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| 2. |
- 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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| 3. |
- Kristan, Matej, et al.
(author)
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The first visual object tracking segmentation VOTS2023 challenge results
- 2023
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In: 2023 IEEE/CVF International conference on computer vision workshops (ICCVW). - : Institute of Electrical and Electronics Engineers Inc.. - 9798350307443 - 9798350307450 ; , s. 1788-1810
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking Segmentation VOTS2023 challenge is the eleventh annual tracker benchmarking activity of the VOT initiative. This challenge is the first to merge short-term and long-term as well as single-target and multiple-target tracking with segmentation masks as the only target location specification. A new dataset was created; the ground truth has been withheld to prevent overfitting. New performance measures and evaluation protocols have been created along with a new toolkit and an evaluation server. Results of the presented 47 trackers indicate that modern tracking frameworks are well-suited to deal with convergence of short-term and long-term tracking and that multiple and single target tracking can be considered a single problem. A leaderboard, with participating trackers details, the source code, the datasets, and the evaluation kit are publicly available at the challenge website1
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| 4. |
- Lensink, Marc F., et al.
(author)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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In: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Journal article (peer-reviewed)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 5. |
- Wang, Nana, et al.
(author)
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Perovskite light-emitting diodes based on solution-processed self-organized multiple quantum wells
- 2016
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In: Nature Photonics. - : NATURE PUBLISHING GROUP. - 1749-4885 .- 1749-4893. ; 10:11, s. 699-
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Journal article (peer-reviewed)abstract
- Organometal halide perovskites can be processed from solutions at low temperatures to form crystalline direct-bandgap semiconductors with promising optoelectronic properties(1-5). However, the efficiency of their electroluminescence is limited by non-radiative recombination, which is associated with defects and leakage current due to incomplete surface coverage(6-9). Here we demonstrate a solution-processed perovskite light-emitting diode (LED) based on self-organized multiple quantum wells (MQWs) with excellent film morphologies. The MQW-based LED exhibits a very high external quantum efficiency of up to 11.7%, good stability and exceptional highpower performance with an energy conversion efficiency of 5.5% at a current density of 100 mA cm(-2). This outstanding performance arises because the lower bandgap regions that generate electroluminescence are effectively confined by perovskite MQWs with higher energy gaps, resulting in very efficient radiative decay. Surprisingly, there is no evidence that the large interfacial areas between different bandgap regions cause luminescence quenching.
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| 6. |
- Yang, Heyi, et al.
(author)
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Composition-Conditioning Agent for Doped Spiro-OMeTAD to Realize Highly Efficient and Stable Perovskite Solar Cells
- 2022
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In: Advanced Energy Materials. - : WILEY-V C H VERLAG GMBH. - 1614-6832 .- 1614-6840. ; 12:44
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Journal article (peer-reviewed)abstract
- The doped Spiro-OMeTAD hole transport layer (HTL) formed using the lithium bis(trifluoromethane) sulfonimide salt and 4-tert-butylpyridine with phenethylammonium iodide surface treatment on a perovskite film has continuously dominated the record power conversion efficiencies (PCEs) of perovskite solar cells (pero-SCs). However, unstable HTL compositions and iodide salts can cause severe device degradation. In this study, an HTL composition-conditioning agent (CCA), Spiro-BD-2OEG, is designed, which contains a Spiro-OMeTAD-like backbone, functional pyridine units, and oligo (ethylene glycol) chains. This finely designed CCA presents good miscibility with Spiro-OMeTAD and its dopants and acts as a conditioning agent through weak bond interactions. As a result, the CCA-regulated HTL shows a pinhole-free and smooth morphology with enhanced Spiro-OMeTAD ordering and improves dopant stability. In addition, the gradient-distributed CCA in the HTL can narrow the energy level offset with the valence band of the perovskite. The resultant pero-SCs exhibit an excellent PCE of 24.19% without any interface treatment and weak size dependence. A remarkable PCE of 22.63% is obtained even for a 1.004-cm(2) device. Importantly, the strategy shows good universality and significantly promotes the long-term stability of the pero-SCs based on the classical doped Spiro-OMeTAD.
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| 7. |
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| 8. |
- Yuan, Jun, et al.
(author)
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Enabling low voltage losses and high photocurrent in fullerene-free organic photovoltaics
- 2019
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In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Journal article (peer-reviewed)abstract
- Despite significant development recently, improving the power conversion efficiency of organic photovoltaics (OPVs) is still an ongoing challenge to overcome. One of the prerequisites to achieving this goal is to enable efficient charge separation and small voltage losses at the same time. In this work, a facile synthetic strategy is reported, where optoelectronic properties are delicately tuned by the introduction of electron-deficient-core-based fused structure into non-fullerene acceptors. Both devices exhibited a low voltage loss of 0.57 V and high short-circuit current density of 22.0 mA cm(-2), resulting in high power conversion efficiencies of over 13.4%. These unconventional electron-deficient-core-based non-fullerene acceptors with near-infrared absorption lead to low non-radiative recombination losses in the resulting organic photovoltaics, contributing to a certified high power conversion efficiency of 12.6%.
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| 9. |
- Bai, Yang, et al.
(author)
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Geometry design of tethered small-molecule acceptor enables highly stable and efficient polymer solar cells
- 2023
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In: Nature Communications. - : NATURE PORTFOLIO. - 2041-1723. ; 14:1
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Journal article (peer-reviewed)abstract
- With the power conversion efficiency of binary polymer solar cells dramatically improved, the thermal stability of the small-molecule acceptors raised the main concerns on the device operating stability. Here, to address this issue, thiophene-dicarboxylate spacer tethered small-molecule acceptors are designed, and their molecular geometries are further regulated via the thiophene-core isomerism engineering, affording dimeric TDY-alpha with a 2, 5-substitution and TDY-beta with 3, 4-substitution on the core. It shows that TDY-alpha processes a higher glass transition temperature, better crystallinity relative to its individual small-molecule acceptor segment and isomeric counterpart of TDY-beta, and amore stablemorphology with the polymer donor. As a result, the TDY-alpha based device delivers a higher device efficiency of 18.1%, and most important, achieves an extrapolated lifetime of about 35000 hours that retaining 80% of their initial efficiency. Our result suggests that with proper geometry design, the tethered small-molecule acceptors can achieve both high device efficiency and operating stability.
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| 10. |
- Cheng, Hao-Wen, et al.
(author)
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Realizing Efficient Charge/Energy Transfer and Charge Extraction in Fullerene-Free Organic Photovoltaics via a Versatile Third Component
- 2019
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In: Nano letters (Print). - : AMER CHEMICAL SOC. - 1530-6984 .- 1530-6992. ; 19:8, s. 5053-5061
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Journal article (peer-reviewed)abstract
- Solution-processed organic photovoltaics (OPVs) based on bulk-heterojunctions have gained significant attention to alleviate the increasing demend of fossil fuel in the past two decades. OPVs combined of a wide bandgap polymer donor and a narrow bandgap nonfullerene acceptor show potential to achieve high performance. However, there are still two reasons to limit the OPVs performance. One, although this combination can expand from the ultraviolet to the near-infrared region, the overall external quantum efficiency of the device suffers low values. The other one is the low open-circuit voltage (V-OC) of devices resulting from the relatively downshifted lowest unoccupied molecular orbital (LUMO) of the narrow bandgap. Herein, the approach to select and incorporate a versatile third component into the active layer is reported. A third component with a bandgap larger than that of the acceptor, and absorption spectra and LUMO levels lying within that of the donor and acceptor, is demonstrated to be effective to conquer these issues. As a result, the power conversion efficiencies (PCEs) are enhanced by the elevated short-circuit current and V-OC; the champion PCEs are 11.1% and 13.1% for PTB7-Th:IEICO-4F based and PBDB-T:Y1 based solar cells, respectively.
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