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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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- Campanella, A., et al.
(författare)
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Additional booster doses in patients with chronic lymphocytic leukemia induce humoral and cellular immune responses to SARS-CoV-2 similar to natural infection regardless ongoing treatments : A study by ERIC, the European Research Initiative on CLL
- 2024
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Ingår i: American Journal of Hematology. - : John Wiley & Sons. - 0361-8609 .- 1096-8652. ; 99:4, s. 745-750
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Profound immune dysregulation and impaired response to the SARS-CoV-2 vaccine put patients with chronic lymphocytic leukemia (CLL) at risk of severe COVID-19. We compared humoral memory and T-cell responses after booster dose vaccination or breakthrough infection. (Green) Quantitative determination of anti-Spike specific antibodies. Booster doses increased seroconversion rate and antibody titers in all patient categories, ultimately generating humoral responses similar to those observed in the postinfection cohort. In detail, humoral response with overscale median antibody titers arose in >80% of patients in watch and wait, off-therapy in remission, or under treatment with venetoclax single-agent. Anti-CD20 antibodies and active treatment with BTK inhibitors (BTKi) represent limiting factors of humoral response, still memory mounted in ~40% of cases following booster doses or infection. (Blue) Evaluation of SARS-CoV-2-specific T-cell responses. Number of T-cell functional activation markers documented in each patient. The vast majority of patients, including those seronegative, developed T-cell responses, qualitatively similar between treatment groups or between vaccination alone and infection cases. These data highlight the efficacy of booster doses in eliciting T-cell immunity independently of treatment status and support the use of additional vaccination boosters to stimulate humoral immunity in patients on active CLL-directed treatments.
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- Pinsky, L., et al.
(författare)
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Measurement of Fragmentation Products including Angular Distributions for 3, 5, and 10 GeV/A C and Si on several nuclear targets at the AGS
- 2010
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Ingår i: 2009 12th International Conference on Nuclear Reaction Mechanisms, NRM 2009; Varenna; Italy; 15 June 2009 through 19 June 2009. - 2078-8835. - 9789290833413 ; 2, s. 431-437
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Konferensbidrag (refereegranskat)abstract
- Motivated by differences in the predicted fragmentation of heavy ions at energies around 5 GeV/A as employed in the event generators used by the FLUKA Monte Carlo Code [1], a set of measurements were carried out at the AGS facility at the Brookhaven National Laboratory to determine as much information as possible about the cross sections to allow harmonization of those event generators for these incident lab energies. The FLUKA Code employs the RQMD event generator of Sorge [2] for heavy ion interactions starting at 100 MeV/A and extending into the region around 5 GeV/A. Above those energies the DPMJET code of Ranft and Roesler [3] is typically employed to simulate such interactions. The detailed predictions of these event generators had some disagreement in the vicinity of this crossover energy and in order to tune these codes to be in closer harmony at the transition, and of course to be simulating nature as closely as possible, data were taken at 3, 5 and 10 GeV/A with beams of Fe, Si and C on a variety of targets including C, A1. Fe and Cu. The Fe data have not been fully analyzed, but results from the C and Si beams are available and the forward fragment spectrum along with a measurement of the charged particle angular distribution in a set of Si strip detectors out to about 45 degrees in the lab are available. These include sufficient statistics to provide the charged particle distributions as a function of the major projectile fragment. The detectors used in this measurement were based on what were reasonably available to us, and as such were limited in capability, and required separate data acquisition systems. Nevertheless, spectra were obtained that should be sufficient to enable the harmonization of the event generator codes at the crossover energy. This paper discusses only the experimental results and not the impact of those results on the FLUKA code.
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- Battistoni, G, et al.
(författare)
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FLUKA Monte Carlo calculations for hadrontherapy application
- 2013
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Ingår i: CERN-Proceedings-2012-002. ; , s. 461-467
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Konferensbidrag (refereegranskat)abstract
- Monte Carlo (MC) codes are increasingly spreading in the hadrontherapy community due to their detailed description of radiation transport and interaction with matter. The suitability of a MC code for application to hadrontherapy demands accurate and reliable physical models for the description of the transport and the interaction of all components of the expected radiation field (ions, hadrons, electrons, positrons and photons). This contribution will address the specific case of the general-purpose particle and interaction code FLUKA. In this work, an application of FLUKA will be presented, i.e. establishing CT (computed tomography)-based calculations of physical and RBE (relative biological effectiveness)-weighted dose distributions in scanned carbon ion beam therapy.
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