| 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. |
- An, Hongbin, et al.
(författare)
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A method of manufacturing microfluidic contact lenses by using irreversible bonding and thermoforming
- 2018
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Ingår i: Journal of Micromechanics and Microengineering. - : IOP PUBLISHING LTD. - 0960-1317 .- 1361-6439. ; 28:10
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we present the development of microfluidic contact lenses, which is based on the advantages of wearable microfluidics and can have great potential in the ophthalmology healthcare field. The development consists of two parts; the manufacturing process and the usability tests of the devices. In the manufacturing process, we firstly extended silane coupling and surface modification to irreversibly bond plastic membranes with microchannel-molded silicone rubber, to form the plastic-PDMS plane assemblies, and then molded the plane into a contact lens by thermoforming. We systematically investigated the effects of thermoforming factors, heating temperatures and the terrace die's sphere radius on channels by using the factorial experiment design. In addition, various tests were conducted to verify the usability of the devices. Through blockage and leakage tests, the devices were proved to be feasible, with no channel-blockages and could stand high pressures. Through a wearing test, the contact lenses were confirmed to be harmless on the living body. Furthermore, by performing the manipulating test, the device was proved to be liquid-controllable. These works provide a foundation for the applications of microfluidic contact lenses in ophthalmology.
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| 4. |
- An, Hongbin, et al.
(författare)
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Microfluidic contact lenses for unpowered, continuous and non-invasive intraocular pressure monitoring
- 2019
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Ingår i: Sensors and Actuators A-Physical. - : Elsevier BV. - 0924-4247 .- 1873-3069. ; 295, s. 177-187
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Tidskriftsartikel (refereegranskat)abstract
- Intraocular pressure (IOP) is a crucial physiological indicator of the visual system and play a key role in the diagnosis and treatment of glaucoma. However, the current handheld single measurement tools for IOP sensing cannot meet the future demands for glaucoma management. Thus, here we present the microfluidic contact lens sensors that could provide unpowered, continuous and non-invasive IOP monitoring. The microfluidic contact lens is comprised of a sensing layer of the micropatterned soft-elastomer and a hard plastic reference layer. The devices use the annular sensing chamber filled with the dyed liquid and a sensing microchannel as the IOP transducer. Resulting from the volume variance of the sensing chamber and caused by the deformation of the sensing layer under pressure, the IOP signal is detected as the displacement change of the dyed liquid's interface in the sensing channel, and in which, the displacement change can be optically observed by using the smart-phone camera. Based on the silicone rubber model eyeball, the sensing mechanism of the devices with different design parameters (the position of the sensing chambers and the dimension of the sensing channels) are explored by using the theoretical analyses and experimental investigations. The characteristics of these microfluidic contact lens sensors are tested, in which, the maximum sensitivity of the device (with the sensing chamber of 8.5 mm in diameter and the sensing channel of 100 x 40 um in size) can be achieved to 0.708 mm/mmHg in a working range of 0 (4) over tilde0 mmHg. Also, cyclical tests were conducted and indicated that the devices had a good reversibility and Long-term stability. Furthermore, the device (with the sensing chamber of 5.0 mm in diameter and the sensing channel of 150 x 40 urn in size) was test on the porcine eyes ex vivo, showing a sensitivity of 0.2832 mm/mmHg in a range of 8 (3) over tilde2 mmHg and, the device had a good reproducibility to its IOP change. This work provides a promising approach for unpowered, continuous and non-invasive monitoring of IOP.
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| 5. |
- Bi, Cheng, et al.
(författare)
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Experimental grazer exclusion increases pollination reliability and influences pollinator-mediated plant-plant interactions in tibetan alpine meadows
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Ingår i: Alpine Botany. - 1664-2201.
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Tidskriftsartikel (refereegranskat)abstract
- 1. Co-flowering plant species often interact through shared pollinators, with effects ranging from positive (facilitation) to negative (competition). It remains unclear how this variation relates to variation in floral density, floral trait distinctiveness, and local environmental conditions. We studied the effect of grazer exclusion, a proposed local management strategy, on pollinator-mediated plant-plant interactions in heavily degraded alpine meadows of the Qinghai-Tibet Plateau. 2. We studied the effect of experimental grazer exclusion on plant reproduction and pollinator-mediated reproductive interactions quantified through pollen transfer networks. We also explored potential mechanisms of pollinator-mediated interspecific pollen transfer and its effect on plant reproductive fitness, including local floral abundance and floral trait distinctiveness among co-flowering species. 3. Grazer exclusion led to greater pollen deposition onto stigmas. The overall quantitative effects of pollinator-mediated interspecific interactions on the receptor species were mainly positive (facilitative) or neutral (with no detectable effect). The frequency of positive relative to negative quantitative effects for pairwise donor-receptor pairs tended to increase after grazer exclusion. Plants with floral traits similar to those of local ‘hub species’ appeared to benefit from pollinator-mediated interactions. 4. Our results suggest an overall positive effect of excluding grazers during the plant growing season on plant reproduction. Facilitative species interactions predominate in harsh environments such as the alpine, and the benefits of pollinator-mediated interactions among plants seemed to exceed the cost of conspecific pollen loss associated with pollinator sharing. This suggest that species invasions into alpine plant communities, an expected consequence of climate change, may not necessarily have negative effects on the reproduction of resident plant species.
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| 6. |
- Fang, Shan, et al.
(författare)
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A Dynamic Transformation Car-Following Model for the Prediction of the Traffic Flow Oscillation
- 2024
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Ingår i: IEEE Intelligent Transportation Systems Magazine. - 1939-1390 .- 1941-1197. ; 16:1, s. 174-198
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Tidskriftsartikel (refereegranskat)abstract
- Car-following (CF) behavior is a fundamental of traffic flow modeling; it can be used for the virtual testing of connected and automated vehicles and the simulation of various types of traffic flow, such as free flow and traffic oscillation. Although existing CF models can replicate the free flow well, they are incapable of simulating complicated traffic oscillation, and it is difficult to strike a balance between accuracy and efficiency. This article investigates the error variation when the traffic oscillation is simulated by the intelligent driver model (IDM). Then, it divides the traffic oscillation into four phases (coasting, deceleration, acceleration, and stationary) by using the space headway of multiple steps. To simulate traffic oscillation between multiple human-driven vehicles, a dynamic transformation CF model is proposed, which includes the long-time prediction submodel [modified sequence-to-sequence (Seq2seq)] model, short-time prediction submodel (Transformer), and their dynamic transformation strategy]. The first submodel is utilized to simulate the coasting and stationary phases, while the second submodel is utilized to simulate the acceleration and deceleration phases. The results of experiments indicated that compared to K-nearest neighbors, IDM, and Seq2seq CF models, the dynamic transformation CF model reduces the trajectory error by 60.79–66.69% in microscopic traffic flow simulations, 7.71–29.91% in mesoscopic traffic flow simulations, and 1.59–18.26% in macroscopic traffic flow simulations. Moreover, the runtime of the dynamic transformation CF model (Inference) decreased by 14.43–66.17% when simulating the large-scale traffic flow.
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| 7. |
- Jiang, Wei, et al.
(författare)
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Rapid manoeuvre of fan worms (Annelida: Sabellidae) through tubes
- 2023
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Ingår i: Journal of Experimental Biology. - 0022-0949. ; 226:9
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Tidskriftsartikel (refereegranskat)abstract
- Multiple variables determine the success of an escape response of an animal, and the rapidity of the escape manoeuvre is often the most important. Fan worms (Annelida: Sabellidae) can rapidly withdraw their tentacles, which are covered in heavily ciliated ramifications called pinnules, into their tubes to protect them from approaching threats. Here, we explore the dynamic and mechanistic features behind this escape manoeuvre. The escape responses of fan worms were recorded by high-speed videography and quantified by computerized motion analysis, showing an ultrahigh retraction speed of 272 ±135 mm s−1 (8±4 body lengths s−1). We found that fan worms possess powerful muscle-driven systems, which can generate contractive forces up to 36 times their body weight. In order to achieve these rapid, forceful movements through seawater without damaging their tentacles, fan worms have developed functional morphological adaptations to reduce fluidic drag, including the flattening of their radiolar pinnules and the deformation of bodily segmental ridges. Our hydrodynamic models indicate that these mechanical processes can decrease fluidic drag by 47%, trapped mass by 75% and friction coefficient by 89%. These strategies allow fan worms to execute rapid escape responses and could inspire the design of fast in-pipe robots.
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| 8. |
- Ma, Ding, Doktorand, 1987-, et al.
(författare)
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Intra-urban scaling properties examined by automatically extracted city hotspots from street data and nighttime light imagery
- 2021
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Ingår i: Remote Sensing. - : MDPI. - 2072-4292. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- A country can be well-comprehended through its core cities. Similarly, we can learn about a city from its hotspots, as they manifest the concentration of urban infrastructures and human activities. Following this philosophy, this paper studies the intra-urban form and function from a complexity science perspective by exploring the power law distribution of hotspot sizes and related socio-economic attributes. To detect hotspots, we rely on spatial clustering of geospatial big data sets, including street data from OpenStreetMap platform and nighttime light (NTL) data from the visible infrared imaging radiometer suite (VIIRS) imagery. Unlike conventional spatial units, which are imposed by governments or authorities (such as census block), the delineation of hotspots is done in a totally bottom-up manner and, more importantly, can help us examine precisely the scaling pattern of urban morphological and functional aspects. This results in two types of urban hotspots—street-based and NTL-based hotspots—being generated across 20 major cities in China. We find that Zipf’s law of hotspot sizes (both types) holds remarkably well for each city, as do the city-size distributions at the country level, indicating a statistically self-similar structure of geographic space. We further find that the urban scaling law can be effectively detected when using NTL-based hotspots as basic units. Furthermore, the comparison between two types of hotspots enables us to gain in-depth insights of urban planning and urban economic development.
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| 9. |
- Ma, Yanjun, et al.
(författare)
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A usable selection range standard based on test suite reduction algorithms
- 2010
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Ingår i: Wuhan University Journal of Natural Sciences. - : Springer Science and Business Media LLC. - 1007-1202 .- 1993-4998. ; 15:3, s. 261-266
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we analyze the features and distinctions of 6 classical algorithms: greedy algorithm (G), greedy evolution algorithm (GE), heuristics algorithm (H), greedy heuristic G (GRE), integer linear programming algorithm (ILP) and genetic algorithm (GA) to ensure the main influencing factors-the performance of algorithms and the running time of algorithms. What's more, we would not only present a research design that aims at gaining deeper understanding about the algorithm classification and its function as well as their distinction, but also make an empirical study in order to obtain a practical range standard that can guide the selection of reduction algorithms. When the size of a test object (product of test requirements and test cases) is smaller than 2000×2000, G algorithm is the commonly recommended algorithm. With the growth of test size, the usage of GE and GRE becomes more general.
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| 10. |
- Qiu, Yizhi, et al.
(författare)
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Proximity to oilseed rape fields affects plant pollination and pollinator-mediated selection on a co-flowering plant on the Tibetan Plateau
- 2023
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Ingår i: Evolutionary Applications. - : Wiley. - 1752-4571. ; 16:4, s. 814-823
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Tidskriftsartikel (refereegranskat)abstract
- The ecological effects of mass-flowering crops on pollinator abundance and species richness of neighbouring habitats are well established, yet the potential evolutionary consequences remain unclear. We studied effects of proximity to a mass-flowering crop on the pollination of local co-flowering plants and on patterns of natural selection on a pollination-generalised plant on the Tibetan Plateau. We recorded pollinator visitation rates and community composition at different distances (near vs. far) to oilseed rape (Brassica napus) fields in two habitat types and quantified pollinator-mediated selection on attractive traits of Trollius ranunculoides. The proximity to oilseed rape increased pollinator visitation in neighbouring alpine meadows and changed pollinator composition in neighbouring shrub meadows. Trollius ranunculoides in the alpine meadow near oilseed rape received three times more pollinator visits (mainly bees) and consequently had a 16.5% increase in seed set but also received slightly more heterospecific pollen per stigma. In contrast, pollinator visitation to T. ranunculoides in the shrub meadow near oilseed rape was three times lower (mainly flies), leading to a 10.7% lower seed despite no effect on pollen deposition. The proximity to the oilseed rape field intensified pollinator-mediated selection on flower size and weakened selection on flower height of T. ranunculoides in the alpine meadow but did not affect phenotypic selection on either trait in the shrub meadow. Our study highlights context-dependent variation in plant–pollinator interactions close to mass-flowering oilseed rape, suggesting potential effects on the evolution of flower traits of native plants through altered pollinator-mediated selection. However, context dependence may make these effects difficult to predict.
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| 11. |
- 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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| 12. |
- Wang, Zhen, et al.
(författare)
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Modeling and field experiments on autonomous vehicle lane changing with surrounding human-driven vehicles
- 2021
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Ingår i: Computer-Aided Civil and Infrastructure Engineering. - : Wiley. - 1093-9687 .- 1467-8667. ; 36:7, s. 877-889
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Tidskriftsartikel (refereegranskat)abstract
- Autonomous vehicle (AV) technology is widely studied in both industrial and academic communities since it is regarded as a promising means for improving transportation safety and efficiency. Lane changing is a critical link for higher-level AV operations. However, few studies on AV lane changing consider the dynamics of surrounding vehicles, particularly in a mixed traffic environment including human-driven vehicles (HVs). Therefore, this article presents a dynamic lane-changing model for AV incorporating human driver behavior in mixed traffic. The proposed model includes four key components: car following (and lane keeping), lane-changing decision, dynamic trajectory generation, and model predictive control (MPC)-based trajectory tracking. AV longitudinal control algorithm is also depicted in detail in this article. Field experiments are conducted on a large-scale test track to test and validate the proposed model. An AV and three HVs are used in the lane-changing experiments. Different human driver behaviors are considered in the experiment settings. Experimental results show that the proposed lane-changing model can complete lane-changing maneuvers efficiently when HVs are cooperative and can also robustly abort them when HVs are uncooperative. Compared with the measured human lane-changing maneuvers, AV lane-changing maneuvers from the proposed model are more comfortable and safer.
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| 13. |
- Xu, Zhigang, et al.
(författare)
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Modeling Relationship between Truck Fuel Consumption and Driving Behavior Using Data from Internet of Vehicles
- 2018
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Ingår i: Computer-Aided Civil and Infrastructure Engineering. - : Wiley. - 1093-9687 .- 1467-8667. ; 33:3, s. 209-219
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Tidskriftsartikel (refereegranskat)abstract
- In this research, by taking advantage of dynamic fuel consumption–speed data from Internet of Vehicles, we develop two novel computational approaches to more accurately estimate truck fuel consumption. The first approach is on the basis of a novel index, named energy consumption index, which is to explicitly reflect the dynamic relationship between truck fuel consumption and truck drivers’ driving behaviors obtained from Internet of Vehicles. The second approach is based on a Generalized Regression Neural Network model to implicitly establish the same relationship. We further compare the two proposed models with three well-recognized existing models: vehicle specific power (VSP) model, Virginia Tech microscopic (VT-Micro) model, and Comprehensive Modal Emission Model (CMEM). According to our validations at both microscopic and macroscopic levels, the two proposed models have stronger performed in predicting fuel consumption in new routes. The models can be used to design more energy-efficient driving behaviors in the soon-to-come era of connected and automated vehicles.
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| 14. |
- 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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| 15. |
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| 16. |
- 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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