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Journal of Integrative Plant Biology 2020年第2期62卷 201-217页

作者： Pengfei Dong Xiaoyu Tu Haoxuan Li Jianhua Zhang Donald Grierson Pinghua Li Silin Zhong State Key Laboratory of Agrobiotechnology School of Life SciencesThe Chinese University of Hong KongHong KongChina Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology Zhejiang UniversityHangzhou 310058China State Key Laboratory of Crop Biology College of AgronomyShandong Agricultural UniversityTai’an 271018China

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation,which is best studied in the mammalian models.Using in situ Hi-C,we have compared the 3D chromatin architectures of rice mesophyll and endosperm,foxtail millet bundle sheath and mesophyll,and maize bundle sheath,mesophyll and endosperm tissues.We found that their global A/B compartment partitions are stable across tissues,while local A/B compartment has tissue-specific dynamic associated with differential gene expression.Plant domains are largely stable across tissues,while new domain border formations are often associated with transcriptional activation in the region.Genes inside plant domains are not conserved across species,and lack significant co-expression behavior unlike those in mammalian TADs.Although we only observed chromatin loops between gene islands in the large genomes,the maize loop gene pairs’syntenic orthologs have shorter physical distances in small genome monocots,suggesting that loops instead of domains might have conserved biological function.Our study showed that plants’chromatin features might not have conserved biological functions as the mammalian ones.

关键词： plant chromatin domains Tissue-specific Hi-C analyses rice

Bioinformatics analyses of differentially expressed genes associated with spinal cord injury:a microarray-based analysis in a mouse model

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Neural Regeneration Research 2019年第7期14卷 1262-1270页

作者： Lei Guo Jing Lv Yun-Fei Huang Ding-Jun Hao Ji-Jun Liu Department of Spinal Surgery Honghui HospitalXi'an Jiaotong University Department of Clinical Laboratory Honghui HospitalXi'an Jiaotong University

Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P < 0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at28 days after spinal cord injury.These key genes screened by bioin

关键词： nerve regeneration spinal cord injury differentially expressed genes bioinformatics analyses Database for Annotation,Visualization and Integrated Discovery analysis inflammation Kyoto Encyclopedia of Genes and Genomes pathway microarray transcription factors neural regeneration

Mathematical analyses of the GPS receiver interference tolerance and mean time to loss lock

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Defence Technology（防务技术） 2019年第3期15卷 440-449页

作者： Ehab M.Shaheen Sherif A.Elgamel Electronic Warfare Department Military Technical College

In this paper, novel mathematical expressions are derived for the Global Positioning System (GPS) receiver interference tolerance in the presence of different types of interference signals such as: continuous wave interference, narrowband interference, partial band interference, broadband interference, match spectrum interference and pulse interference. Also, in this paper the mean time to loss lock is determined in order to analyse the mentioned interferences effect on the GPS receiver. These derived analytical expressions are validated with the aid of extensive simulation experiments.

关键词： Mathematical analyses GPS receiver interference tolerance

Further analyses of variation of ribosome DNA copy number and polymorphism in ciliates provide insights relevant to studies of both molecular ecology and phylogeny

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Science China(Life Sciences) 2019年第2期62卷 203-214页

作者： Yurui Wang Chundi Wang Yaohan Jiang Laura A.Katz Feng Gao Ying Yan Institute of Evolution & Marine Biodiversity Ocean University of China Key Laboratory of Mariculture Ocean University of China Ministry of Education Department of Biological Sciences Smith College

Sequence-based approaches, such as analyses of ribosome DNA(rDNA) clone libraries and high-throughput amplicon sequencing, have been used extensively to infer evolutionary relationships and elucidate the biodiversity in microbial communities.However, recent studies demonstrate both r DNA copy number variation and intra-individual(intra-genomic) sequence variation in many organisms, which challenges the application of the rDNA-based surveys. In ciliates, an ecologically important clade of microbial eukaryotes, rDNA copy number and sequence variation are rarely studied. In the present study, we estimate the intraindividual small subunit rDNA(SSU r DNA) copy number and sequence variation in a wide range of taxa covering nine classes and 18 orders of the phylum Ciliophora. Our studies reveal that:(i) intra-individual sequence variation of SSU rDNA is ubiquitous in all groups of ciliates detected and the polymorphic level varies among taxa;(ii) there is a most common version of SSU rDNA sequence in each cell that is highly predominant and may represent the germline micronuclear template;(iii)compared with the most common version, other variant sequences differ in only 1–3 nucleotides, likely generated during macronuclear(somatic) amplification;(iv) the intra-cell sequence variation is unlikely to impact phylogenetic analyses;(v) the rDNA copy number in ciliates is highly variable, ranging from 103 to 106, with the highest record in Stentor roeselii. Overall,these analyses indicate the need for careful consideration of SSU r DNAvariation in analyses of the role of ciliates in ecosystems.

关键词： ciliates SSU rDNA sequence variation phylogenetic analyses rDNA copy number ecological significance

A glimpse of endocrine pancreas development from single-cell analyses

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Journal of Molecular Cell Biology 2019年第6期11卷 433-434页

作者： Ce Gao Jinrong Peng Nutrition College of Animal Sciences Zhejiang University Hangzhou 310058 China

Diabetes is a global public health concern in the 21st century. According to the report in the International Diabetes Federation Diabetes Atlas in 2015, 415 million adults suffer from diabetes globally. Although considerable progress has made in the treatment of diabetes, such as insulin administration, researchers are still looking for alternative therapeutic approaches, e.g. islet transplantation from cadaveric donors, for its radical cure. However, this approach is limited due to the scarcity of donors and availability of islet cells.

关键词： endocrine pancreas development single-cell analyses International Diabetes Federation Diabetes Atlas

Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses

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International Journal of Oral Science 2018年第4期10卷 263-272页

作者： Susan Yost Philip Stashenko Yoonhee Choi Maria Kukuruzinska Caroline A.Genco Andrew Salama Ellen O.Weinberg Carolyn D.Kramer Jorge Frias-Lopez Forsyth Institute 245 First StreetCambridgeMA 02142USA Boston University Henry M.Goldman School of Dental Medicine 100 East Newton StreetBostonMA 02118USA Department of Integrative Physiology and Pathobiology Tufts University School of Medicine136 Harrison AvenueBostonMA 02111USA Department of Oral Biology College of DentistryUniversity of Florida1395 Center DriveGainesvilleFL 32610-0424USA

Oral squamous cell carcinoma(OSCC) is the most prevalent and most commonly studied oral cancer. However, there is a void regarding the role that the oral microbiome may play in OSCC. Although the relationship between microbial community composition and OSCC has been thoroughly investigated, microbial profiles of the human microbiome in cancer are understudied. Here we performed a small pilot study of community-wide metatranscriptome analysis to profile mRNA expression in the entire oral microbiome in OSCC to reveal molecular functions associated with this disease. Fusobacteria showed a statistically significantly higher number of transcripts at tumour sites and tumour-adjacent sites of cancer patients compared to the healthy controls analysed. Regardless of the community composition, specific metabolic signatures were consistently found in disease. Activities such as iron ion transport, tryptophanase activity, peptidase activities and superoxide dismutase were over-represented in tumour and tumour-adjacent samples when compared to the healthy controls. The expression of putative virulence factors in the oral communities associated with OSCC showed that activities related to capsule biosynthesis, flagellum synthesis and assembly, chemotaxis, iron transport, haemolysins and adhesins were upregulated at tumour sites. Moreover, activities associated with protection against reactive nitrogen intermediates, chemotaxis, flagellar and capsule biosynthesis were also upregulated in non-tumour sites of cancer patients. Although they are preliminary, our results further suggest that Fusobacteria may be the leading phylogenetic group responsible for the increase in expression of virulence factors in the oral microbiome of OSCC patients.

关键词： profiles analyses

Entropy resistance analyses of a two-stream parallel flow heat exchanger with viscous heating

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Chinese Physics B 2013年第8期22卷 361-364页

作者：程雪涛梁新刚 Key Laboratory for Thermal Science and Power Engineering of Ministry of Education School of Aerospace Tsinghua University

Heat exchangers are widely used in industry, and analyses and optimizations of the performance of heat exchangers are important topics. In this paper, we define the concept of entropy resistance based on the entropy generation analyses of a one-dimensional heat transfer process. With this concept, a two-stream parallel flow heat exchanger with viscous heating is analyzed and discussed. It is found that the minimization of entropy resistance always leads to the maximum heat transfer rate for the discussed two-stream parallel flow heat exchanger, while the minimizations of entropy generation rate, entropy generation numbers, and revised entropy generation number do not always.

关键词： entropy generation minimization heat exchanger entropy resistance analyses

Theory and Implementation of Sensitivity analyses Based on Their Algebraic Representation in the Graph Model

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Journal of Systems Science and Systems Engineering 2019年第5期28卷 580-601页

作者： Jinshuai Zhao Haiyan Xu Keith W.Hipel Baohua Yang College of Economics and Management Nanjing University of Aeronautics and Astronautics Nanjing 211106 China College of Computer Science and Technology Jiangsu Normal University Xuzhou 221116 China Department of Systems Design Engineering University of Waterloo Waterloo Canada School of Business Jiangsu Normal University Xuzhou 221116 China

Sensitivity analyses based on an algebraic representation in the graph model for conflict resolution (GMCR) are generalized for ascertaining the robustness of stability results by varying decision makers' preference ranking.The ordinal preferences in GMCR are advantageous to carry out sensitivity analyses with respect to systematically identifying the influence of preference alterations upon the four basic stabilities consisting of Nash stability,general metarationality,symmetric metarationality and sequential stability.The proposed algebraic representation of the four basic stabilities is not only effective and convenient for computer implementation of sensitivity analysis,but also makes it easier to understand the meaning of the four stabilities when compared with the existing matrix representation.Further,these sensitivity analyses results are embedded into the latest version of the decision support system NUAAGMCR,which can be used to study real-world conflicts.To illustrate how these contributions to sensitivity analyses can be applied in practice and provide valuable strategic insights,they are used to investigate the civil war conflict in South Sudan.

关键词： Sensitivity analyses algebraic expression graph model ordinal preference conflict resolution

analyses on Marketing Strategies of Penglai's Tourism

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海外英语 2013年第7X期 285-288页

作者：徐宜华西南科技大学外国语学院四川绵阳621010

Although tourism marketing has made great progress in recent years,researches on it are far from enough.Current re searches on tourism marketing at home and abroad lack pertinence and mostly provide theoretical basis for tourism development within a wide range.The researches on tourism marketing of Penglai are few and far between.Based on previous studies and the status quo of tourism marketing strategy,the below statements tries to find out existing problems of Penglai's tourism,put for ward countermeasures and propose feasible marketing patterns suitable for its tourism development.It subsequently concludes that it can make contribution to the sustainable development of Penglai's tourism and provide other county-level tourism cities with reference for marketing tourism marketing strategies.

关键词： Penglai tourism marketing strategy analyses

FURTHER EXPLORING THE POTENTIAL FOR ASSIMILATION OF UNMANNED AIRCRAFT OBSERVATIONS TO BENEFIT HURRICANE analyses AND FORECASTS

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Tropical Cyclone Research and Review 2015年第2期4卷 64-70页

作者： JASON ASIPPEL FUQING ZHANG YONGHUI WENG SCOTT ABRAUN DANIEL JCECIL IM Systems Group RockvilleMarylandUSA National Oceanographic and Atmospheric Administration Environmental Modeling CenterCollege ParkMarylandUSA Department of Meteorology The Pennsylvania State UniversityPennsylvaniaUSA Laboratory for Atmospheres NASA Goddard Space Flight CenterMarylandUSA NASA Marshall Space Flight Center AlabamaUSA

This study explores the potential of assimilating data from multiple instruments onboard high-altitude,longendurance unmanned aircraft to improve hurricane analyses and forecasts.A recent study found a signifi cant positive impact on analyses and forecasts of Hurricane Karl when an ensemble Kalman fi lter was used to assimilate data from the High-altitude Imaging Wind and Rain Airborne Profi ler(HIWRAP),a new Doppler radar onboard the NASA Global Hawk(GH)unmanned airborne system.The GH can also carry other useful instruments,including dropsondes and the Hurricane Imaging Radiometer(HIRAD),which is a new radiometer that estimates large swaths of wind speeds and rainfall at the ocean surface.The primary fi nding is that simultaneously assimilating data from HIWRAP and the other GH-compatible instruments results in further analysis and forecast improvement for Karl.The greatest improvement comes when HIWRAP,HIRAD,and dropsonde data are simultaneously assimilated.

关键词： VWP FURTHER EXPLORING THE POTENTIAL FOR ASSIMILATION OF UNMANNED AIRCRAFT OBSERVATIONS TO BENEFIT HURRICANE analyses AND FORECASTS