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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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| 5. |
- Bregu, Endri, et al.
(författare)
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Reactive control of autonomous drones
- 2016
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Ingår i: MobiSys 2016 - Proceedings of the 14th Annual International Conference on Mobile Systems, Applications, and Services. - New York, NY, USA : Association for Computing Machinery, Inc. - 9781450342698 ; , s. 207-219
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Konferensbidrag (refereegranskat)abstract
- Aerial drones, ground robots, and aquatic rovers enable mobile applications that no other technology can realize with comparable flexibility and costs. In existing platforms, the low-level control enabling a drone's autonomous movement is currently realized in a time-triggered fashion, which simplifies implementations. In contrast, we conceive a notion of reactive control that supersedes the time-triggered approach by leveraging the characteristics of existing control logic and of the hardware it runs on. Using reactive control, control decisions are taken only upon recognizing the need to, based on observed changes in the navigation sensors. As a result, the rate of execution dynamically adapts to the circumstances. Compared to time-triggered control, this allows us to: i) attain more timely control decisions, ii) improve hardware utilization, iii) lessen the need to overprovision control rates. Based on 260+ hours of real-world experiments using three aerial drones, three different control logic, and three hardware platforms, we demonstrate, for example, up to 41% improvements in control accuracy and up to 22% improvements in flight time.
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| 7. |
- Kamnitsas, Konstantinos, et al.
(författare)
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Transductive Image Segmentation : Self-training and Effect of Uncertainty Estimation
- 2021
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Ingår i: Domain Adaptation and Representation Transfer, and Affordable Healthcare and AI for Resource Diverse Global Health - 3rd MICCAI Workshop, DART 2021, and 1st MICCAI Workshop, FAIR 2021, Held in Conjunction with MICCAI 2021, Proceedings. - Cham : Springer International Publishing. - 1611-3349 .- 0302-9743. - 9783030877217 ; 12968 LNCS, s. 79-89
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Konferensbidrag (refereegranskat)abstract
- Semi-supervised learning (SSL) uses unlabeled data during training to learn better models. Previous studies on SSL for medical image segmentation focused mostly on improving model generalization to unseen data. In some applications, however, our primary interest is not generalization but to obtain optimal predictions on a specific unlabeled database that is fully available during model development. Examples include population studies for extracting imaging phenotypes. This work investigates an often overlooked aspect of SSL, transduction. It focuses on the quality of predictions made on the unlabeled data of interest when they are included for optimization during training, rather than improving generalization. We focus on the self-training framework and explore its potential for transduction. We analyze it through the lens of Information Gain and reveal that learning benefits from the use of calibrated or under-confident models. Our extensive experiments on a large MRI database for multi-class segmentation of traumatic brain lesions shows promising results when comparing transductive with inductive predictions. We believe this study will inspire further research on transductive learning, a well-suited paradigm for medical image analysis.
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| 8. |
- Morrison, Kathleen D., et al.
(författare)
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Mapping past human land use using archaeological data : A new classification for global land use synthesis and data harmonization
- 2021
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 16:4
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Tidskriftsartikel (refereegranskat)abstract
- In the 12,000 years preceding the Industrial Revolution, human activities led to significant changes in land cover, plant and animal distributions, surface hydrology, and biochemical cycles. Earth system models suggest that this anthropogenic land cover change influenced regional and global climate. However, the representation of past land use in earth system models is currently oversimplified. As a result, there are large uncertainties in the current understanding of the past and current state of the earth system. In order to improve representation of the variety and scale of impacts that past land use had on the earth system, a global effort is underway to aggregate and synthesize archaeological and historical evidence of land use systems. Here we present a simple, hierarchical classification of land use systems designed to be used with archaeological and historical data at a global scale and a schema of codes that identify land use practices common to a range of systems, both implemented in a geospatial database. The classification scheme and database resulted from an extensive process of consultation with researchers worldwide. Our scheme is designed to deliver consistent, empirically robust data for the improvement of land use models, while simultaneously allowing for a comparative, detailed mapping of land use relevant to the needs of historical scholars. To illustrate the benefits of the classification scheme and methods for mapping historical land use, we apply it to Mesopotamia and Arabia at 6 kya (c. 4000 BCE). The scheme will be used to describe land use by the Past Global Changes (PAGES) LandCover6k working group, an international project comprised of archaeologists, historians, geographers, paleoecologists, and modelers. Beyond this, the scheme has a wide utility for creating a common language between research and policy communities, linking archaeologists with climate modelers, biodiversity conservation workers and initiatives.
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| 9. |
- Muschitiello, Francesco, et al.
(författare)
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Fennoscandian freshwater control on Greenland hydroclimate shifts at the onset of the Younger Dryas
- 2015
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Sources and timing of freshwater forcing relative to hydroclimate shifts recorded in Greenland ice cores at the onset of Younger Dryas, similar to 12,800 years ago, remain speculative. Here we show that progressive Fennoscandian Ice Sheet (FIS) melting 13,100-12,880 years ago generates a hydroclimate dipole with drier-colder conditions in Northern Europe and wetter-warmer conditions in Greenland. FIS melting culminates 12,880 years ago synchronously with the start of Greenland Stadial 1 and a large-scale hydroclimate transition lasting similar to 180 years. Transient climate model simulations forced with FIS freshwater reproduce the initial hydroclimate dipole through sea-ice feedbacks in the Nordic Seas. The transition is attributed to the export of excess sea ice to the subpolar North Atlantic and a subsequent southward shift of the westerly winds. We suggest that North Atlantic hydroclimate sensitivity to FIS freshwater can explain the pace and sign of shifts recorded in Greenland at the climate transition into the Younger Dryas.
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| 10. |
- Qu, Yuangao, et al.
(författare)
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Carbonaceous biosignatures of diverse chemotrophic microbial communities from chert nodules of the Ediacaran Doushantuo Formation
- 2017
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Ingår i: Precambrian Research. - : Elsevier BV. - 0301-9268 .- 1872-7433. ; 290, s. 184-196
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Tidskriftsartikel (refereegranskat)abstract
- The Ediacaran Doushantuo Formation (DST) is renowned for exceptionally preserved Precambrian fossils including metazoans. Some of these fossils, particularly microfossils such as multicellular algae and acanthomorphic acritarchs, are preserved in DST chert nodules. To better understand the geomicrobiological processes that contributed to the authigenic formation of DST chert nodules and facilitated exceptional fossil preservation, we analyzed organic matter in these chert nodules and the surrounding matrix (calcareous mudstone) using multiple in-situ techniques: confocal laser Raman spectroscopy, micro-Fourier transform infrared spectroscopy (FTIR), and secondary ion mass spectroscopy (SIMS). We found strong ultrastructural, chemical, and isotopic heterogeneities in the organic matter as indicated by the Raman spectral parameter I-1350/1600 ranging from 0.49 to 0.88, the infrared spectral index R3/2 from 0.12 to 0.90, and an estimated δ13Corg-SIMS range of 44‰ (V-PDB). These micron-scale heterogeneities imply that the organic matter preserved in the DST chert nodules is derived from different carbonaceous sources in a diverse microbial ecosystem, including eukaryotic and/or prokaryotic photoautotrophs, as well as chemotrophs involved in the fermentation and probably anaerobic oxidation of organic remains. Thus, the microbial ecosystems in Ediacaran ocean waters and sediments were more complex than previously thought, and these microbial processes controlled dynamic micro-environments in DST sediments where chert nodules were formed and fossils were mineralized. The results also show that variations in the relative abundances, activities, and interactions of co-existing microorganisms in DST sediments may have modulated δ13Corg shifts, causing local decoupling between δ13Corg and δ13Ccarb as measured in bulk samples.
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