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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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| 3. |
- Singh, Vijay Kumar, et al.
(författare)
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Novel Genetic Algorithm (GA) based hybrid machine learning-pedotransfer Function (ML-PTF) for prediction of spatial pattern of saturated hydraulic conductivity
- 2022
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Ingår i: Engineering Applications of Computational Fluid Mechanics. - : Taylor & Francis. - 1994-2060 .- 1997-003X. ; 16:1, s. 1082-1099
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Tidskriftsartikel (refereegranskat)abstract
- Saturated hydraulic conductivity (Ks) is an important soil characteristic that controls water moves through the soil. On the other hand, its measurement is difficult, time-consuming, and expensive; hence Pedotransfer Functions (PTFs) are commonly used for its estimation. Despite significant development over the years, the PTFs showed poor performance in predicting Ks. Using Genetic Algorithm (GA), two hybrid Machine Learning based PTFs (ML-PTF), i.e. a combination of GA with Multilayer Perceptron (MLP-GA) and Support Vector Machine (SVM-GA), were proposed in this study. We compared the performances of four machine learning algorithms for different sets of predictors. The predictor combination containing sand, clay, Field Capacity, and Wilting Point showed the highest accuracy for all the ML-PTFs. Among the ML-PTFs, the SVM-GA algorithm outperformed the rest of the PTFs. It was noticed that the SVM-GA PTF demonstrated higher efficiency than the MLP-GA algorithm. The reference model for hydraulic conductivity prediction was selected as the SVM-GA PTF paired with the K-5 predictor variables. The proposed PTFs were compared with 160 models from past literature. It was found that the algorithms advocated were an improvement over these PTFs. The current model would help in efficient spatio-temporal measurement of hydraulic conductivity using pre-available databases.
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