| 1. |
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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. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Grøn, Ole, et al.
(author)
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Acoustic mapping of submerged stone age sites—A HALD approach
- 2021
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In: Remote Sensing. - : MDPI AG. - 2072-4292. ; 13:3
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Journal article (peer-reviewed)abstract
- Acoustic response from lithics knapped by humans has been demonstrated to facilitate effective detection of submerged Stone Age sites exposed on the seafloor or embedded within its sediments. This phenomenon has recently enabled the non-invasive detection of several hitherto unknown submerged Stone Age sites, as well as the registration of acoustic responses from already known localities. Investigation of the acoustic-response characteristics of knapped lithics, which appear not to be replicated in naturally cracked lithic pieces (geofacts), is presently on-going through laboratory experiments and finite element (FE) modelling of high-resolution 3D-scanned pieces. Experimental work is also being undertaken, employing chirp sub-bottom systems (reflection seismic) on known sites in marine areas and inland water bodies. Fieldwork has already yielded positive results in this initial stage of development of an optimised Human-Altered Lithic Detection (HALD) method for mapping submerged Stone Age sites. This paper reviews the maritime archaeological perspectives of this promising approach, which potentially facilitates new and improved practice, summarizes existing data, and reports on the present state of development. Its focus is not reflection seismics as such, but a useful resonance phenomenon induced by the use of high-resolution reflection seismic systems.
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| 5. |
- Ji, Zhong-Hai, et al.
(author)
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High-throughput screening and machine learning for the efficient growth of high-quality single-wall carbon nanotubes
- 2021
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In: Nano Reseach. - : Tsinghua University Press. - 1998-0124 .- 1998-0000. ; 14, s. 4610-4615
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Journal article (peer-reviewed)abstract
- It has been a great challenge to optimize the growth conditions toward structure-controlled growth of single-wall carbon nanotubes (SWCNTs). Here, a high-throughput method combined with machine learning is reported that efficiently screens the growth conditions for the synthesis of high-quality SWCNTs. Patterned cobalt (Co) nanoparticles were deposited on a numerically marked silicon wafer as catalysts, and parameters of temperature, reduction time and carbon precursor were optimized. The crystallinity of the SWCNTs was characterized by Raman spectroscopy where the featured G/D peak intensity (IG/ID) was extracted automatically and mapped to the growth parameters to build a database. 1,280 data were collected to train machine learning models. Random forest regression (RFR) showed high precision in predicting the growth conditions for high-quality SWCNTs, as validated by further chemical vapor deposition (CVD) growth. This method shows great potential in structure-controlled growth of SWCNTs. [Figure not available: see fulltext.].
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| 6. |
- Liu, Zhigang, et al.
(author)
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Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment
- 2020
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1, s. 855-
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Journal article (peer-reviewed)abstract
- Cognitive decline is one of the complications of type 2 diabetes (T2D). Intermittent fasting (IF) is a promising dietary intervention for alleviating T2D symptoms, but its protective effect on diabetes-driven cognitive dysfunction remains elusive. Here, we find that a 28-day IF regimen for diabetic mice improves behavioral impairment via a microbiota-metabolites-brain axis: IF enhances mitochondrial biogenesis and energy metabolism gene expression in hippocampus, re-structures the gut microbiota, and improves microbial metabolites that are related to cognitive function. Moreover, strong connections are observed between IF affected genes, microbiota and metabolites, as assessed by integrative modelling. Removing gut microbiota with antibiotics partly abolishes the neuroprotective effects of IF. Administration of 3-indolepropionic acid, serotonin, short chain fatty acids or tauroursodeoxycholic acid shows a similar effect to IF in terms of improving cognitive function. Together, our study purports the microbiota-metabolites-brain axis as a mechanism that can enable therapeutic strategies against metabolism-implicated cognitive pathophysiologies.
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| 7. |
- Petrache, C. M., et al.
(author)
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Evidence of chiral bands in even-even nuclei
- 2018
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In: Physical Review C. - : American Physical Society. - 2469-9985 .- 2469-9993. ; 97:4
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Journal article (peer-reviewed)abstract
- Evidence for chiral doublet bands has been observed for the first time in the even-even nucleus Nd136. One chiral band was firmly established. Four other candidates for chiral bands were also identified, which can contribute to the realization of the multiple pairs of chiral doublet bands (MχD) phenomenon. The observed bands are investigated by the constrained and tilted axis cranking covariant density functional theory (TAC-CDFT). Possible configurations have been explored. The experimental energy spectra, angular momenta, and B(M1)/B(E2) values for the assigned configurations are globally reproduced by TAC-CDFT. Calculated results support the chiral interpretation of the observed bands, which correspond to shapes with maximum triaxiality induced by different multiquasiparticle configurations in Nd136.
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| 8. |
- Ren, Bo, et al.
(author)
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A Carbohydrate- Anion Recognition System in Aprotic Solvents
- 2014
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In: Chemistry - An Asian Journal. - : Wiley. - 1861-4728 .- 1861-471X. ; 9:5, s. 1298-1304
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Journal article (peer-reviewed)abstract
- A carbohydrate-anion recognition system in nonpolar solvents is reported, in which complexes form at the B-faces of -D-pyranosides with H1-, H3-, and H5-cis patterns similar to carbohydrate- interactions. The complexation effect was evaluated for a range of carbohydrate structures; it resulted in either 1:1 carbohydrate-anion complexes, or 1:2 complex formation depending on the protection pattern of the carbohydrate. The interaction was also evaluated with different anions and solvents. In both cases it resulted in significant binding differences. The results indicate that complexation originates from van der Waals interactions or weak CHA(-) hydrogen bonds between the binding partners and is related to electron-withdrawing groups of the carbohydrates as well as increased hydrogen-bond-accepting capability of the anions.
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| 9. |
- Ren, Bo, et al.
(author)
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An Iron(III) Catalyst with Unusually Broad Substrate Scope in Regioselective Alkylation of Diols and Polyols
- 2016
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In: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 22:7, s. 2481-2486
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Journal article (peer-reviewed)abstract
- In this study, [Fe(dibm)(3)] (dibm=diisobutyrylmethane) is shown to have unusually broad scope as a catalyst for the selective monoalkylation of a diverse set of 1,2- and 1,3-diol-containing structures. The mechanism is proposed to proceed via a cyclic dioxolane-type intermediate, formed between the iron(III) species and two adjacent hydroxyl groups. This approach represents the first transition-metal catalysts that are able to replace stoichiometric amounts of organotin reagents in regioselective alkylation. The reactions generally lead to very high regioselectivities and high yields, on par with, or better than, previous methods used for regioselective alkylation.
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| 10. |
- Ren, Bo, et al.
(author)
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Regioselective Acetylation of Diols and Polyols by Acetate Catalysis: Mechanism and Application.
- 2014
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In: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 79:17, s. 8134-8142
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Journal article (peer-reviewed)abstract
- We propose a principle for H-bonding activation in acylation of hydroxyl groups, where the acylation is activated by the formation of hydrogen bonds between hydroxyl groups and anions. With the guidance of this principle, we demonstrate a method for the selective acylation of carbohydrates. By this method, diols and polyols are regioselectively acetylated in high yields under mild conditions using catalytic amts. of acetate. In comparison to other methods involving reagents such as organotin, organoboron, organosilicon, organobase, and metal salts, this method is more environmentally friendly, convenient, and efficient and is also assocd. with higher regioselectivity. We have performed a thorough quantum chem. study to decipher the mechanism, which suggests that acetate first forms a dual H-bond complex with a diol, which enables subsequent monoacylation by acetic anhydride under mild conditions. The regioselectivity appears to originate from the inherent structure of the diols and polyols and their specific interactions with the coordinating acetate catalyst. [on SciFinder(R)]
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| 11. |
- Ren, Weixi, et al.
(author)
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An intelligent optimization method for the facility environment on rural roads
- 2024
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In: Computer-Aided Civil and Infrastructure Engineering. - 1093-9687 .- 1467-8667. ; 39:17, s. 2559-2580
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Journal article (peer-reviewed)abstract
- This study develops an intelligent optimization method of the facility environment (i.e., road facilities and surrounding landscapes) from drivers’ visual perception to adjust operation speeds on rural roads. Different from previous methods that heavily rely on expert experience and are time-consuming, this method can rapidly generate optimized visual images of the facility environment and promptly verify the optimization effects. In this study, a visual road schema model is established to quantify the facility environment from drivers’ visual perception, and an automated optimization scheme determination approach considering the original facility environment characteristics is proposed using self-explaining theory. Then, Cycle-consistent generative adversarial network is used to automatically generate optimized facility environment images. To verify the optimization effect, operation speeds of the optimized facility environments are predicted using random forest. The case study shows that this method can effectively optimize the facility environment where original operation speeds are more than 20% over the speed limits, and the whole process only takes 1 h far less than several months or years in previous ways. Overall, this study advances the intelligence level in optimizing the facility environment and enhances rural road safety.
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| 12. |
- Ren, Weixi, et al.
(author)
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Divergent Effects of Factors on Crash Severity under Autonomous and Conventional Driving Modes Using a Hierarchical Bayesian Approach
- 2022
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In: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 19:18
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Journal article (peer-reviewed)abstract
- Influencing factors on crash severity involved with autonomous vehicles (AVs) have been paid increasing attention. However, there is a lack of comparative analyses of those factors between AVs and human-driven vehicles. To fill this research gap, the study aims to explore the divergent effects of factors on crash severity under autonomous and conventional (i.e., human-driven) driving modes. This study obtained 180 publicly available autonomous vehicle crash data, and 39 explanatory variables were extracted from three categories, including environment, roads, and vehicles. Then, a hierarchical Bayesian approach was applied to analyze the impacting factors on crash severity (i.e., injury or no injury) under both driving modes with considering unobserved heterogeneities. The results showed that some influencing factors affected both driving modes, but their degrees were different. For example, daily visitors' flowrate had a greater impact on the crash severity under the conventional driving mode. More influencing factors only had significant impacts on one of the driving modes. For example, in the autonomous driving mode, mixed land use increased the severity of crashes, while daytime had the opposite effects. This study could contribute to specifying more appropriate policies to reduce the crash severity of both autonomous and human-driven vehicles especially in mixed traffic conditions.
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| 13. |
- Ren, Weixi, et al.
(author)
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Self-explaining analysis of facility environments on 2-lane rural roads with an improved lightweight CNN considering drivers’ visual perception
- 2024
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In: International Journal of Transportation Science and Technology. - 2046-0449 .- 2046-0430. ; In Press
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Journal article (peer-reviewed)abstract
- Speeding is one of the primary contributors to rural road crashes. Self-explaining theory offers a solution to reduce speeding, which suggests that well-designed facility environments (i.e., road facilities and surrounding landscapes) can automatically guide drivers to choose appropriate speeds on different road categories. This study proposes an improved lightweight convolutional neural network (LW-CNN) that includes drivers’ visual perception characteristics (i.e., depth perception and dynamic vision) to conduct the self-explaining analysis of the facility environment on 2-lane rural roads. Data for this study are gathered through naturalistic driving experiments on 2-lane rural roads across five Chinese provinces. A total of 3,502 visual facility environment images, alongside their corresponding operation speeds and speed limits, are collected. The improved LW-CNN exhibits high accuracy and efficiency in predicting operation speeds with these visual facility environment images, achieving a train loss of 0.05% and a validation loss of 0.15%. The semantics of facility environments affecting operation speeds are further identified by combining this LW-CNN with the Gradient-weighted class activation mapping algorithm and the semantic segmentation network. Then, six typical 2-lane rural road categories perceived by drivers with different operation speeds and speeding probability are summarized using k-means clustering. An objective and comprehensive analysis of each category's semantic composition and depth features is conducted to evaluate their influence on drivers’ speeding probability and road category perception. The findings of this study can be directly applied to optimize facility environments from drivers’ visual perception to decrease speeding-related crashes.
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| 14. |
- Wen, Bo, et al.
(author)
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IPeak : An open source tool to combine results from multiple MS/MS search engines
- 2015
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In: Proteomics. - : Wiley-VCH Verlagsgesellschaft. - 1615-9853 .- 1615-9861. ; 15:17, s. 2916-2920
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Journal article (peer-reviewed)abstract
- Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/.
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| 15. |
- Wu, Rong Chang, et al.
(author)
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Conodont faunal dynamics across the middle and upper ordovician boundary in the Yichang area, western Hubei province, South China
- 2016
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In: Canadian Journal of Earth Sciences. - : Canadian Science Publishing. - 0008-4077 .- 1480-3313. ; 53:8, s. 856-864
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Journal article (peer-reviewed)abstract
- A total of 6094 conodont specimens, assigned to 18 genera and 27 species, have been recovered from the uppermost Kuniutan and Miaopo formations, spanning the latest Darriwilian - early Sandbian in age, at the Jieling section, Yichang, Hubei Province. Three conodont zones have been recognized, i.e., in ascending order, the Pygodus serra Zone, the Pygodus anserinus - Yangtzeplacognathus jianyeensis Zone, and the Baltoniodus alobatus Zone. The conodont biodiversity in the Miaopo Formation shows a decreasing trend at Jieling. Multivariate statistical analysis of the conodont fauna from the Jieling section shows that the Baltoniodus and Periodon biofacies are present in the uppermost Kuniutan Formation, and the Periodon and Scabbardella biofacies can be recognized in the Miaopo Formation.
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| 16. |
- Wu, Wei, et al.
(author)
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Whole-exome sequencing identified four loci influencing craniofacial morphology in northern Han Chinese
- 2019
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In: Human Genetics. - : SPRINGER. - 0340-6717 .- 1432-1203. ; 138:6, s. 601-611
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Journal article (peer-reviewed)abstract
- Facial shape differences are one of the most significant phenotypes in humans. It is affected largely by skull shape. However, research into the genetic basis of the craniofacial morphology has rarely been reported. The present study aimed to identify genetic variants influencing craniofacial morphology in northern Han Chinese through whole-exome sequencing (WES). Phenotypic data of the volunteers' faces and skulls were obtained through three-dimensional CT scan of the skull. A total of 48 phenotypes (35 facial and 13 cranial phenotypes) were used for the bioinformatics analysis. Four genetic loci were identified affecting the craniofacial shapes. The four candidate genes are RGPD3, IGSF3, SLC28A3, and USP40. Four single-nucleotide polymorphism (SNP) site mutations in RGPD3, IGSF3, and USP40 were significantly associated with the skull shape (p<1x10(-6)), and three SNP site mutations in RGPD3, IGSF3, and SLC28A3 were significantly associated with the facial shape (p<1x10(-6)). The rs62152530 site mutation in the RGPD3 gene may be closely associated with the nasal length, ear length, and alar width. The rs647711 site mutation in the IGSF3 gene may be closely associated with the nasal length, mandibular width, and width between the mental foramina. The rs10868138 site mutation in the SLC28A3 gene may be associated with the nasal length, alar width, width between tragus, and width between the mental foramina. The rs1048603 and rs838543 site mutations in the USP40 gene may be closely associated with the pyriform aperture width. Our findings provide useful genetic information for the determination of face morphology.
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| 17. |
- Zhang, Bo lun, et al.
(author)
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Experimental study on film cooling performance of a turbine blade tip with a trapezoidal slot cooling scheme in transonic flow using PSP technique
- 2022
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In: Experimental Thermal and Fluid Science. - : Elsevier BV. - 0894-1777. ; 130
-
Research review (peer-reviewed)abstract
- A turbine blade tip with a trapezoidal slot cooling scheme is first proposed in the current paper. The film cooling characteristics of a turbine blade tip with a trapezoidal slot scheme are experimentally studied by the pressure sensitive paint (PSP) technique in transonic flow. Varieties of density ratio, tip clearance gap and position of the trapezoidal slot scheme are selected as investigation parameters. The mainstream Reynolds number is 370,000 based on the blade axial chord length. The cascade exit Mach numbers are is 1.05. The results indicate that increasing the density ratio has a positive effect on the film cooling effectiveness of the whole blade tip with a pressure side trapezoidal slot scheme at a small tip clearance gap, whereas it decreases the film cooling effectiveness upstream of the blade tip at the large tip clearance gap. For the blade tip with a pressure side trapezoidal slot scheme, the film cooling effectiveness of the tip clearance gap of 1.5% near the trailing edge is higher than that of the other tip clearance gaps at the same density ratio condition. Changing the trapezoidal slot position from the tip pressure side to the tip midline increases the film cooling effectiveness near the trailing edge.
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| 18. |
- Zhang, Xiangnan, et al.
(author)
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Gut Bacterial Indole-3-acetic Acid Induced Immune Promotion Mediates Preventive Effects of Fu Brick Tea Polyphenols on Experimental Colitis
- 2023
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In: Journal of Agricultural and Food Chemistry. - : American Chemical Society (ACS). - 0021-8561 .- 1520-5118. ; 71:2, s. 1201-1213
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Journal article (peer-reviewed)abstract
- Ulcerative colitis has been consistently associated with gut microbiota imbalance and disturbed immune system. Emerging research suggests a protective function of polyphenols on prevention and treatment of ulcerative colitis, yet underlying mechanisms remain unclear. Fu brick tea, a postfermented tea, contains abundant polyphenols with anti-inflammatory and antioxidant properties. In the present study, we found that prophylactic supplementation of polyphenols extracted from Fu brick tea (FBTP) dose-dependently alleviated colitis symptoms, immune cells infiltration, and pro-inflammatory cytokines secretion in mice suffering dextran sulfate sodium induced murine colitis. FBTP substantially reshaped gut microbiota and promoted microbial transformation of tryptophan into indole-3-acetic acid (I3A), thereafter leading to aryl hydrocarbon receptor (AHR)-mediated protection from colitis through enhanced expressions of IL-22 and tight junction proteins (i.e., ZO-1, occluding and claudin-1) in colon. Multiomics integration analyses revealed strong connections between I3A, tryptophan-metabolizing bacteria, AHR activity, and pathological phenotypes of colitis. Notably, FBTP failed to significantly alleviate colitis symptoms in the absence of gut microbiota, while intragastric administration of I3A could imitate benefits of FBTP on colitis alleviation and intestinal epithelial homeostasis through a direct enhancement in AHR activity in microbiota-depleted mice. These findings further determine the key role of gut microbiota controlled I3A-AHR signaling in mediating the FBTP on colitis alleviation. This study provides the first data proposing the FBTP as a natural prebiotic for colitis alleviation through the gut microbiota-dependent modulation of the AHR pathway. Most importantly, we also identified I3A as a key microbial metabolite targeted by FBTP for exhibiting health-promoting effects.
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| 19. |
- Zhou, Yixuan, et al.
(author)
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H-Bonding Activation in Highly Regioselective Acetylation of Diols.
- 2013
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In: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 78:22, s. 11618-11622
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Journal article (peer-reviewed)abstract
- H-bonding activation in the regioselective acetylation of vicinal and 1,3-diols is presented. Herein, the acetylation of the hydroxyl group with acetic anhydride can be activated by the formation of H-bonds between the hydroxyl group and anions. The reaction exhibits high regioselectivity when a catalytic amt. of tetrabutylammonium acetate is employed. Mechanistic studies indicated that acetate anion forms dual H-bonding complexes with the diol, which facilitates the subsequent regioselective monoacetylation. [on SciFinder(R)]
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