| 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. |
- Liu, Zhigang, et al.
(författare)
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Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 11:1, s. 855-
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Duan, Jinpei, et al.
(författare)
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Dual-Circulant Modulation for Modular Multilevel DC/DC Converters With Inherent Balance Capability
- 2023
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Ingår i: IEEE transactions on power electronics. - : Institute of Electrical and Electronics Engineers (IEEE). - 0885-8993 .- 1941-0107. ; 38:7, s. 7958-7963
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Tidskriftsartikel (refereegranskat)abstract
- Modular multilevel dc/dc converters (MMDC) have emerged recently for medium-voltage dc applications. Under single-circulant modulation, the submodule (SM) capacitor voltages in MMDC are found to be evenly divided only at some specific modulation coefficients. To obtain the inherent balance capability under all modulation coefficients and expand the application range of circulant modulation, a simple dual-circulant modulation is proposed in this letter. On the basis of single-circulant modulation, the self-balancing of the SM capacitor voltages is realized by using the additional switching patterns generated by a simple circulant permutation method. The theoretical analysis of the proposed method is presented, and the inherent balance capability of MMDC under the dual-circulant modulation method is verified by experiments.
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| 4. |
- Santangelo, James S., et al.
(författare)
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Global urban environmental change drives adaptation in white clover
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Tidskriftsartikel (refereegranskat)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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| 5. |
- Wang, Guanqun, et al.
(författare)
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Predictability of Vehicle Fuel Consumption Using LSTM: Findings from Field Experiments
- 2023
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Ingår i: Journal of Transportation Engineering Part A: Systems. - 2473-2893 .- 2473-2907. ; 149:5
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Tidskriftsartikel (refereegranskat)abstract
- It has been well-recognized that driving behaviors significantly impact the fuel consumption of vehicles. To explore how well deep learning methods can predict fuel consumption precisely and efficiently and then guide drivers to go in an energy-saving way, we propose a fuel consumption prediction model, namely FuelNet, based on long short-term memory (LSTM) neural networks in this study. First, we develop the proposed FuelNet model with numerous vehicle kinematics data and corresponding fuel consumption data collected in the test field and real-world scenarios. And we analyze the relationship between the prediction accuracy and different combinations of input variables, training set size, and the sampling interval of the raw data. Second, we conduct intensive field tests to demonstrate the applicability of our model to fuel consumption prediction for different speed conditions and vehicle types. Furthermore, the superior prediction performance of FuelNet is shown by comparing it with five other types of models, such as the physical model, statistical and regression model, conventional neural networks model, and other deep learning models. Finally, we apply it to three real case studies, which verify that FuelNet can precisely predict fuel consumption for different driving trajectories in many scenarios such as signalized intersection (average value of RE is 0.049), campus environments (RE is 0.030), urban roads (RE is 0.077), and highways (RE is 0.097), as well as can contribute to detecting abnormal fuel consumption.
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| 6. |
- Xu, Zhigang, et al.
(författare)
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Trajectory Optimization for a Connected Automated Traffic Stream: Comparison Between an Exact Model and Fast Heuristics
- 2021
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Ingår i: IEEE Transactions on Intelligent Transportation Systems. - 1524-9050 .- 1558-0016. ; 22:5, s. 2969-2978
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Tidskriftsartikel (refereegranskat)abstract
- Numerous fast heuristic algorithms, including shooting heuristics (SH), have been developed for real-time trajectory optimization, although their optimality has not yet been quantified. This paper compares the performance between fast heuristics and exact optimization models. We investigate a core trajectory optimization problem as a building block for numerous trajectory optimization problems, i.e., guiding movements of connected automated vehicles on a one-lane highway when the arrival and departure times and velocity are given. To apply the SH algorithm to this problem, we adapt it to a fast-simplified shooting heuristic (FSSH) model to solve the trajectory smoothing problems with different arrival and departure velocities. An exact trajectory optimization (ETO) model is formulated that takes the vehicle position and velocity as the decision variables, and the fuel consumption and driving comfort as the objective function. The constraints of the model are based on the limits and safety of the vehicle dynamics between consecutive vehicles. We demonstrate the convexity of the ETO objective function, ensuring the solvability of the ETO model at the true optimum using gradient descent algorithms supplied by the MATLAB optimization toolbox. Six groups of numerical experiments using different input parameters and one experiment using real Next Generation Simulation (NGSIM) data are conducted. ETO can improve the objective values by a few to tens of percentage points. However, FSSH achieves a greater solution efficiency with an average solution time of less than 0.1 s compared to similar to 450 s for ETO.
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| 7. |
- Yao, Mingguang, et al.
(författare)
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Raman signature to identify the structural transition of single-wall carbon nanotubes under high pressure
- 2008
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - : American Physical Society. - 1098-0121 .- 1550-235X. ; 78:20
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Tidskriftsartikel (refereegranskat)abstract
- Raman spectra of single-walled carbon nanotubes (SWNTs) with diameters of 0.6–1.3 nm have been studied under high pressure. A “plateau” in the pressure dependence of the G-band frequencies was observed in all experiments, both with and without pressure transmission medium. Near the onset of the G-band plateau, the corresponding radial breathing mode (RBM) lines become very weak. A strong broadening of the full width at half maximum of the RBMs just before the onset of the G-band plateau suggests that a structural transition starts in the SWNTs. Raman spectra from SWNTs released from different pressures also indicate that a significant structural transition occurs during the G-band plateau process. Simulations of the structural changes and the corresponding Raman modes of a nanotube under compression show a behavior similar to the experimental observations. Based on the experimental results and the theoretical simulation, a detailed model is suggested for the structural transition of SWNTs, corresponding to the experimentally obtained Raman results in the high-pressure domain.
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| 8. |
- Zhao, Xiangmo, et al.
(författare)
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Field experiments on longitudinal characteristics of human driver behavior following an autonomous vehicle
- 2020
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Ingår i: Transportation Research, Part C: Emerging Technologies. - : Elsevier BV. - 0968-090X. ; 114, s. 205-224
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Tidskriftsartikel (refereegranskat)abstract
- Although mixed traffic, including both autonomous vehicles (AV) and human-driven vehicles (HV), is expected to prevail in the foreseeable future, our current understanding of the longitudinal characteristics of mixed traffic is limited and, in particular, lacks evidence from field experiments. To bridge this gap, we designed and conducted a set of field experiments to reveal differences in car-following behaviors between a human driver following-AV and following-HV on both constant speed traffic characteristics with discrete speeds ({10,20,…,60}km/h) and dynamic car-following behaviors with continuous speeds (within 0–60 km/h) in both the indifferentiable and differentiable appearance settings of the AV. We recruited 10 drivers for the experiment (14 runs for each driver and collected position and speed data of the tested vehicles along their complete trajectories based on vehicle gaps, headways, and standard deviations of vehicle speed. A K-means clustering algorithm was applied to classify drivers based on their responses in following-AV vs. following-HV with both constant speed and dynamic speed characteristics. The analyses of the differentiable appearance setting show that different drivers exhibit different behaviors in following-AV vs. following-HV: some are AV-believers, some are AV-skeptics, and the others are insensitive. Yet in the indifferentiable appearance setting, there is no significant difference between following a lead AV and following a lead HV. This reveals that drivers’ response to the lead vehicle depends on their subjective trusts on AV technologies rather than the actual driving behavior. The results suggest that, depending on the characteristics and composition of the drivers, classic car-following behavior in pure HV traffic may need to be updated for modeling mixed traffic in the near future.
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| 9. |
- Allardyce, Benjamin J., et al.
(författare)
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Comparative acoustic performance and mechanical properties of silk membranes for the repair of chronic tympanic membrane perforations
- 2016
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Ingår i: Journal of The Mechanical Behavior of Biomedical Materials. - : Elsevier BV. - 1751-6161 .- 1878-0180. ; 64, s. 65-74
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Tidskriftsartikel (refereegranskat)abstract
- The acoustic and mechanical properties of silk membranes of different thicknesses were tested to determine their suitability as a repair material for tympanic membrane perforations. Membranes of different thickness (10-100 mu m) were tested to determine their frequency response and their resistance to pressure loads in a simulated ear canal model. Their mechanical rigidity to pressure loads was confirmed by tensile testing. These membranes were tested alongside animal cartilage, currently the strongest available myringoplasty graft as well as paper, which is commonly used for simpler procedures. Silk membranes showed resonant frequencies within the human hearing range and a higher vibrational amplitude than cartilage, suggesting that silk may offer good acoustic energy transfer characteristics. Silk membranes were also highly resistant to simulated pressure changes in the middle ear, suggesting they can resist retraction, a common cause of graft failure resulting from chronic negative pressures in the middle ear. Part of this strength can be explained by the substantially higher modulus of silk films compared with cartilage. This allows for the production of films that are much thinner than cartilage, with superior acoustic properties, but that still provide the same level of mechanical support as thicker cartilage. Together, these in vitro results suggest that silk membranes may provide good hearing outcomes while offering similar levels of mechanical support to the reconstructed middle ear.
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| 10. |
- Borthakur, Dulal, et al.
(författare)
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Current status and trends in forest genomics
- 2022
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Ingår i: Forestry Research. - : Maximum Academic Press. - 2767-3812. ; 2
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Forskningsöversikt (refereegranskat)abstract
- Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.
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