| 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. |
- Ebersole, Charles R., et al.
(författare)
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Many Labs 5: Testing Pre-Data-Collection Peer Review as an Intervention to Increase Replicability
- 2020
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Ingår i: Advances in Methods and Practices in Psychological Science. - : Sage. - 2515-2467 .- 2515-2459. ; 3:3, s. 309-331
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Tidskriftsartikel (refereegranskat)abstract
- Replication studies in psychological science sometimes fail to reproduce prior findings. If these studies use methods that are unfaithful to the original study or ineffective in eliciting the phenomenon of interest, then a failure to replicate may be a failure of the protocol rather than a challenge to the original finding. Formal pre-data-collection peer review by experts may address shortcomings and increase replicability rates. We selected 10 replication studies from the Reproducibility Project: Psychology (RP:P; Open Science Collaboration, 2015) for which the original authors had expressed concerns about the replication designs before data collection; only one of these studies had yielded a statistically significant effect (p < .05). Commenters suggested that lack of adherence to expert review and low-powered tests were the reasons that most of these RP:P studies failed to replicate the original effects. We revised the replication protocols and received formal peer review prior to conducting new replication studies. We administered the RP:P and revised protocols in multiple laboratories (median number of laboratories per original study = 6.5, range = 3-9; median total sample = 1,279.5, range = 276-3,512) for high-powered tests of each original finding with both protocols. Overall, following the preregistered analysis plan, we found that the revised protocols produced effect sizes similar to those of the RP:P protocols (Delta r = .002 or .014, depending on analytic approach). The median effect size for the revised protocols (r = .05) was similar to that of the RP:P protocols (r = .04) and the original RP:P replications (r = .11), and smaller than that of the original studies (r = .37). Analysis of the cumulative evidence across the original studies and the corresponding three replication attempts provided very precise estimates of the 10 tested effects and indicated that their effect sizes (median r = .07, range = .00-.15) were 78% smaller, on average, than the original effect sizes (median r = .37, range = .19-.50).
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| 3. |
- Amin, Samir, et al.
(författare)
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Der Kapitalismus ist senil geworden
- 2002
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Ingår i: Mittelweg 36. ; :4
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- Abstract in German Verliert der Kapitalismus seine Progressivität und entfaltet stattdessen zerstörerische Kräfte? Ein Gespräch mit zwei der führenden Kapitalismuskritiker über die Zukunft des kapitalistischen Systems und den unterschiedlichen Formen von Gegenentwürfen.
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| 4. |
- Amin, Samir, et al.
(författare)
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Kako je kapitalizam posenilio
- 2002
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Ingår i: Rec. ; :68/14, s. 263-270
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- Abstract in Uncoded languages Da li kapitalizam gubi svoju progresivnost i postaje destruktivan? Da li je moguce da se cak blizi svom kraju? Ovakvo razmisljanje zvuci poznato, ali se o ovim pitanjima danas razgovara mnogo vise nego ikada pre. Majkl Hart i Samir Amin, obojica medu vodecim kriticarima savremenog kapitalizma, razgovaraju o buducnosti sistema, pokretima otpora sistemu i alternativama koje ti pokreti nude.
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| 5. |
- Amin, Samir, et al.
(författare)
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Så blev kapitalismen senil
- 2002
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Ingår i: Arena. - 1652-0556. ; :2, s. 33-37
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- Arena har mött Michael Hardt och Samir Amin, två av världens mest kända systemkritiker, i ett samtal om framtiden.
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| 6. |
- Eisenacher, Martin, et al.
(författare)
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Getting a grip on proteomics data - Proteomics Data Collection (ProDaC)
- 2009
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 9:15, s. 3928-3933
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Tidskriftsartikel (refereegranskat)abstract
- In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community-wide data collection. The objectives of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data. Ending in March 2009, ProDaC has delivered a comprehensive toolbox of standards and computer programs to achieve these goals.
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| 7. |
- Eisenacher, Martin, et al.
(författare)
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Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea
- 2008
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 8:7, s. 1326-1330
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Tidskriftsartikel (refereegranskat)abstract
- Proteomics Data Collection (ProDaC) is an EU-funded Coordination Action within the 6th framework programme. It aims to simplify the publication, dissemination and utilization of proteomics data by establishing standards that will support broad data collection from the research community. As a part of ProDaC, regular workshops are organized on a half-yearly basis to enable communication and discussion of the involved partners and to report on project progress. After the kick-off meeting (October 2006) in Long Beach, CA, USA and the 1st workshop in Lyon, France (April 2007), the 2nd ProDaC workshop took place at the COEX InterContinental Hotel in Seoul, Korea, on 5th October 2007, shortly before the HUPO World Congress. The progress achieved within the first year was presented by the leaders of the work packages. Additionally, a Journal's representative talked about his experiences and future plans concerning Proteomics standards; and two further external speakers presented their research related to data handling and Proteomics repositories.
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| 8. |
- Eisenacher, Martin, et al.
(författare)
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Proteomics Data Collection - 3rd ProDaC Workshop April 22nd 2008, Toledo, Spain
- 2008
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 8:20, s. 4163-4167
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Tidskriftsartikel (refereegranskat)abstract
- The "Coordination Action" ProDaC (Proteomics Data Collection) - funded by the EU within the 6(th) framework programme - was created to support the dissemination, utilization and publication of proteomics data. Within this international consortium, standards are developed and maintained to support extensive data collection by the proteomics community. An important part of ProDaC are workshops organized on a regular basis (two per year) to allow discussions and communication between the ProDaC partners and to report on the progress of the project. The kick-off meeting took place in October 2006 in Long Beach, CA, USA. The 1(st) ProDaC workshop was held in Lyon, France (April 2007) and the 2(nd) in Seoul, Korea in October 2007. ProDaC organized the 3(rd) ProDaC workshop at the Beatriz Hotel, Toledo, on 22(nd) April, 2008, directly before the HUPO - PSI spring meeting (Human Proteome Organisation - Proteomics Standards Initiative). The work package coordinators presented talks about the progress achieved during the past six months. Additionally four external speakers presented their work on data conversion and data repositories. The concluding discussion session was chaired by the journal's representative.
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| 9. |
- Eisenacher, Martin, et al.
(författare)
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Proteomics Data Collection-5th ProDaC Workshop
- 2009
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Ingår i: Proteomics. - : Wiley. - 1615-9861 .- 1615-9853. ; 9:14, s. 3626-3629
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Tidskriftsartikel (refereegranskat)abstract
- The Proteomics Data Collection (ProDaC) consortium, a "Coordination Action" funded by the 6th EU Framework Programme, started in October 2006. Its aim was to facilitate the collection and distribution of proteomics data and the public availability of data sets from proteomics experiments. Within the consortium standard formats are created and tools are developed to allow extensive data collection within the proteomics community. An important part of ProDaC is the organization of workshops twice a year to inform about the consortium's progress and to stimulate communication between the ProDaC partners and between partners and interested members of the proteomics community. ProDaC ends on March 31, 2009. The most recent (and final) workshop was the 5th ProDaC workshop held on March 4, 2009 in Kolympari, Crete, Greece. The progress since the last meeting and an overall summary was presented by the work package coordinators and partners. Four external speakers presented talks about their work in relation to ProDaC.
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| 10. |
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| 11. |
- Hardt, Michael, et al.
(författare)
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Geopolitik och nya allianser
- 2004
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Ingår i: Fronesis. - 1404-2614. ; :16-17, s. 211-220
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Tidskriftsartikel (populärvet., debatt m.m.)
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