| 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. |
- Jin, Ying-Hui, et al.
(författare)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 3. |
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| 4. |
- 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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| 5. |
- Chen, Yu-Xiang, et al.
(författare)
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Selective translation by alternative bacterial ribosomes
- 2020
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 117:32, s. 19487-19496
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Tidskriftsartikel (refereegranskat)abstract
- Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species, but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes from Mycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in protein synthesis, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Furthermore, a strain of M. smegmatis in which the alternative ribosome protein operon is deleted grows poorly in iron-depleted medium, uncovering a role for alternative ribosomes in iron homeostasis. Our work confirms the distinct and nonredundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.
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| 6. |
- Gu, Shi-Ran, et al.
(författare)
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Phylogeny and re-circumscription of Cheniella (Leguminosae: Cercidoideae) based on plastome data and morphology, with description of three new species
- 2024
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Ingår i: TAXON. - 0040-0262 .- 1996-8175. ; 73:2, s. 475-502
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Tidskriftsartikel (refereegranskat)abstract
- Subfamily Cercidoideae is an early-diverging lineage of Leguminosae, within which the number and classification of genera have been controversial. Cheniella is a recently described genus in the Cercidoideae which requires revision and testing of its monophyly and circumscription. Here we infer the phylogenetic position and infrageneric relationships of Cheniella as well as the intergeneric relationships of Cercidoideae using 48 newly sequenced plastid genomes, including 34 individuals representing all species of Cheniella. Our phylogenetic analyses yield a well-resolved tree of Cercidoideae with robust support at most nodes. We also present morphological studies through field work and herbarium studies to re-assess the classification and circumscription of the genus. Based on the results of molecular analyses and morphological studies combined with distribution data, we broaden the circumscription of Cheniella to comprise a total of 15 species and 3 subspecies, including three new species (C. hechiensis, C. longistaminea, C. pubicarpa), one new combination (C. tianlinensis) and one new status and combination (C. longipes).
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| 7. |
- Wen, Tian-Jiao, et al.
(författare)
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Non-fused medium bandgap electron acceptors for efficient organic photovoltaics
- 2022
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Ingår i: Journal of Energy Challenges and Mechanics. - : ELSEVIER. - 2056-9386. ; 70, s. 576-582
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Tidskriftsartikel (refereegranskat)abstract
- The cost-effective organic semiconductors are strongly needed in organic photovoltaics (OPVs). Herein, two medium bandgap (MBG) electron acceptors, TPT4F and TPT4Cl are developed via the new design of multi-noncovalent interaction assisted unfused core, flanked with two electron withdrawing end groups. These fullly non-fused MBG acceptors adapt the planar and rigid conformation in solid, therefore exhibiting the ordered face-on stacking and strong photoluminescence in films. As results, TPT4Cl-based OPVs, upon blending with the PBDB-TF polymer donor, have achieved a power conversion efficiency of 10.16% with a low non-radiative loss of 0.27 eV, representing one of the best fullly non-fused medium bandgap acceptors with desirable cost-efficiency balance. (c) 2022 Science Press and Dalian Institute of Chemical Physics, Chinese Academy of Sciences. Published by ELSEVIER B.V. and Science Press. All rights reserved.
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| 8. |
- Zhang, Zhi-Fei, et al.
(författare)
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The Cambrian brachiopod fauna from the first-trilobite age Shuijingtuo Formation in the Three Gorges area of China
- 2016
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Ingår i: Palaeoworld. - : Elsevier BV. - 1871-174X .- 1875-5887. ; 25:3, s. 333-355
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Tidskriftsartikel (refereegranskat)abstract
- The Yangtze platform of South China offers evidence within its Ediacaran–Cambrian geological record of the Cambrian explosion and diversificationevents in metazoan history. To understand the explosive radiation of animals and the environments in which it took place, the basalCambrian fauna succession of the Aijiahe section in the Three Gorges area, western Hubei Province, has been studied, revealing the earliestbrachiopod fauna (Tsunyidiscus trilobite Zone) in this region, which was dominated numerically by acrotretoids. This is accompanied by abundantskeletal fossils including minute well-preserved phosphatized archaeocyath cups and an assortment of abundant sponge spicules, chancelloriids,mollusks, hyoliths, and bradoriids, retrieved by acid-etching limestone interbeds in the black shale-dominated Shuijingtuo Formation (Series 2).The brachiopods comprise two species of acrotretoids, two types of botsfordiids (Botsfordiidae gen. et sp. indet. A and B), and four species oflinguloids. Of the latter, Spinobolus popovi n. gen. n. sp. is strikingly distinctive and typified by spine-like ornamentation seen for the first time in thelower Cambrian; the remaining three linguloid genera, Palaeobolus, Eoobolus, and Lingulellotreta, have a trans-paleocontinental distribution. TheThree Gorges Shuijingtuo brachiopod assemblage differs from that of the upper Atdabanian Stage (Cambrian Stage 3) in Siberia and South China,but shows great similarities with those discovered in the Tsanglangpuan (equivalent to Botoman or Stage 4) Stage of eastern Yunnan Province,Siberia, and South Australia, suggesting a much more prolonged sedimentary hiatus in basalmost Shuijingtuo Formation of the Three Gorges areathan previously expected. The presence of such unconformities provides a caveat to stable isotope-based correlations that involve a number ofdiscussions of global ocean geochemical changes across the time interval that witnessed Cambrian explosion of metazoans.
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| 9. |
- Zhang, Zhuo-Zhi, et al.
(författare)
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A suspended silicon single-hole transistor as an extremely scaled gigahertz nanoelectromechanical beam resonator
- 2020
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Ingår i: Advanced Materials. - : Wiley. - 0935-9648 .- 1521-4095. ; 32:52
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Tidskriftsartikel (refereegranskat)abstract
- Suspended single-hole transistors (SHTs) can also serve as nanoelectromechanical resonators, providing an ideal platform for investigating interactions between mechanical vibrations and charge carriers. Demonstrating such a device in silicon (Si) is of particular interest, due to the strong piezoresistive effect of Si and potential applications in Si-based quantum computation. Here, a suspended Si SHT also acting as a nanoelectromechanical beam resonator is demonstrated. The resonant frequency and zero-point motion of the device are approximate to 3 GHz and 0.2 pm, respectively, reaching the best level among similar devices demonstrated with Si-containing materials. The mechanical vibration is transduced to electrical readout by the SHT. The signal transduction mechanism is dominated by the piezoresistive effect. A giant apparent effective piezoresistive gauge factor with strong correlation to single-hole tunneling is extracted in this device. The results show the great potential of the device in interfacing charge carriers with mechanical vibrations, as well as investigating potential quantum behavior of the vibration phonon mode.
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| 10. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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