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| 2. |
- 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. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 5. |
- Hong, Sanghee, et al.
(författare)
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Community health status and outcomes after allogeneic hematopoietic cell transplantation in the United States
- 2021
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Ingår i: Cancer. - : John Wiley & Sons. - 0008-543X .- 1097-0142. ; 127:4, s. 609-618
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Tidskriftsartikel (refereegranskat)abstract
- Background: The association of community factors and outcomes after hematopoietic cell transplantation (HCT) has not been comprehensively described. Using the County Health Rankings and Roadmaps (CHRR) and the Center for International Blood and Marrow Transplant Research (CIBMTR), this study evaluated the impact of community health status on allogeneic HCT outcomes.Methods: This study included 18,544 adult allogeneic HCT recipients reported to the CIBMTR by 170 US centers in 2014-2016. Sociodemographic, environmental, and community indicators were derived from the CHRR, an aggregate community risk score was created, and scores were assigned to each patient (patient community risk score [PCS]) and transplant center (center community risk score [CCS]). Higher scores indicated less healthy communities. The impact of PCS and CCS on patient outcomes after allogeneic HCT was studied.Results: The median age was 55 years (range, 18-83 years). The median PCS was -0.21 (range, -1.37 to 2.10; standard deviation [SD], 0.42), and the median CCS was -0.13 (range, -1.04 to 0.96; SD, 0.40). In multivariable analyses, a higher PCS was associated with inferior survival (hazard ratio [HR] per 1 SD increase, 1.04; 99% CI, 1.00-1.08;P= .0089). Among hematologic malignancies, a tendency toward inferior survival was observed with a higher PCS (HR, 1.04; 99% CI, 1.00-1.08;P= .0102); a higher PCS was associated with higher nonrelapse mortality (NRM; HR, 1.08; 99% CI, 1.02-1.15;P= .0004). CCS was not significantly associated with survival, relapse, or NRM.Conclusions: Patients residing in counties with a worse community health status have inferior survival as a result of an increased risk of NRM after allogeneic HCT. There was no association between the community health status of the transplant center location and allogeneic HCT outcomes.
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| 6. |
- Kirkpatrick, Christine L., et al.
(författare)
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The "PepSAVI-MS" Pipeline for Natural Product Bioactive Peptide Discovery
- 2017
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 89:2, s. 1194-1201
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Tidskriftsartikel (refereegranskat)abstract
- The recent increase in extensively drug-resistant bacterial pathogens and the associated increase of morbidity and mortality demonstrate the immediate need for new antibiotic backbones with novel mechanisms of action. Here, we report the development of the PepSAVI-MS pipeline for bioactive peptide discovery. This highly versatile platform employs mass spectrometry and statistics to identify bioactive peptide targets from complex biological samples. We validate the use of this platform through the successful identification of known bioactive peptides from a botanical species, Viola odorata. Using this pipeline, we have widened the known antimicrobial spectrum for V. odorata cyclotides, including antibacterial activity of cycloviolacin O2 against A. baumannii. We further demonstrate the broad applicability of the platform through the identification of novel anticancer activities for cycloviolacins by their cytotoxicity against ovarian, breast, and prostate cancer cell lines.
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| 7. |
- Pascal, Mathilde M.V., et al.
(författare)
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DOLORisk : Study protocol for a multi-centre observational study to understand the risk factors and determinants of neuropathic pain [version 2; referees: 2 approved]
- 2019
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Ingår i: Wellcome Open Research. - : F1000 Research Ltd. - 2398-502X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Neuropathic pain is an increasingly prevalent condition and has a major impact on health and quality of life. However, the risk factors for the development and maintenance of neuropathic pain are poorly understood. Clinical, genetic and psychosocial factors all contribute to chronic pain, but their interactions have not been studied in large cohorts. The DOLORisk study aims to study these factors. Protocol: Multicentre cross-sectional and longitudinal cohorts covering the main causes leading to neuropathic pain (e.g. diabetes, surgery, chemotherapy, traumatic injury), as well as rare conditions, follow a common protocol for phenotyping of the participants. This core protocol correlates answers given by the participants on a set of questionnaires with the results of protocol for phenotyping of the participants. This core protocol correlates answers given by the participants on a set of questionnaires with the results of their genetic analyses. A smaller number of participants undergo deeper phenotyping procedures, including neurological examination, nerve conduction studies, threshold tracking, quantitative sensory testing, conditioned pain modulation and electroencephalography. Ethics and dissemination: All studies have been approved by their regional ethics committees as required by national law. Results are disseminated through the DOLORisk website, scientific meetings, open-access publications, and in partnership with patient organisations. Strengths and limitations: • Large cohorts covering many possible triggers for neuropathic pain • Multi-disciplinary approach to study the interaction of clinical, psychosocial and genetic risk factors • High comparability of the data across centres thanks to harmonised protocols • One limitation is that the length of the questionnaires might reduce the response rate and quality of responses of participants.
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| 8. |
- Testor, Pierre, et al.
(författare)
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OceanGliders: A component of the integrated GOOS
- 2019
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
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Forskningsöversikt (refereegranskat)abstract
- The OceanGliders program started in 2016 to support active coordination and enhancement of global glider activity. OceanGliders contributes to the international efforts of the Global Ocean Observation System (GOOS) for Climate, Ocean Health and Operational Services. It brings together marine scientists and engineers operating gliders around the world: (1) to observe the long-term physical, biogeochemical, and biological ocean processes and phenomena that are relevant for societal applications; and, (2) to contribute to the GOOS through real-time and delayed mode data dissemination. The OceanGliders program is distributed across national and regional observing systems and significantly contributes to integrated, multi-scale and multi-platform sampling strategies. OceanGliders shares best practices, requirements, and scientific knowledge needed for glider operations, data collection and analysis. It also monitors global glider activity and supports the dissemination of glider data through regional and global databases, in real-time and delayed modes, facilitating data access to the wider community. OceanGliders currently supports national, regional and global initiatives to maintian and expand the capabilities and application of gliders to meet key global challenges such as improved measurement of ocean boundary currents, water transformation and storm forecast.
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| 9. |
- Chung, Steve, et al.
(författare)
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Examining the clinical utility of lacosamide: pooled analyses of three phase II/III clinical trials.
- 2010
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Ingår i: CNS drugs. - : Springer Science and Business Media LLC. - 1172-7047. ; 24:12, s. 1041-54
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Tidskriftsartikel (refereegranskat)abstract
- Lacosamide is an antiepileptic drug (AED) approved for the adjunctive treatment of partial-onset seizures in adults. Completed phase II/III clinical trials of lacosamide provide a valuable opportunity to evaluate clinically relevant aspects of the resulting large patient pool.
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| 10. |
- Frisk, Henrik, 1969-, et al.
(författare)
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Intersubjective knowledge through artistic research : approaches to transcultural dialogue through stimulated recall
- 2020
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Konferensbidrag (refereegranskat)abstract
- In this panel discussion we address the theme of “Working together” in relation to the following question: How can intersubjective understanding and new knowledge be drawn from artistic collaboration? The presentation explores the method of stimulated recall, such as it has been used and developed within the work of the Vietnamese/Swedish group The Six Tones.The group was created in 2006 and in 2009, the group took part in their first artistic research project, (re)thinking Improvisation. As part of their work in the project, the group studied their interactions through stimulated recall, using video documentation of rehearsals and performances as a source. The material recorded in 2009 has been coded and re-coded in several periods across the years, and most recently in 2019, when creating a new analysis of the working process for a chapter in Stefan Östersjö’s book Listening To The Other (2020).The structure of the panel is based on sharing materials from earlier work of the group, in the form of video clips and parts of analysis produced. We provide a background to qualitative analysis of video through stimulated recall in music research, but the panel first and foremost aims to create a dialogue with the participants in the conference on these perspectives on knowledge and methods in artistic research. Video clips from previous analysis and earlier coding and annotations, as well as more extended analytical approaches will be presented, also by the participants in the panel again viewing some of these source videos and reflecting on them, thereby enacting a stimulated recall session. How can the collaborative methods that we developed through (re)thinking Improvisation be understood, in terms of the broader context of music scholarship, as innovative forms of knowledge development? Since the time of Pythagoras and Plato, scholars have theorized ways that the communicative nature of musical sound might best be explained. Even since Medieval times, empirical studies of music, such as those documented by Al Farabi in Kitab al-Musiqa al-Kabir (The Great Book of Music), were deemed sufficiently important to constitute a distinct field, ultimately known as musicology, resulting in a division of music studies into musica practica and musica theoretica with its bifurcation of performers and theorists. From the late 19th century, many empirical researchers emphasized behavioral approaches, with a focus on documentation of the array of precise measurable actions connected to musical activity. Such approaches have produced many important insights, yet do not take into account the perceptions and experiences of performers. Other kinds of researchers, such as ethnographers and phenomenologists, made extensive use of interviews, sometimes in combination with observations. Interviews lead to insights of a different kind, but are notoriously unreliable for an array of reasons, including personal biases and tainted interpretations, self-censorship, memory issues, and researcher effects. The historical division of musica practica and musica theoretica started to be directly challenged in the mid-20th century with the rise of the “bimusicality” movement among ethnomusicologists, and – a few decades later later—the “artistic research” movement among academic artists of all kinds, as artistic and academic projects were increasingly intertwined, resulting in new perspectives regarding what counts as musical knowledge. It is within the context of artistic research and ethnomusicology that our project has introduced applications of a method known as video stimulated recall. Stimulated recall first began entering musical study as a method that was pioneered in the field of psychology. By presenting participants with video-recorded actions to reflect upon, stimulated recall as a method seeks to improve the richness and precision of interviews, so their capacity to produce deep insights is greatly enhanced by reference to automatically recorded behaviors. Depending on how it is defined, “stimulated recall” may be understood as associated with the use of images in therapy sessions as part of psychological research as early as the 1950s. However, in music research stimulated recall is typically understood today as a strategy that employs the use of audio or audiovisual recordings as a basis from which to stimulate precise discussion of musical techniques.How exactly have previous music-related studies made new insights by pioneering the application of video stimulated recall strategies, and what has our project done to extend further with methodological innovation? As recent as 2009, a study in the international journal Music Education Research was able to identify previous studies in education that used stimulated recall method, but not any in music (Rowe, 2009). However, across the past decade various music studies have made use of video stimulated recall methods, including from the very year that Rowe’s study was published (Heikinheimo, 2009), a significant proportion of which are from the Nordic countries (e.g. Falthin, 2015; Heikinheimo, 2009; Soderman & Folkestad, 2004, etc.). Moreover, while the term “video stimulated recall” was not explicitly used at the time, some innovative studies of musical interaction in jazz from the perspective of communication theory were developed as early as the late 1980s by Bastien & Hostager (1988, 1992, 1996) that might best be understood as pioneering the use of stimulated recall methods in music. In these studies, jazz musicians were videotaped in the course of improvised performance and later asked to explain the processes observed. More recently, notable studies have included doctoral dissertations in Europe (Falthin, 2015) on meaning-making processes among young music students, and in North America (Bell, 2013) on interaction with technologies in the music recording process. Articles using this method in major journals have examined such topics as the views of expressive performance among young music students (Meissner, Timmers & Pitts, 2020) and how music teachers and students view the role of creativity in music performance (James, Wise, & Rink, 2010). There have thus far been relatively few stimulated recall studies of advanced musicians and situations in which musicians are negotiating between different musical traditions across a cultural divide, yet stimulated recall methods promise insights in these areas as well. Our work may be among the first to use stimulated recall methods to examine intercultural music making, although not the first to use these strategies for study of other aspects of music making nor intercultural issues. In fact, there are previous examples of this method being used for cross-cultural research in Vietnam, although not in the field of music (Nguyen & Tangen, 2017). Rather, what makes the approach used in our study unique is that the robust capabilities of stimulated recall strategies are used to explicate complex experiences and processes are brought to bear on aesthetic decision making associated in both traditional and experimental musicianship in the context of an intercultural project. In such a way, the work of the Six Tones in this project has extended significantly on previous methods and research findings. Our initial motivation for developing the methods for analysis of our artistic practice was the challenge we faced as a group of musicians involved in intercultural collaboration. In The Six Tones, musicians from traditional Vietnamese music would engage with musicians from the west, negotiating musical practices as the practice is unfolding. At the early stages of this process the language barrier highlighted the different perspectives and the need to make these perspectives a central aspect of the artistic process. At the bottom line, the challenge we experienced was rooted in how our listening, as professional musicians, is socio-culturally situated, and therefore biased. An extra effort is therefore necessary to move beyond stereotypical interaction, and the aim of the method we developed was to accommodate new forms of listening that engender more dynamic artistic exchange. As developed for artistic research purposes by the group, it would be a mistake to see the method of stimulated recall as primarily aiming for the production of discursive analytical layers, i.e. the coding and annotations. In the practice of The Six Tones, it is instead the ways in which the shared listening, enhanced through the method, has created a new listening practice within the group: a transformed listening. The process of verbalizing and signifying the experience of repeated listening is an important part of the process, but not the final goal. Rather, it is this transformed listening, and the ability to establish modes of interaction with musical Others beyond cultural prejudice, which has been the central ambition. The panel discusses how such a listening practice emerged within the group, but also gives examples of how such forms of listening has subsequently been shared with other musicians in intercultural collaboration. Our reference is the work carried out in the ongoing research project Musical Transformations, involving master performers in a tradition in the south of Vietnam, and how they describe experiences of transformed listening, through the process of intercultural music making, and the use of stimulated recall. We understand a musician’s listening as embodied, and therefore situated in the interaction with their instruments, and other musical tools, such as tonal systems and forms of notation. A transformed performance practice can be seen as evidence of a transformed listening. We also argue that novel modes of listening can be evidenced in the interaction between musicians in performance. When artistic research is manifested in performance, its outcomes must also be assessed through its force and effec
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