| 1. |
- Kanai, M, et al.
(author)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(author)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
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| 5. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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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| 6. |
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| 7. |
- Hudson, T., et al.
(author)
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Managing collaboration in the nanoManipulator
- 2004
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In: Presence. ; 13:2
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Journal article (peer-reviewed)abstract
- We designed, developed, deployed, and evaluated the Collaborative nanoManipulator (CnM), a system supporting remote collaboration between users of the nanoManipulator interface to atomic force microscopes. To be accepted by users, the shared nanoManipulator application had to have the same high level of interactivity as the single user system and the application had to support a user’s ability to interleave working privately and working collaboratively. This paper briefly describes the entire collaboration system, but focuses on the shared nanoManipulator application. Based on our experience developing the CnM, we present: a method of analyzing applications to characterize the requirements for sharing data between collaborating sites, examples of data structures that support collaboration, and guidelines for selecting appropriate synchronization and concurrency control schemes.
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| 8. |
- Sonnenwald, Diane H., et al.
(author)
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Designing to support situational awareness across distances : An example from a scientific collaboratory
- 2004
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In: Information Processing & Management. ; 40:6, s. 989-
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Journal article (peer-reviewed)abstract
- When collaborating individuals rely on situation awareness (the gathering, incorporation and utilization of environmental information) to help them combine their unique knowledge and skills and achieve their goals. When collaborating across distances, situation awareness is mediated by technology. There are few guidelines to help system analysts design systems or applications that support the creation and maintenance of situation awareness for teams or groups. We propose a framework to guide design decisions to enhance computer-mediated situation awareness during scientific research collaboration. The foundation for this framework is previous research in situation awareness and virtual reality, combined with our analysis of interviews and observations of collaborating scientists. The framework suggests that situation awareness is comprised of contextual, task and process, and socio-emotional information. Research in virtual reality systems suggests control, sensory, distraction and realism attributes of technology contribute to a sense of presence (Witmer & Singer, 1998). We suggest that consideration of these attributes with respect to contextual, task and process, and socio-emotional information provides insights to guide design decisions. We used the framework when designing a scientific collaboratory system. Results from a controlled experimental evaluation of the collaboratory system help illustrate the framework's utility.
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| 9. |
- Sonnenwald, Diane H., et al.
(author)
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Evaluating a scientific collaboratory : Results of a controlled experiment
- 2003
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In: ACM Transactions on Human Computer Interaction. ; 10:2, s. 150-
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Journal article (peer-reviewed)abstract
- The evaluation of scientific collaboratories has lagged behind their development. Do the capabilities afforded by collaboratories outweigh their disadvantages? To evaluate a scientific collaboratory system, we conducted a repeated-measures controlled experiment that compared the outcomes and process of scientific work completed by 20 pairs of participants (upper level undergraduate science students) working face-to-face and remotely. We collected scientific outcomes (graded lab reports) to investigate the quality of scientific work, post-questionnaire data to measure the adoptability of the system, and post-interviews to understand the participants' views of doing science under both conditions. We hypothesized that study participants would be less effective, report more difficulty, and be less favorably inclined to adopt the system when collaborating remotely. Contrary to expectations, the quantitative data showed no statistically significant differences with respect to effectiveness and adoption. The qualitative data helped explain this null result: participants reported advantages and disadvantages working under both conditions and developed work-arounds to cope with the perceived disadvantages of collaborating remotely. While the data analysis produced null results, considered as a whole, the analysis leads us to conclude there is positive potential for the development and adoption of scientific collaboratory systems.
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| 10. |
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