thus fosters the growth of commensal bacteria that compete with C. difficile for the nutritional niche.
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| 15. |
- Sips, A. C. C., et al.
(författare)
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An international database for the study of the formation of ITBs in tokamaks
- 2002
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Ingår i: Plasma Physics and Controlled Fusion. - 0741-3335 .- 1361-6587. ; 44, s. A391-A398
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Tidskriftsartikel (refereegranskat)abstract
- For the first time, data from eight,different tokamaks have been combined in an international database for internal transport barriers (ITBs). An analysis of the data for the formation of an ITB with dominant ion heating shows a clear dependence of the threshold power on the minor radius and line-averaged electron density for the formation of ion ITBs. The dependence of ITB formation on the toroidal magnetic field is weak. For the formation of ITBs with dominant electron heating, the database is smaller, but for the threshold power a strong increase with plasma size and a weak toroidal field dependence could also be identified. Based on these results, an expression for the power required to form an ITB is given using global variables only. These results give a basis for the analysis of the database using local values (like magnetic shear) and a detailed comparison with theory-based models.
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| 16. |
- Stajich, Jason E., et al.
(författare)
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Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
- 2010
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 107:26, s. 11889-11894
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Tidskriftsartikel (refereegranskat)abstract
- The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
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| 17. |
- Villforth, C., et al.
(författare)
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Variability and stability in blazar jets on time-scales of years : optical polarization monitoring of OJ 287 in 2005-2009
- 2010
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 402:3, s. 2087-2111
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Tidskriftsartikel (refereegranskat)abstract
- OJ 287 is a BL Lac object at redshift z = 0.306 that has shown double-peaked bursts at regular intervals of similar to 12 yr during the last similar to 40 yr. We analyse optical photopolarimetric monitoring data from 2005 to 2009, during which the latest double-peaked outburst occurred. The aim of this study is twofold: firstly, we aim to analyse variability patterns and statistical properties of the optical polarization light curve. We find a strong preferred position angle in optical polarization. The preferred position angle can be explained by separating the jet emission into two components: an optical polarization core and chaotic jet emission. The optical polarization core is stable on time-scales of years and can be explained as emission from an underlying quiescent jet component. The chaotic jet emission sometimes exhibits a circular movement in the Stokes plane. We find six such events, all on the time-scales of 10-20 d. We interpret these events as a shock front moving forwards and backwards in the jet, swiping through a helical magnetic field. Secondly, we use our data to assess different binary black hole models proposed to explain the regularly appearing double-peaked bursts in OJ 287. We compose a list of requirements a model has to fulfil to explain the mysterious behaviour observed in OJ 287. The list includes not only characteristics of the light curve but also other properties of OJ 287, such as the black hole mass and restrictions on accretion flow properties. We rate all existing models using this list and conclude that none of the models is able to explain all observations. We discuss possible new explanations and propose a new approach to understanding OJ 287. We suggest that both the double-peaked bursts and the evolution of the optical polarization position angle could be explained as a sign of resonant accretion of magnetic field lines, a 'magnetic breathing' of the disc.
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