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| 1 | Space-Air-Ground Integrated Network (SAGIN) for 6G: Requirements, Architecture and Challenges显示文摘As the fifth-generation(5G)mobile communication network may not meet the requirements of emerging technologies and applications,including ubiquitous coverage,industrial internet of things(IIoT),ubiquitous artificial intelligence(AI),digital twins(DT),etc.,this paper aims to explore a novel space-air-ground integrated network(SAGIN)architecture to support these new requirements for the sixth-generation(6G)mobile communication network in a flexible,low-latency and efficient manner.Specifically,we first review the evolution of the mobile communication network,followed by the application and technology requirements of 6G.Then the current 5G non-terrestrial network(NTN)architecture in supporting the new requirements is deeply analyzed.After that,we proposes a new flexible,low-latency and flat SAGIN architecture,and presents corresponding use cases.Finally,the future research directions are discussed. | Huanxi Cui Jun Zhang Yuhui Geng Zhenyu Xiao Tao Sun Ning Zhang Jiajia Liu Qihui Wu Xianbin Cao | 2022 | China Communications2022，19，2： | 11 |
| 2 | Distributed learning particle swarm optimizer for global optimization of multimodal problems显示文摘 | Geng ZHANG Yangmin LI Yuhui SHI | 2018 | Frontiers of Computer Science2018，12，1： | 5 |
| 3 | Crystal structure of the African swine fever virus structural protein p35 reveals its role for core shell assembly显示文摘Dear Editor,The African swine fever(ASF)is a highly contagious hemorrhagic and lethal disease in domestic pigs.The ASF outbreaks of in many Asia countries,including China,Vietnam,Mongolia,and South Korea,have posed a huge threat to the pig indusry.In the attempt to stop ASF from spreading further in China's Mainland,more than 10 million pigs have been culled since August 2018.The causative agent for ASF is a DNA virus,African swine fever virus(ASFV).Although this deadly disease has been reported in Kenya nearly one hundred years ago,there has been no vaccine for protection from ASFV infection or effective treatments to cure ASF until now. | Guobang Li Dan Fu Guangshun Zhang Dongming Zhao Mingyu Li Xue Geng Dongdong Sun Yuhui Wang Cheng Chen Peng Jiao Lin Cao Yu Guo Zihe Rao | 2020 | Protein & Cell2020，11，8： | 3 |
| 4 | Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea显示文摘Agrocybe cylindracea,an edible mushroom,is widely cultivated for its abundance of nutrients and flavor,and many of its metabolites are reported to have beneficial roles,such as medicinal effects on tumors and chronical illnesses.However,the lack of genomic information has hindered further molecular studies on this fungus.Here,we present a genome assembly of A.cylindracea together with comparative genomics and pathway analyses of Agaricales species.The draft,generated from both next-generation sequencing(NGS)and single-molecule real-time(SMRT)sequencing platforms to overcome high genetic heterozygosity,is composed of a56.5 Mb sequence and 15,384 predicted genes.This mushroom possesses a complex reproductive system,including tetrapolar heterothallic and secondary homothallic mechanisms,and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources.Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances,including B vitamins,unsaturated fatty acids,and N-acetylglucosamine.RNA-seq data show that A.cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage,whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis.These results reflect diverse functions of the two anatomical structures of the fruiting body.Our comprehensive genomic and transcriptomic data,as well as preliminary comparative analyses,provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components. | Yuan Liang Dengxue Lu Sen Wang Yuhui Zhao Shenghan Gao Rongbing Han Jun Yu Weili Zheng Jianing Geng Songnian Hu | 2020 | Genomics, Proteomics & Bioinformatics2020，18，3： | 2 |
| 5 | A noise and artifact suppression using resampling(NASR)method to facilitate de novo protein structure determination显示文摘Background The search of heavy atoms is crucial to the de novo determination of protein structures.Typically,the difference Patterson map is calculated as a first step to solve substructure.However,the pseudo-peaks and noises inherent in such maps arising from the high symmetry and large size of protein structures accompanied with the data collection errors inevitably pose a challenge in accurate real space-based substructure determination.Purpose In order to mitigate such pseudo-peaks and noises and further improve signal-to-noise ratio(SNR)of the difference Patterson map,the noise and artifact suppression using resampling(NASR)method originally proposed in nuclear magnetic resonance is introduced into protein crystallography in this work to optimize the difference Patterson map.Methods The NASR method makes use of the statistical learning theory,which in this work repeatedly samples a fixed portion of diffraction data(sub-dataset)randomly followed by a statistical analysis of the multiple calculated difference Patterson maps to discard pseudo-peaks and noises.Its feasibility is based on the fact that the true vector peaks of the heavy atoms keep static in the multiple random sub-datasets,whereas the pseudo-peaks and noises fluctuate remarkably.And the key of this method lies in the design of a weighting function to distinguish true vector peaks from pseudo-peaks and noises,as well as a proper selection of the parameters associated with the function.Results The introduced NASR method is both numerically and experimentally demonstrated to be feasible in suppressing spurious peaks and non-correlative noises intrinsic to the difference Patterson maps.As a result,the SNR of the difference Patterson maps can be enhanced to some extent to facilitate real space-based substructure determination.Conclusion It is therefore anticipated that the proposed method may provide a meaningful insight into how to denoise the difference Patterson maps,which in turn assists in locating heavy atoms and further facilitates de novo protein structure determination. | Menglu Hu Zengqiang Gao Qiang Zhou Zhi Geng Yuhui Dong | 2019 | Radiation Detection Technology and Methods2019，3，3： | 1 |
| 6 | Identification and characterization of MeERF genes and their targets in pathogen response by cassava(Manihot esculenta)显示文摘Cassava,Manihot esculenta Crantz (Me),is a major dietary source of calories for over 700 million people in tropical regions.The production of cassava is constantly threatened by cassava bacterial blight (CBB),caused by Xanthomonas axonopodis pv.manihotis (Xam).The gene resources for CBB-resistant breeding of cassava are limited.In model plant species,ethylene response factors play important roles in response to pathogen infection.In this study,cassava ethylene response factors (MeERFs) were identified and characterized as the first step in studying their potential for CBB-resistant breeding of cassava.In the cassava genome 155 MeERFs were identified,of which 23 were induced by Xam infection.The promoter regions of204 genes harbored GCC-box that had the potential to interact with MeERFs.Using 37 transcriptomes derived from Xam infection treatment,four gene co-expression modules for the MeERFs and GCC-box containing genes were constructed.Six MeERFs were associated with two GCC-box containing genes:transcription initiation factor TFIIE subunit beta (MeTFIIE),and histone-lysine N-methyltransferase ASHR1 (MeASHR1).Dual-luciferase reporter assays showed that MeERF10 and MeERF58 positively regulated Me TFIIE;MeERF137 negatively regulated Me TFIIE;MeERF10 and MeERF137 positively regulated Me ASHR1;and MeERF35 negatively regulated Me ASHR1.The four MeERFs may mediate pathogen response by regulating the expression of the two GCC-box containing genes. | Yuhui Hong Yong Xiao Na Song Shousong Zhu Rui Zhao Ke Li Mengting Geng Xiaohui Yu Honggang Wang Wei Xia Yinhua Chen | 2021 | The Crop Journal2021，9，5： | 1 |
| 7 | Intra-host Ebola viral adaption during human infection显示文摘The onsite next generation sequencing(NGS)of Ebola virus(EBOV)genomes during the 2013–2016 Ebola epidemic in Western Africa provides an opportunity to trace the origin,transmission,and evolution of this virus.Herein,we have diagnosed a cohort of EBOV patients in Sierra Leone in 2015,during the late phase of the outbreak.The surviving EBOV patients had a recovery process characterized by decreasing viremia,fever,and biochemical parameters.EBOV genomes sequenced through the longitudinal blood samples of these patients showed dynamic intra-host substitutions of the virus during acute infection,including the previously described short stretches of 13 serial TNC mutations.Remarkably,within individual patients,samples collected during the early phase of infection possessed Ts at these nucleotide sites,whereas they were replaced by Cs in samples collected in the later phase,suggesting that these short stretches of TNC mutations could emerge independently.In addition,up to a total of 35 nucleotide sites spanning the EBOV genome were mutated coincidently.Our study showed the dynamic intra-host adaptation of EBOV during patient recovery and gave more insight into the complex EBOV-host interactions. | William JLiu Weifeng Shi Wuyang Zhu Cong Jin Shumei Zou Ji Wang Yuehua Ke Xiaofeng Li Mi Liu Tao Hu Hang Fan Yigang Tong Xiang Zhao Wenbin Chen Yuhui Zhao Di Liu Gary Wong Chengchao Chen Chunyu Geng Weiwei Xie Hui Jiang Idrissa Laybor Kamara Abdul Kamara Matt Lebby Brima Kargbo Xiangguo Qiu Yu Wang Xiaofeng Liang Mifang Liang Xiaoping Dong Guizhen Wu George F.Gao Yuelong Shu | 2019 | Biosafety and Health2019，1，1： | 1 |
| 8 | The Association Between H3K4me3 and Antisense Transcription显示文摘Histone H3 lysine 4 trimethylation(H3K4me3) is well known to occur in the promoter region of genes for transcription activation.However,when investigating the H3K4me3 profiles in the mouse cerebrum and testis,we discovered that H3K4me3 also has a significant enrichment at the 3 0 end of actively transcribed(sense) genes,named as 3 0-H3K4me3.3 0-H3K4me3 is associated with 15% of protein-coding genes in both tissues.In addition,we examined the transcriptional initiation signals including RNA polymerase II(RNAPII) binding sites and 5 0-CAGE-tag that marks transcriptional start sites.Interestingly,we found that 3 0-H3K4me3 is associated with the initiation of antisense transcription.Furthermore,3 0-H3K4me3 modification levels correlate positively with the antisense expression levels of the associated sense genes,implying that 3 0-H3K4me3 is involved in the activation of antisense transcription.Taken together,our findings suggest that H3K4me3 may be involved in the regulation of antisense transcription that initiates from the 3 0 end of sense genes.In addition,a positive correlation was also observed between the expression of antisense and the associated sense genes with 3 0-H3K4me3 modification.More importantly,we observed the 3 0-H3K4me3 enrichment among genes in human,fruitfly and Arabidopsis,and found that the sequences of 3 0-H3K4me3-marked regions are highly conserved and essentially indistinguishable from known promoters in vertebrate.Therefore,we speculate that these 3 0-H3K4me3-marked regions may serve as potential promoters for antisense transcription and 3 0-H3K4me3 appear to be a universal epigenetic feature in eukaryotes.Our results provide a novel insight into the epigenetic roles of H3K4me3 and the regulatory mechanism of antisense transcription. | Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Feng Ding Chengqi Xin Jianing Geng Shuhui Song Fanglin Sun Songnian Hu Jun Yu | 2012 | Genomics, Proteomics & Bioinformatics2012，10，2： | 1 |
| 9 | Boosting fire safety and mechanical performance of thermoplastic polyurethane by the face-to-face two-dimensional phosphorene/MXene architecture显示文摘Black phosphorus(BP), as one of the most promising fillers for flame retarding polymer, has been seriously limited in practical application, due to the agglomeration and poor structural stability challenges.Here, the BP was modified by MXene and polydopamine(PDA) via ultrasonication and dopamine modification strategy to improve the structural stability and dispersibility in the matrix. Then, the obtained(BP-MXene@PDA) nanohybrid was employed to promote the mechanical performance, thermal stability,and flame retardancy of thermoplastic polyurethane elastomer(TPU). The resultant TPU composite containing 2 wt.% of BP1-MXene2@PDA showed a 19.2% improvement in the tensile strength and a 13.8%increase in the elongation at break compared to those of the pure TPU. The thermogravimetric analysis suggested that BP-MXene@PDA clearly enhances the thermal stability of TPU composites. Furthermore,the introduction of the BP-MXene@PDA nanohybrids could considerably improve the flame retardancy of TPU composite, i.e., 64.2% and 27.3% decrease in peak heat release rate and total heat release, respectively. The flame-retardant mechanisms of TPU/BP-MXene@PDA in the gas phase and condensed phase were investigated systematically. This work provides a novel strategy to simultaneously enhance the fire safety and mechanical properties of TPU, thus expanding its industrial applications. | Yong Luo Yuhui Xie Wei Geng Junhan Chu Hua Wu Delong Xie Xinxin Sheng Yi Mei | 2022 | Journal of Materials Science & Technology2022，，34： | 1 |
| 10 | Network Element Placement for Space-Air-Ground Integrated Network:A Tutorial显示文摘With the demand for Internet connectivity in remote areas,the space-air-ground integrated network(SAGIN)was proposed to achieve ubiquitous coverage and enhance service capabilities of extant terrestrial networks.The paradigm of virtual network element placement(NEP)is applied into SAGIN.It can save energy and operating costs by placing specific network elements(NEs)as software instances.In addition,it helps to provide services in end-to-end networks with its ability to allocate and manage resources flexibly.However,NEP faces some challenges in SAGIN.The network topologies can be dynamic,and links such as the satellite-to-ground and air-to-ground ones are prone to fail.These will make NEP management more complicated.Moreover,the static NEP schemes are hard to accommodate the time-varying traffic.In this context,this work explains the NEP problem in SAGIN from three aspects,i.e.,the SAGIN radio access network(RAN),the SAGIN core network(CN),and the SAGIN barrier network(BN).First,the physical and networking architectures of SAGIN are introduced.Then the status of the network element placement and corresponding challenges are described from these two aspects.Finally,this paper discusses future research directions and key technical challenges. | GENG Yuhui CAO Xianbin CUI Huanxi XIAO Zhenyu | 2022 | Chinese Journal of Electronics2022，31，6： | 0 |
| 11 | An ultra-low concentration electrolyte with fluorine-free bulky anions for stable potassium metal batteries显示文摘Potassium metal battery is a promising alternative to Li-ion battery for large-scale energy storage due to the abundant potassium resources and high energy density.However,it suffers from rapid capacity fading and safety issues due to the uncontrolled dendrite growth.Herein,we design a fluorine-free ultra-low concentration electrolyte(ULCE)with the super bulky[BPh_(4)]^(−) anions for stable potassium metal battery.In this special electrolyte,the migration rate of K+in the electrolyte is about six times faster than that of the[BPh_(4)]^(−) anions because of the super bulky structure of the[BPh_(4)]^(−) anions,thus resulting in a high K^(+)transference number of 0.76.This high transference number can effectively make up for the deficiency of K^(+)in ULCE for ensuring the normal operation of the potassium metal battery.In addition,the improved transference number can also promote the uniform distribution of K^(+)flux on the surface of the K metal anode,resulting in uniform K deposition.As a result,this electrolyte achieves a high K plating/stripping Coulombic efficiency of 92.6%over 200 cycles and a stable discharging/charging for 100 cycles under the full battery configuration(K used as the anode and perylene-3,4,9,10-tetracarboxylic dianhydride used as the cathode). | Qinguang Liu Mei Geng Ting Yu Li Zhang Changdong Wu Jie Liu Shulin Zhao Qingxin Yang Robin Song Jingjuan Ye Fenfen Wang Yuping Wu Dengji Xiao Yuhui Chen | 2023 | Nano Research2023，16，6： | 0 |
| 12 | Electron densitymap evaluation functions for determining the quality of protein crystal structures显示文摘Background Finding methods to judge the quality of X-ray crystallographic information is an active research topic.The quality of electron density maps reconstructed by Fourier transform is always limited by the finite resolution,the amplitude/phase error and the completeness of diffraction data.At present,the R value and effective resolution are common ways of evaluating the quality of electron density maps.Unfortunately,the current evaluation methods are only dependent on diffraction amplitude,without any phase information.Methods Advanced evaluation functions in real space are designed to estimate the electron density map quality.The electron density map definition evaluation function relies on the atomicity of the electron density distribution.We use the power spectrum electron density entropy in protein crystallography for the first time.These two functions include both structure factor amplitudes and phases via the Fourier transform of electron density map.Results We carry out tests on synthetic data sets of known structures,varying the resolution and error,and draw the quality curves of electron density maps with theoretical,noisy and experimental diffraction data by two evaluation functions at different resolutions.The curves reveal the optimum structure and resolution of proteins clearly.Conclusions The work presented here offers new methods to evaluate the qualities of the electron density maps of proteins with slight differences,and brand new indicators to select the optimum diffraction resolution of protein structures. | Tianyi Zhang Zhi Geng Heng Zhang Liang Zhou Yuhui Dong | 2018 | Radiation Detection Technology and Methods2018，2，2： | 0 |
| 13 | Service Function Chain Migration in LEO Satellite Networks显示文摘With the advancements of software defined network(SDN)and network function virtualization(NFV),service function chain(SFC)placement becomes a crucial enabler for flexible resource scheduling in low earth orbit(LEO)satellite networks.While due to the scarcity of bandwidth resources and dynamic topology of LEO satellites,the static SFC placement schemes may cause performance degradation,resource waste and even service failure.In this paper,we consider migration and establish an online migration model,especially considering the dynamic topology.Given the scarcity of bandwidth resources,the model aims to maximize the total number of accepted SFCs while incurring as little bandwidth cost of SFC transmission and migration as possible.Due to its NP-hardness,we propose a heuristic minimized dynamic SFC migration(MDSM)algorithm that only triggers the migration procedure when new SFCs are rejected.Simulation results demonstrate that MDSM achieves a performance close to the upper bound with lower complexity. | Geng Yuhui Wang Niwei Chen Xi Xu Xiaofan Zhou Changsheng Yang Junyi Xiao Zhenyu Cao Xianbin | 2024 | China Communications2024，21，3： | 0 |
| 14 | An iterative refinement method combining detector geometry optimization and diffraction model refinement in serial femtosecond crystallography显示文摘Background Recent advances in serial femtosecond crystallography(SFX)using X-ray free electron lasers(XFELs)have facilitated accurate structure determination for biological macromolecules.However,given the many fluctuations inherent in SFX,the acquisition of SFX data of sufficiently high quality still remains challenging.Method Aimed at enhancing the accuracy of SFX data,this study proposes an iterative refinement method to optimally match pairs of the observed and predicted reflections on the detector plane.This method features a combination of detector geometry optimization and diffraction model refinement in an alternate manner,concomitant with a cycle-by-cycle peak selection procedure.Result To demonstrate whether this iterative method is convergent and feasible,both numerical simulations and experimental tests have been performed.The results reveal that this method can gradually improve overall quality of the integrated SFX data and therefore accelerate the convergence of Monte Carlo integration,while simultaneously suppressing correlations inherent in certain parameters and precluding outliers to some extent during the refinement.Conclusion We have demonstrated that our iterative refinement method is applicable to both simulated and experimental SFX data.It is expected that this method could provide meaningful insights into the refinement of SFX data and take the step forward toward more accurate Monte Carlo integration. | Zhi Geng Menglu Hu Zhun She Qiang Zhou Zengqiang Gao Yuhui Dong | 2018 | Radiation Detection Technology and Methods2018，2，1： | 0 |
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