| 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. |
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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- Han, Ridong, et al.
(författare)
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Document-level Relation Extraction with Relation Correlations
- 2024
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Ingår i: Neural Networks. - Oxford : Elsevier. - 0893-6080 .- 1879-2782. ; 171, s. 14-24
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Tidskriftsartikel (refereegranskat)abstract
- Document-level relation extraction faces two often overlooked challenges: long-tail problem and multi-label problem. Previous work focuses mainly on obtaining better contextual representations for entity pairs, hardly address the above challenges. In this paper, we analyze the co-occurrence correlation of relations, and introduce it into the document-level relation extraction task for the first time. We argue that the correlations can not only transfer knowledge between data-rich relations and data-scarce ones to assist in the training of long-tailed relations, but also reflect semantic distance guiding the classifier to identify semantically close relations for multi-label entity pairs. Specifically, we use relation embedding as a medium, and propose two co-occurrence prediction sub-tasks from both coarse- and fine-grained perspectives to capture relation correlations. Finally, the learned correlation-aware embeddings are used to guide the extraction of relational facts. Substantial experiments on two popular datasets (i.e., DocRED and DWIE) are conducted, and our method achieves superior results compared to baselines. Insightful analysis also demonstrates the potential of relation correlations to address the above challenges. The data and code are released at https://github.com/RidongHan/DocRE-Co-Occur. © 2023 Elsevier Ltd
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| 5. |
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| 6. |
- Reimers, Jeffrey R., et al.
(författare)
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Challenges facing an understanding of the nature of low-energy excited states in photosynthesis
- 2016
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1857:9, s. 1627-1640
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Forskningsöversikt (refereegranskat)abstract
- While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
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| 7. |
- Tang, Hu, et al.
(författare)
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Boron-Rich Molybdenum Boride with Unusual Short-Range Vacancy Ordering, Anisotropic Hardness, and Superconductivity
- 2020
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Ingår i: Chemistry of Materials. - : AMER CHEMICAL SOC. - 0897-4756 .- 1520-5002. ; 32:1, s. 459-467
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Tidskriftsartikel (refereegranskat)abstract
- Determination of the structures of materials involving more light elements such as boron-rich compounds is challenging and technically important in understanding their varied compositions and superior functionalities. Here we resolve the long-standing uncertainties in structure and composition about the highest boride (termed MoB4, Mo1-xB3, or MoB3) through the rapid formation of large sized boron-rich molybdenum boride under pressure. Using high-quality single-crystal X-ray diffraction analysis and aberration-corrected scanning transmission electron microscopy, we reveal that boron-rich molybdenum boride with a composition of Mo0.757B3 exhibits P6(3)/mmc symmetry with a partial occupancy of 0.514 in 211 Mo sites (Mol), and direct observations reveal the short-range ordering of cation vacancies in (010) crystal planes. Large anisotropic Young's moduli and Vickers hardness are seen for Mo0.757B3, which may be attributed by its two-dimensional boron distributions. Mo0.757B3 is also found to be superconducting with a transition temperature (T-c) of 2.4 K, which was confirmed by measurements of resistivity and magnetic susceptibility. Theoretical calculations suggest that the partial occupancy of Mo atoms plays a crucial role in the emergence of superconductivity.
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| 8. |
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| 9. |
- Wang, Wei, et al.
(författare)
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Enhanced edge detection for polarimetric SAR images using a directional span-driven adaptive window
- 2018
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Ingår i: International Journal of Remote Sensing. - : TAYLOR & FRANCIS LTD. - 0143-1161 .- 1366-5901. ; 39:19, s. 6340-6357
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Tidskriftsartikel (refereegranskat)abstract
- Automatic edge detection for polarimetric synthetic aperture radar (PolSAR) images plays a fundamental role in various PolSAR applications. The classic methods apply the fixed-shape windows to detect the edges, whereas their performance is limited in heterogeneous areas. This article presents an enhanced edge detection method for PolSAR data based on the directional span-driven adaptive (DSDA) window. The DSDA window has variable sizes and flexible shapes, and is constructed by adaptively selecting samples that follow the same statistical distribution. Therefore, it can overcome the limitation of classic fixed-shape windows. To obtain refined and reliable edge detection results in heterogeneous urban areas, we adopt the spherically invariant random vector (SIRV) product model since the complex Wishart distribution is often not met. In addition, a span ratio is combined with the SIRV distance to highlight the dissimilarity measure and to improve the robustness of the proposed method. The simulated PolSAR data and three real data sets from experimental synthetic aperture radar, electromagnetics institute synthetic aperture radar, and Radarsat-2 systems are used to validate the performance of the enhanced edge detector. Both quantitative evaluation and visual presentation of the results demonstrate the effectiveness of the proposed method and its superiority over the classic edge detectors.
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| 10. |
- Wang, Wei, et al.
(författare)
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Enhanced Edge Detection for Polarimetric SAR Images Using Directional Span-Driven Adaptive Window
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Automatic edge detection for polarimetric synthetic aperture radar (PolSAR) images plays a fundamental role in various PolSAR applications. The classic methods apply the fixed-shape windows to detect the edges, whereas their performance is limited in heterogeneous areas. This paper presents an enhanced edge detection method for PolSAR data based on the directional span-driven adaptive (DSDA) window. The DSDA window has variable sizes and flexible shapes, and is constructed by adaptively selecting samples which follow the same statistical distribution. Therefore, it can overcome the limitation of classic fixed-shape windows. To obtain refined and reliable edge detection results in heterogeneous urban areas, we adopt the spherically invariant random vector (SIRV) product model, since the complex Wishart distribution is often not met. In addition, a span ratio is combined with the SIRV distance to highlight the dissimilarity measure and to improve the robustness of the proposed method. The simulated PolSAR data and three real data sets from ESAR, EMISAR and RADARSAT-2 systems are used to validate the performance of the enhanced edge detector. Both quantitative evaluation and visual presentation of the results demonstrate the effectiveness of the proposed method and its superiority over the classic edge detectors.
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