| 1. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
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.
|
|
| 2. |
|
|
| 3. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
|
|
| 4. |
- Cheng, Shi-Ping, et al.
(författare)
-
Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
-
Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
-
Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
|
|
| 5. |
- Kristan, Matej, et al.
(författare)
-
The Sixth Visual Object Tracking VOT2018 Challenge Results
- 2019
-
Ingår i: Computer Vision – ECCV 2018 Workshops. - Cham : Springer Publishing Company. - 9783030110086 - 9783030110093 ; , s. 3-53
-
Konferensbidrag (refereegranskat)abstract
- The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).
|
|
| 6. |
|
|
| 7. |
- Chang, Kuang Yu, et al.
(författare)
-
Observational constraints reduce model spread but not uncertainty in global wetland methane emission estimates
- 2023
-
Ingår i: Global Change Biology. - 1354-1013. ; 29:15, s. 4298-4312
-
Tidskriftsartikel (refereegranskat)abstract
- The recent rise in atmospheric methane (CH4) concentrations accelerates climate change and offsets mitigation efforts. Although wetlands are the largest natural CH4 source, estimates of global wetland CH4 emissions vary widely among approaches taken by bottom-up (BU) process-based biogeochemical models and top-down (TD) atmospheric inversion methods. Here, we integrate in situ measurements, multi-model ensembles, and a machine learning upscaling product into the International Land Model Benchmarking system to examine the relationship between wetland CH4 emission estimates and model performance. We find that using better-performing models identified by observational constraints reduces the spread of wetland CH4 emission estimates by 62% and 39% for BU- and TD-based approaches, respectively. However, global BU and TD CH4 emission estimate discrepancies increased by about 15% (from 31 to 36 TgCH4 year−1) when the top 20% models were used, although we consider this result moderately uncertain given the unevenly distributed global observations. Our analyses demonstrate that model performance ranking is subject to benchmark selection due to large inter-site variability, highlighting the importance of expanding coverage of benchmark sites to diverse environmental conditions. We encourage future development of wetland CH4 models to move beyond static benchmarking and focus on evaluating site-specific and ecosystem-specific variabilities inferred from observations.
|
|
| 8. |
- Chen, Zhibin, et al.
(författare)
-
Summary of the 3rd International Workshop on Gas-Dynamic Trap based Fusion Neutron Source (GDT-FNS)
- 2022
-
Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 62:6
-
Tidskriftsartikel (refereegranskat)abstract
- The 3rd International Workshop on Gas-Dynamic Trap-based Fusion Neutron Source (GDT-FNS) was held through the hybrid mode on 13-14 September 2021 in Hefei, China, jointly organized by the Hefei Institutes of Physical Science (HFIPS), Chinese Academy of Sciences (CAS), and the Budker Institute of Nuclear Physics (BINP), Russian Academy of Sciences (RAS). It followed the 1st GDT-FNS Workshop held in November 2018 in Hefei, China, and the 2nd taking place in November 2019 in Novosibirsk, Russian Federation. With the financial support from CAS and China Association for Science and Technology (CAST), this workshop was attended by more than 80 participants representing 20 institutes and universities from seven countries, with oral presentations broadcast via the Zoom conferencing system. Twenty-two presentations were made with topics covering design and key technologies, simulation and experiments, steady-state operation, status of the ALIANCE project, multi applications of neutron sources, and other concepts (Tokamaks, Mirrors, FRC, Plasma Focus, etc). The workshop consensus was made including the establishment of the ALIANCE International Working Group. The next GDT-FNS workshop is planned to be held in May 2022 in Novosibirsk.
|
|
| 9. |
- Cheng, Benyuan, et al.
(författare)
-
Pressure-induced metallization and amorphization in VO2(A) nanorods
- 2016
-
Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 93:18
-
Tidskriftsartikel (refereegranskat)abstract
- A metallic state enabled by the metal-insulator transition (MIT) in single crystal VO2(A) nanorods is demonstrated, which provides important physical foundation in experimental understanding of MIT in VO2. The observed tetragonal metallic state at ∼28 GPa should be interpreted as a distinct metastable state, while increasing pressure to ∼32 GPa, it transforms into a metallic amorphous state completely. The metallization is due to V 3d orbital electrons delocalization, and the amorphization is attributed to the unique variation of V-O-V bond angle. A metallic amorphous VO2 state is found under pressure, which is beneficial to explore the phase diagram of VO2. Furthermore, this work proves the occurrence of both the metallization and amorphization in octahedrally coordinated materials.
|
|
| 10. |
- Cui, Wen, et al.
(författare)
-
Reversible pressure-induced polymerization of Fe(C5H5)(2) doped C-70
- 2013
-
Ingår i: Carbon. - : Pergamon-Elsevier Science. - 0008-6223 .- 1873-3891. ; 62, s. 447-454
-
Tidskriftsartikel (refereegranskat)abstract
- High pressure Raman, IR and X-ray diffraction (XRD) studies have been carried out on C-70(Fe(C5H5)(2))(2) (hereafter, "C-70(Fc)(2)") sheets. Theoretical calculation is further used to analyze the Electron Localization Function (ELF) and charge transfer in the crystal and thus to understand the transformation of C-70(Fc)(2) under pressure. Our results show that even at room temperature dimeric phase and one dimensional (1D) polymer phase of C-70 molecules can be formed at about 3 and 8 GPa, respectively. The polymerization is found to be reversible Upon decompression and the reversibility is related to the pressure-tuned charge transfer, as well as the overridden steric repulsion of counter ions. According to the layered structure of the intercalated ferrocene molecules formed in the crystal, we suggest that ferrocene acts as not only a spacer to restrict the polymerization of C-70 molecules within a layer, but also as charge reservoir to tune the polymerization process. This supplies a possible way for us to design the polymerization of fullerenes at suitable conditions.
|
|
