| 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. |
- de Jong, Yde, et al.
(författare)
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PESI - a taxonomic backbone for Europe
- 2015
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Ingår i: Biodiversity Data Journal. - 1314-2836 .- 1314-2828. ; 3, s. 1-51
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Tidskriftsartikel (refereegranskat)abstract
- Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.
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| 3. |
- Hussey, Daniel K, et al.
(författare)
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Scoring the Current Risk Stratification Guidelines in Follow-up Evaluation of Patients After Metal-on-Metal Hip Arthroplasty: A Proposal for a Metal-on-Metal Risk Score Supporting Clinical Decision-Making.
- 2016
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Ingår i: The Journal of bone and joint surgery. American volume. - 1535-1386. ; 98:22, s. 1905-1912
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Tidskriftsartikel (refereegranskat)abstract
- In the follow-up evaluation of patients with metal-on-metal (MoM) hip replacements, current evidence suggests that orthopaedic surgeons should avoid reliance on any single investigative tool. Current risk stratification guidelines can be difficult to interpret because they do not provide guidance when there are several risk factors in different groups (high and low risk). To improve the clinical utility of risk stratification guidelines, we designed a scoring system to assess the risk of revision.The study population consisted of 1,709 patients (1,912 hips) enrolled in a multicenter follow-up study of a recalled MoM hip replacement. Eleven scoring criteria were determined on the basis of existing follow-up algorithm recommendations and consisted of patient-related factors, symptoms, clinical status, implant type, metal ion levels, and radiographic imaging results. Forward stepwise logistic regression was conducted to determine the minimum set of predictive variables for the risk of revision and to assign variable weights. The MoM risk score for each hip was then created by averaging the weighted values of each predictive variable.Receiver operating characteristic curve analysis yielded good discrimination between all revised and unrevised hips, with an area under the curve of 0.82 (p < 0.001). The odds of revision for the group with a high MoM risk score were increased by 5.8-fold (95% confidence interval [CI], 3.1 to 11.0) relative to the moderate risk group and by 21.8-fold (95% CI, 9.9 to 48.0) compared with the low risk group.Although the use of MoM hip arthroplasty has been limited since 2010, we continue to be faced with the follow-up and risk assessment of thousands of patients who have not had a revision. As more knowledge about risk stratification is gained, the complexity of the algorithms is expected to increase. We propose the use of the MoM risk score as a tool to aid in the clinical decision-making process.Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
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