| 1. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 2. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 3. |
- Gong, Ze, et al.
(författare)
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The Association Between Quadriceps Strength and Synovitis in Knee Osteoarthritis : An Exploratory Study From the Osteoarthritis Initiative
- 2023
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Ingår i: The Journal of rheumatology. - : The Journal of Rheumatology. - 0315-162X .- 1499-2752. ; 50:4, s. 548-555
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The aim of this study was to explore the association between quadriceps strength and synovitis in knee osteoarthritis (KOA). METHODS: This study was derived from the Osteoarthritis Initiative (OAI), which recruited adults from the OAI cohort with or at risk of KOA. Knees with complete records of isometric quadriceps strength and effusion-synovitis and Hoffa-synovitis assessments were included. Quadriceps strength was measured isometrically at baseline. Effusion-synovitis and Hoffa-synovitis were measured using the Magnetic Resonance Imaging Osteoarthritis Knee Score at baseline and at 1-year and 2-year follow-ups. Generalized estimating equations were used to analyze the associations of baseline quadriceps strength with changes in effusion-synovitis and Hoffa-synovitis in multivariable analyses. Additionally, analyses were stratified by synovitis-driven inflammatory phenotypes. RESULTS: A total of 1513 knees were included in this study. In total, 61% of the subjects were female; subjects had an average age of 61.9 (SD 8.8) years and a mean BMI of 29.4 (SD 4.7). Regarding the whole population, baseline quadriceps strength was negatively associated with baseline effusion-synovitis and follow-up changes in effusion-synovitis (odds ratio [OR] 0.77-0.86), but no significant association was observed in terms of Hoffa-synovitis. Stratified by synovitis-driven inflammatory phenotype, baseline quadriceps strength was significantly associated with follow-up changes in effusion-synovitis-but not in Hoffa-synovitis-in the population with existing effusion-synovitis (OR 0.75-0.79). CONCLUSION: Higher baseline quadriceps strength was negatively associated with changes in effusion-synovitis-but not in Hoffa-synovitis-especially in the population with existing effusion-synovitis. Our findings suggested a potential protective role of the quadriceps in effusion-synovitis.
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| 4. |
- Liu, Shiping, et al.
(författare)
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Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears
- 2014
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 157:4, s. 785-794
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Tidskriftsartikel (refereegranskat)abstract
- Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.
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| 5. |
- Buchholz, Angela, et al.
(författare)
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Insights into the O : C-dependent mechanisms controlling the evaporation of alpha-pinene secondary organic aerosol particles
- 2019
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 19:6, s. 4061-4073
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Tidskriftsartikel (refereegranskat)abstract
- The volatility of oxidation products of volatile organic compounds (VOCs) in the atmosphere is a key factor to determine if they partition into the particle phase contributing to secondary organic aerosol (SOA) mass. Thus, linking volatility and measured particle composition will provide insights into SOA formation and its fate in the atmosphere. We produced alpha-pinene SOA with three different oxidation levels (characterized by average oxygen-to-carbon ratio; (O:C) over bar = 0.53, 0.69, and 0.96) in an oxidation flow reactor. We investigated the particle volatility by isothermal evaporation in clean air as a function of relative humidity (RH < 2 %, 40 %, and 80 %) and used a filter-based thermal desorption method to gain volatility and chemical composition information. We observed reduced particle evaporation for particles with increasing <(O:C )over bar> ratio, indicating that particles become more resilient to evaporation with oxidative aging. Particle evaporation was increased in the presence of water vapour and presumably particulate water; at the same time the resistance of the residual particles to thermal desorption was increased as well. For SOA with (O:C ) over bar = 0.96, the unexpectedly large increase in mean thermal desorption temperature and changes in the thermogram shapes under wet conditions (80 % RH) were an indication of aqueous phase chemistry. For the lower (O:C ) over bar cases, some water-induced composition changes were observed. However, the enhanced evaporation under wet conditions could be explained by the reduction in particle viscosity from the semi-solid to liquid-like range, and the observed higher desorption temperature of the residual particles is a direct consequence of the increased removal of high-volatility and the continued presence of low-volatility compounds.
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| 6. |
- Gong, Zijun, et al.
(författare)
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A Machine Learning-Based Approach for Auto-Detection and Localization of Targets in Underwater Acoustic Array Networks
- 2020
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Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; 69:12, s. 15857-15866
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Tidskriftsartikel (refereegranskat)abstract
- The localization and tracking of underwater objects have many applications. In a proactive underwater sensor array, some nodes will periodically broadcast linear frequency modulated (LFM) signals, which will hit the targets, get reflected and received by the other nodes. Depending on the target's position and velocity, the received signals will also be LFM signals of different frequencies and frequency rates. We can use the Fractional Fourier Transform (FrFT) to analyze the received signal's spectrum and find the peak. Based on the location of the peak, the target's distance and radial velocity can be estimated. However, the accuracy is highly dependent on the sampling interval of the spectrum. Smaller sampling interval leads to higher accuracy but also induces considerable complexity. To overcome this issue, we propose a machine learning-based approach to automatically detect the existence of the target, and roughly estimate the peak's location if targets exist. Then over-sampling can be conducted for a small area around the peak, leading to improved accuracy and reduced complexity. The idea is based on the following observation: if a target exists, we will be able to observe an "X" pattern on the spectrum. Extensive simulations are conducted to verify the effectiveness of the proposed architecture.
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| 7. |
- Gong, Zijun, et al.
(författare)
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Data-Aided Doppler Compensation for High-Speed Railway Communications over mmWave Bands
- 2021
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Ingår i: IEEE Transactions on Wireless Communications. - 1558-2248 .- 1536-1276. ; 20:1, s. 520-534
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Tidskriftsartikel (refereegranskat)abstract
- IEEE Millimeter wave communications show great potentials in many applications, one of which is the high-speed railway (HSR) communication system. However, a major challenge is the Doppler effect caused by the relative-movement between the train and the base station (BS), which leads to fast channel variation. To compensate for the Doppler shift, an accurate channel model is indispensable, and the far-field channel model is generally employed, which assumes that the dimensions of the antenna arrays are negligible compared to the distance between transmitter and receiver. This model is widely used in Cellular systems, but the underlining assumption is not always true for railway communication systems. In this paper, the modeling of the Doppler effect for millimeter wave in HSR communications is conducted, and data-aided Doppler estimation and compensation algorithms are designed based on the new model. We show that the conventional far-field channel model is based on the first-order Taylor expansion of the actually channel, and the second-order component cannot be ignored for HSR communications. Extensive simulations are conducted to verify the validity of the new model and the effectiveness of the proposed algorithms.
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| 8. |
- Gong, Zijun, et al.
(författare)
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Simultaneous Localization and Communications With Massive MIMO-OTFS
- 2023
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Ingår i: IEEE Journal on Selected Areas in Communications. - Piscataway, NJ : IEEE. - 0733-8716 .- 1558-0008. ; 41:12, s. 3908-3924
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Tidskriftsartikel (refereegranskat)abstract
- Next generation cellular network is expected to provide the simultaneous high-accuracy localization and ultra-reliable communication services, even in high mobility scenarios. To that end, the novel orthogonal time frequency space (OTFS) modulation has been developed as a promising physical-layer transmission technique, evident by the outstanding performance in terms of robustness against time-frequency selective fading over the orthogonal frequency division multiplexing (OFDM) counterpart. However, when OTFS meets massive multiple-input multiple-output (MIMO), the specific conditions, under which the delay-Doppler (DD) domain channel model holds, are not identified. In addition, the channel estimation and localization performance in such system is rarely studied. In this work, we target at these new challenges, and conduct comprehensive modelling, performance analysis, and algorithm design for massive MIMO-OTFS based simultaneous localization and communications. Specifically, we derive new channel models for the massive MIMO-OTFS system, which captures both time-frequency dispersion and spatial wideband effects. The specific conditions, under which the new models hold has been unveiled as well. Based on the new models, we establish the theoretical foundations for channel estimation and localization, by deriving the Cramer-Rao lower bounds of channel parameter and location estimation errors. Such bounds have been achieved with the newly designed low-complexity channel estimation and localization algorithms. Numerical simulations of the proposed framework with prevailing pulse functions are also conducted and the results validate the proposed designs and analysis. © 1983-2012 IEEE.
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| 9. |
- Gong, Zijun, et al.
(författare)
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Smart AUV-Assisted Localization and Time Synchronization of Underwater Acoustic Devices
- 2022
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Ingår i: Smart Ships. - Boca Raton : CRC Press. - 9781003025924 ; , s. 133-168
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The localization and time synchronization of Underwater Acoustic Devices (UADs) have many potential applications in industry and scientific research. This can be done by deploying location-aware fixed anchors on the sea surface or bottom. However, this solution has poor accuracy and induces huge costs. In recent years, with the surge of Autonomous Underwater Vehicles (AUVs), the possibility of employing smart AUVs as mobile anchors have been extensively discussed. In this chapter, three smart AUV-assisted underwater localization and time synchronization techniques will be introduced, based on ToA (Time of Arrival), Doppler shift, and linear frequency modulated signals. The system model will be presented in detail, and the corresponding algorithms will be briefly discussed. For each of them, some preliminary numerical evaluations are conducted to directly show their performance.
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| 10. |
- Su, Ruoyu, et al.
(författare)
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A Mobile Node Assisted Localization System for Wireless Sensor Networks
- 2021
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Ingår i: IWCMC 2021: 2021 17TH INTERNATIONAL WIRELESS COMMUNICATIONS & MOBILE COMPUTING CONFERENCE (IWCMC). - 2376-6492. - 9781728186160 ; , s. 1716-1720
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Konferensbidrag (refereegranskat)abstract
- Wireless sensor network (WSN), consisting of several sensor nodes, is one of the most promising technologies emerged in the past decade. The positioning system for WSN is particularly meaningful and widely used in the military surveillance, air-sea rescue, traffic monitoring, and etc. However, the traditional positioning system always suffers from deployment and maintenance of anchors. In this paper, we propose a positioning system employing a Raspberry Pi platform attached to a DJI drone as a mobile anchor. The DJI drone can serve as multiple virtual anchors by moving and broadcasting its location information periodically. Thus, it is possible to localize sensor node by itself when the sensor node collects the drone's position. A Gauss-Newton method is applied to improve the accuracy of the proposed positioning system. We also elaborate the adaption of the Gauss-Newton method with the geodetic coordinates. The goal of the proposed positioning system is to achieve higher accuracy and higher coverage at lower cost.
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