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Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences
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作者 Lihini Sandaleka Muthukumarana Methsala Madurangi Wedage +1 位作者 Samanthika Rathnayake Nissanka Kolitha De Silva 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2024年第5期214-225,I0004-I0038,共47页
Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Tran... Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B. 展开更多
关键词 Molecular systematics ITS2 COI DNA sequences Phylogeny PHYLOGEOGRAPHY
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Safety assessment of a novel marine multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 according to phenotype and whole genome-sequencing analysis
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作者 Xueyan Mo Mengcheng Zhou +8 位作者 Yanmei Li Lili Yu Huashang Bai Peihong Shen Xing Zhou Haojun Zhu Huijie Sun Ru Bu Chengjian Jiang 《Food Science and Human Wellness》 SCIE CAS CSCD 2024年第4期2048-2059,共12页
The application of microorganisms as probiotics is limited due to lack of safety evaluation.Here,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from ... The application of microorganisms as probiotics is limited due to lack of safety evaluation.Here,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from marine mangrove microorganisms.Its safety and probiotic properties were assessed in accordance with phenotype and whole-genome sequencing analysis.Results showed that the genes and phenotypic expression of related virulence,antibiotic resistance and retroelement were rarely found.Hyphal morphogenesis genes(SIT4,HOG1,SPA2,ERK1,ICL1,CST20,HSP104,TPS1,and RHO1)and phospholipase secretion gene(VPS4)were annotated.True hyphae and phospholipase were absent.Only one retroelement(Tad1-65_BG)was found.Major biogenic amines(BAs)encoding genes were absent,except for spermidine synthase(JA9_002594),spermine synthase(JA9_004690),and tyrosine decarboxylase(inx).The production of single BAs and total BAs was far below the food-defined thresholds.GXDK6 had no resistance to common antifungal drugs.Virulence enzymes,such as gelatinase,DNase,hemolytic,lecithinase,and thrombin were absent.Acute toxicity test with mice demonstrated that GXDK6 is safe.GXDK6 has a good reproduction ability in the simulation gastrointestinal tract.GXDK6 also has a strong antioxidant ability,β-glucosidase,and inulinase activity.To sum up,GXDK6 is considered as a safe probiotic for human consumption and food fermentation. 展开更多
关键词 Meyerozyma guilliermondii Safety assessment PROBIOTICS Marine mangrove microorganisms Whole-genome sequencing analysis
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Action of circulating and infiltrating B cells in the immune microenvironment of colorectal cancer by single-cell sequencing analysis
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作者 Jing-Po Zhang Bing-Zheng Yan +1 位作者 Jie Liu Wei Wang 《World Journal of Gastrointestinal Oncology》 SCIE 2024年第6期2683-2696,共14页
BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer(CRC),one of the most prevalent malignancies worldwide.In this study,multi-omics and single-cell sequencing t... BACKGROUND The complexity of the immune microenvironment has an impact on the treatment of colorectal cancer(CRC),one of the most prevalent malignancies worldwide.In this study,multi-omics and single-cell sequencing techniques were used to investigate the mechanism of action of circulating and infiltrating B cells in CRC.By revealing the heterogeneity and functional differences of B cells in cancer immunity,we aim to deepen our understanding of immune regulation and provide a scientific basis for the development of more effective cancer treatment strategies.AIM To explore the role of circulating and infiltrating B cell subsets in the immune microenvironment of CRC,explore the potential driving mechanism of B cell development,analyze the interaction between B cells and other immune cells in the immune microenvironment and the functions of communication molecules,and search for possible regulatory pathways to promote the anti-tumor effects of B cells.METHODS A total of 69 paracancer(normal),tumor and peripheral blood samples were collected from 23 patients with CRC from The Cancer Genome Atlas database(https://portal.gdc.cancer.gov/).After the immune cells were sorted by multicolor flow cytometry,the single cell transcriptome and B cell receptor group library were sequenced using the 10X Genomics platform,and the data were analyzed using bioinformatics tools such as Seurat.The differences in the number and function of B cell infiltration between tumor and normal tissue,the interaction between B cell subsets and T cells and myeloid cell subsets,and the transcription factor regulatory network of B cell subsets were explored and analyzed.RESULTS Compared with normal tissue,the infiltrating number of CD20+B cell subsets in tumor tissue increased significantly.Among them,germinal center B cells(GCB)played the most prominent role,with positive clone expansion and heavy chain mutation level increasing,and the trend of differentiation into memory B cells increased.However,the number of plasma cells in the tumor microenvironment decreased significantly,and the plasma cells secreting IgA antibodies decreased most obviously.In addition,compared with the immune microenvironment of normal tissues,GCB cells in tumor tissues became more closely connected with other immune cells such as T cells,and communication molecules that positively regulate immune function were significantly enriched.CONCLUSION The role of GCB in CRC tumor microenvironment is greatly enhanced,and its affinity to tumor antigen is enhanced by its significantly increased heavy chain mutation level.Meanwhile,GCB has enhanced its association with immune cells in the microenvironment,which plays a positive anti-tumor effect. 展开更多
关键词 Colorectal cancer Multi-omics analysis Single-cell sequencing analysis Immune microenvironment Infiltrating B cells
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Integration of Sequence Stratigraphic Analysis and 3D Geostatistical Modeling of Pliocene–Pleistocene Delta,F3 Block,Netherlands
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作者 Haris Ahmed KHAN Ali Asghar SHAHID +3 位作者 Muhammad Jahangir KHAN Taher ZOUAGHI Maria Dolores ALVAREZ Syed Danial Mehdi NAQVI 《Acta Geologica Sinica(English Edition)》 SCIE CAS CSCD 2023年第1期256-268,共13页
This research is focused on the analysis of the sequence stratigraphic units of F3 Block,within a wave-dominated delta of Plio–Pleistocene age.Three wells of F3 block and a 3D seismic data,are utilized in this resear... This research is focused on the analysis of the sequence stratigraphic units of F3 Block,within a wave-dominated delta of Plio–Pleistocene age.Three wells of F3 block and a 3D seismic data,are utilized in this research.The conventional techniques of 3D seismic interpretation were utilized to mark the 11 surfaces on the seismic section.Integration of seismic sequence stratigraphic interpretation,using well logs,and subsequent 3D geostatistical modeling,using seismic data,aided to evaluate the shallow hydrocarbon traps.The resulting models were obtained using System Tract and Facies models,which were generated by using sequential stimulation method and their variograms made by spherical method,moreover,these models are validated via histograms.The CDF curve generated from upscaling of well logs using geometric method,shows a good relation with less percentage of errors(1 to 2 for Facies and 3 to 4 for System Tract models)between upscaled and raw data that complements the resulted models.These approaches help us to delineate the best possible reservoir,lateral extent of system tracts(LST and/or HST)in the respective surface,and distribution of sand and shale in the delta.The clinoform break points alteration observed on seismic sections,also validates the sequence stratigraphic interpretation.The GR log-based Facies model and sequence stratigraphy-based System Tract model of SU-04-2 showed the reservoir characteristics,presence of sand bodies and majorly LST,respectively,mainly adjacent to the main fault of the studied area.Moreover,on the seismic section,SU-04-2 exhibits the presence of gas pockets at the same location that also complements the generated Facies and System Tract models.The generated models can be utilized for any similar kind of study and for the further research in the F3 block reservoir characterization. 展开更多
关键词 sequence stratigraphy facies modeling system tract modeling F3 block North Sea
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Lagrangian coherent structure analysis on transport of Acetes chinensis along coast of Lianyungang,China 被引量:1
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作者 Kexin WANG Xueqing ZHANG +2 位作者 Qi LOU Xusheng XIANG Ying XIONG 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第1期345-359,共15页
Spatial heterogeneity or“patchiness”of plankton distributions in the ocean has always been an attractive and challenging scientific issue to oceanographers.We focused on the accumulation and dynamic mechanism of the... Spatial heterogeneity or“patchiness”of plankton distributions in the ocean has always been an attractive and challenging scientific issue to oceanographers.We focused on the accumulation and dynamic mechanism of the Acetes chinensis in the Lianyungang nearshore licensed fishing area.The Lagrangian frame approaches including the Lagrangian coherent structures theory,Lagrangian residual current,and Lagrangian particle-tracking model were applied to find the transport pathways and aggregation characteristics of Acetes chinensis.There exist some material transport pathways for Acetes chinensis passing through the licensed fishing area,and Acetes chinensis is easy to accumulate in the licensed fishing area.The main mechanism forming this distribution pattern is the local circulation induced by the nonlinear interaction of topography and tidal flow.Both the Lagrangian coherent structure analysis and the particle trajectory tracking indicate that Acetes chinensis in the licensed fishing area come from the nearshore estuary.This work contributed to the adjustment of licensed fishing area and the efficient utilization of fishery resources. 展开更多
关键词 plankton accumulation hydrodynamic model Lagrangian particle-tracking model Lagrangian analysis
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Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning
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作者 Xiaolu Li Ye Yang +3 位作者 Senming Xu Yuchang Gui Jianmin Chen Jianwen Xu 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第12期2723-2734,共12页
Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is s... Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022). 展开更多
关键词 bioinformatics analysis BIOMARKER CIBERSORT GEO dataset LASSO miRNA-mRNA network RNA sequencing spinal cord injury SVM-RFE weighted gene co-expression network analysis
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Model reduction of fractional impedance spectra for time–frequency analysis of batteries, fuel cells, and supercapacitors 被引量:1
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作者 Weiheng Li Qiu-An Huang +6 位作者 Yuxuan Bai Jia Wang Linlin Wang Yuyu Liu Yufeng Zhao Xifei Li Jiujun Zhang 《Carbon Energy》 SCIE EI CAS CSCD 2024年第1期108-141,共34页
Joint time–frequency analysis is an emerging method for interpreting the underlying physics in fuel cells,batteries,and supercapacitors.To increase the reliability of time–frequency analysis,a theoretical correlatio... Joint time–frequency analysis is an emerging method for interpreting the underlying physics in fuel cells,batteries,and supercapacitors.To increase the reliability of time–frequency analysis,a theoretical correlation between frequency-domain stationary analysis and time-domain transient analysis is urgently required.The present work formularizes a thorough model reduction of fractional impedance spectra for electrochemical energy devices involving not only the model reduction from fractional-order models to integer-order models and from high-to low-order RC circuits but also insight into the evolution of the characteristic time constants during the whole reduction process.The following work has been carried out:(i)the model-reduction theory is addressed for typical Warburg elements and RC circuits based on the continued fraction expansion theory and the response error minimization technique,respectively;(ii)the order effect on the model reduction of typical Warburg elements is quantitatively evaluated by time–frequency analysis;(iii)the results of time–frequency analysis are confirmed to be useful to determine the reduction order in terms of the kinetic information needed to be captured;and(iv)the results of time–frequency analysis are validated for the model reduction of fractional impedance spectra for lithium-ion batteries,supercapacitors,and solid oxide fuel cells.In turn,the numerical validation has demonstrated the powerful function of the joint time–frequency analysis.The thorough model reduction of fractional impedance spectra addressed in the present work not only clarifies the relationship between time-domain transient analysis and frequency-domain stationary analysis but also enhances the reliability of the joint time–frequency analysis for electrochemical energy devices. 展开更多
关键词 battery fuel cell supercapacitor fractional impedance spectroscopy model reduction time-frequency analysis
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The Application of Nicotiana benthamiana as a Transient Expression Host to Clone the Coding Sequences of Plant Genes
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作者 Jianzhong Huang Peng Jia +3 位作者 Xiaoju Zhong Xiuying Guan Hongbin Zhang Honglei Ruan 《American Journal of Molecular Biology》 CAS 2024年第2期54-65,共12页
Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using co... Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes. 展开更多
关键词 Coding sequence Genomic sequence Nicotiana benthamiana Plant Genes
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Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice
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作者 Weilin Tan Jun Ma +9 位作者 Jiayuanyuan Fu Biying Wu Ziyu Zhu Xuekang Huang Mengran Du Chenrui Wu Ehab Balawi Qiang Zhou Jie Zhang Zhengbu Liao 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第1期171-179,共9页
Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate trau... Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway. 展开更多
关键词 axon guidance bioinformatics analysis competing endogenous RNA ERYTHROPOIETIN Gene Ontology Kyoto Encyclopedia of Genes and Genomes non-coding RNA RNA sequencing TRANSCRIPTOMICS traumatic brain injury
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Application of Isogeometric Analysis Method in Three-Dimensional Gear Contact Analysis
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作者 Long Chen Yan Yu +2 位作者 Yanpeng Shang Zhonghou Wang Jing Zhang 《Computer Modeling in Engineering & Sciences》 SCIE EI 2024年第4期817-846,共30页
Gears are pivotal in mechanical drives,and gear contact analysis is a typically difficult problem to solve.Emerging isogeometric analysis(IGA)methods have developed new ideas to solve this problem.In this paper,a thre... Gears are pivotal in mechanical drives,and gear contact analysis is a typically difficult problem to solve.Emerging isogeometric analysis(IGA)methods have developed new ideas to solve this problem.In this paper,a threedimensional body parametric gear model of IGA is established,and a theoretical formula is derived to realize single-tooth contact analysis.Results were benchmarked against those obtained from commercial software utilizing the finite element analysis(FEA)method to validate the accuracy of our approach.Our findings indicate that the IGA-based contact algorithmsuccessfullymet theHertz contact test.When juxtaposed with the FEA approach,the IGAmethod demonstrated fewer node degrees of freedomand reduced computational units,all whilemaintaining comparable accuracy.Notably,the IGA method appeared to exhibit consistency in analysis accuracy irrespective of computational unit density,and also significantlymitigated non-physical oscillations in contact stress across the tooth width.This underscores the prowess of IGA in contact analysis.In conclusion,IGA emerges as a potent tool for addressing contact analysis challenges and holds significant promise for 3D gear modeling,simulation,and optimization of various mechanical components. 展开更多
关键词 Contact analysis involute gear isogeometric analysis finite element analysis
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Preliminary electromagnetic analysis of the COOL blanket for CFETR
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作者 鲁帅领 马学斌 刘松林 《Plasma Science and Technology》 SCIE EI CAS CSCD 2024年第1期101-108,共8页
The supercritical CO_(2)cOoled Lithium-Lead(COOL)blanket has been designed as one advanced blanket candidate for the Chinese Fusion Engineering Test Reactor(CFETR).This work focuses on the electromagnetic(EM)loads(Max... The supercritical CO_(2)cOoled Lithium-Lead(COOL)blanket has been designed as one advanced blanket candidate for the Chinese Fusion Engineering Test Reactor(CFETR).This work focuses on the electromagnetic(EM)loads(Maxwell force and Lorentz force)acting on the COOL blanket,which are important mechanical loads in further structural analysis of the COOL blanket.A 3D electromagnetic analysis is performed using the ANSYS finite element method to obtain EM loads on the COOL blanket in this study.At first,the magnetic scalar potential(MSP)method is used to obtain the magnetic field and the Maxwell force on the COOL blanket.Then,the magnetic vector potential(MVP)method is performed during a plasma disruption event to get the eddy current distribution.At last,a multi-step method is adopted for the calculation of the Lorentz force and the torque.The maximum Lorentz forces of inboard and outboard blanket structural components are 5624 kN and 2360 kN respectively. 展开更多
关键词 CFETR COOL blanket finite element analysis electromagnetic analysis
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Automatic area estimation of algal blooms in water bodies from UAV images using texture analysis
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作者 Ajmeria Rahul Gundu Lokesh +2 位作者 Siddhartha Goswami R.N.Ponnalagu Radhika Sudha 《Water Science and Engineering》 EI CAS CSCD 2024年第1期62-71,共10页
Algal blooms,the spread of algae on the surface of water bodies,have adverse effects not only on aquatic ecosystems but also on human life.The adverse effects of harmful algal blooms(HABs)necessitate a convenient solu... Algal blooms,the spread of algae on the surface of water bodies,have adverse effects not only on aquatic ecosystems but also on human life.The adverse effects of harmful algal blooms(HABs)necessitate a convenient solution for detection and monitoring.Unmanned aerial vehicles(UAVs)have recently emerged as a tool for algal bloom detection,efficiently providing on-demand images at high spatiotemporal resolutions.This study developed an image processing method for algal bloom area estimation from the aerial images(obtained from the internet)captured using UAVs.As a remote sensing method of HAB detection,analysis,and monitoring,a combination of histogram and texture analyses was used to efficiently estimate the area of HABs.Statistical features like entropy(using the Kullback-Leibler method)were emphasized with the aid of a gray-level co-occurrence matrix.The results showed that the orthogonal images demonstrated fewer errors,and the morphological filter best detected algal blooms in real time,with a precision of 80%.This study provided efficient image processing approaches using on-board UAVs for HAB monitoring. 展开更多
关键词 Algal bloom Image processing Texture analysis Histogram analysis Unmanned aerial vehicles
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Erratum to:Vibration analysis of a gear-rotor-bearing system with outer-ring spalling and misalignment
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作者 徐宏阳 赵翔 +3 位作者 马辉 罗忠 韩清凯 闻邦椿 《Journal of Central South University》 SCIE EI CAS CSCD 2024年第3期1032-1032,共1页
Because of an unfortunate mistake during the production of this article,Figure 13 was wrongly inserted.The corrected Figure 13 is shown as follows.
关键词 FIGURE outer analysis
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Advances in microfluidic-based DNA methylation analysis
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作者 Jiwen Li Tiechuan Li Xuexin Duan 《Nanotechnology and Precision Engineering》 EI CAS CSCD 2024年第1期116-134,共19页
DNA methylation has been extensively investigated in recent years,not least because of its known relationship with various diseases.Progress in analytical methods can greatly increase the relevance of DNA methylation ... DNA methylation has been extensively investigated in recent years,not least because of its known relationship with various diseases.Progress in analytical methods can greatly increase the relevance of DNA methylation studies to both clinical medicine and scientific research.Microflu-idic chips are excellent carriers for molecular analysis,and their use can provide improvements from multiple aspects.On-chip molecular analysis has received extensive attention owing to its advantages of portability,high throughput,low cost,and high efficiency.In recent years,the use of novel microfluidic chips for DNA methylation analysis has been widely reported and has shown obvious superiority to conventional methods.In this review,wefirst focus on DNA methylation and its applications.Then,we discuss advanced microfluidic-based methods for DNA methylation analysis and describe the great progress that has been made in recent years.Finally,we summarize the advantages that microfluidic technology brings to DNA methylation analysis and describe several challenges and perspectives for on-chip DNA methylation analysis.This review should help researchers improve their understanding and make progress in developing microfluidic-based methods for DNA methylation analysis. 展开更多
关键词 Microfluidic chip DNA methylation analysis Molecular analysis High throughput Low cost
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Stability Analysis of Inverse Lax-Wendroff Procedure for a High order Compact Finite Difference Schemes
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作者 Tingting Li Jianfang Lu Pengde Wang 《Communications on Applied Mathematics and Computation》 EI 2024年第1期142-189,共48页
This paper considers the finite difference(FD)approximations of diffusion operators and the boundary treatments for different boundary conditions.The proposed schemes have the compact form and could achieve arbitrary ... This paper considers the finite difference(FD)approximations of diffusion operators and the boundary treatments for different boundary conditions.The proposed schemes have the compact form and could achieve arbitrary even order of accuracy.The main idea is to make use of the lower order compact schemes recursively,so as to obtain the high order compact schemes formally.Moreover,the schemes can be implemented efficiently by solving a series of tridiagonal systems recursively or the fast Fourier transform(FFT).With mathematical induction,the eigenvalues of the proposed differencing operators are shown to be bounded away from zero,which indicates the positive definiteness of the operators.To obtain numerical boundary conditions for the high order schemes,the simplified inverse Lax-Wendroff(SILW)procedure is adopted and the stability analysis is performed by the Godunov-Ryabenkii method and the eigenvalue spectrum visualization method.Various numerical experiments are provided to demonstrate the effectiveness and robustness of our algorithms. 展开更多
关键词 Compact scheme Diffusion operators Inverse Lax-Wendroff(ILW) Fourier analysis Eigenvalue analysis
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Molecular cloning,characterization and promoter analysis of LbgCWIN1 and its expression profiles in response to exogenous sucrose during in vitro bulblet initiation in lily
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作者 Cong Gao Shiqi Li +4 位作者 Yunchen Xu Yue Liu Yiping Xia Ziming Ren Yun Wu 《Horticultural Plant Journal》 SCIE CAS CSCD 2024年第2期545-555,共11页
Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellul... Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellular space, are key enzymes participating in sucrose allocation in higher plants. Previous studies have shown that CWINs play an essential role in bulblet initiation process in bulbous crops, but the underlying molecular mechanism remains unclear. Here, a CWIN gene of Lilium brownii var. giganteum(Lbg) was identified and amplified from genomic DNA. Quantitative RT-PCR assays revealed that the expression level of LbgCWIN1 was highly upregulated exactly when the endogenous starch degraded in non-sucrose medium during in vitro bulblet initiation in Lbg. Phylogenetic relationship, motif, and domain analysis of LbgCWIN1 protein and CWINs in other plant species showed that all sequences of these CWIN proteins were highly conserved. The promoter sequence of LbgCWIN1 possessed a number of alpha-amylase-, phytohormone-, light-and stress-responsive cis-elements. Meanwhile, β-glucuronidase(GUS) assay showed that the 459 bp upstream fragment from the translational start site displayed maximal promoter activity. These results revealed that LbgCWIN1 might function in the process of in vitro bulblet initiation and be in the response to degradation of endogenous starch. 展开更多
关键词 Lilium brownii var.giganteum LbgCWIN1 Phylogenetic analysis Promoter analysis Bulblet initiation
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Privacy Protection in COVID Data Tracking: Textual Analysis of the Literature
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作者 Antonella Massari Viviana D’Addosio +1 位作者 Vittoria Claudia De Nicolò Samuela L’Abbate 《Applied Mathematics》 2024年第3期235-255,共21页
The literary review presented in the following paper aims to analyze the tracking tools used in different countries during the period of the COVID-19 pandemic. Tracking apps that have been adopted in many countries to... The literary review presented in the following paper aims to analyze the tracking tools used in different countries during the period of the COVID-19 pandemic. Tracking apps that have been adopted in many countries to collect data in a homogeneous and immediate way have made up for the difficulty of collecting data and standardizing evaluation criteria. However, the regulation on the protection of personal data in the health sector and the adoption of the new General Data Protection Regulation in European countries has placed a strong limitation on their use. This has not been the case in non-European countries, where monitoring methodologies have become widespread. The textual analysis presented is based on co-occurrence and multiple correspondence analysis to show the contact tracing methods adopted in different countries in the pandemic period by relating them to the issue of privacy. It also analyzed the possibility of applying Blockchain technology in applications for tracking contagions from COVID-19 and managing health data to provide a high level of security and transparency, including through anonymization, thus increasing user trust in using the apps. 展开更多
关键词 TRACKING PRIVACY Blockchain Textual analysis
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Trends and hotspots in gastrointestinal neoplasms risk assessment: A bibliometric analysis from 1984 to 2022
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作者 Qiang-Qiang Fu Le Ma +5 位作者 Xiao-Min Niu Hua-Xin Zhao Xu-Hua Ge Hua Jin De-Hua Yu Sen Yang 《World Journal of Gastrointestinal Oncology》 SCIE 2024年第6期2842-2861,共20页
BACKGROUND Gastrointestinal neoplasm(GN)significantly impact the global cancer burden and mortality,necessitating early detection and treatment.Understanding the evolution and current state of research in this field i... BACKGROUND Gastrointestinal neoplasm(GN)significantly impact the global cancer burden and mortality,necessitating early detection and treatment.Understanding the evolution and current state of research in this field is vital.AIM To conducts a comprehensive bibliometric analysis of publications from 1984 to 2022 to elucidate the trends and hotspots in the GN risk assessment research,focusing on key contributors,institutions,and thematic evolution.METHODS This study conducted a bibliometric analysis of data from the Web of Science Core Collection database using the"bibliometrix"R package,VOSviewer,and CiteSpace.The analysis focused on the distribution of publications,contributions by institutions and countries,and trends in keywords.The methods included data synthesis,network analysis,and visualization of international collaboration networks.RESULTS This analysis of 1371 articles on GN risk assessment revealed a notable evolution in terms of research focus and collaboration.It highlights the United States'critical role in advancing this field,with significant contributions from institutions such as Brigham and Women's Hospital and the National Cancer Institute.The last five years,substantial advancements have been made,representing nearly 45%of the examined literature.Publication rates have dramatically increased,from 20 articles in 2002 to 112 in 2022,reflecting intensified research efforts.This study underscores a growing trend toward interdisciplinary and international collaboration,with the Journal of Clinical Oncology standing out as a key publication outlet.This shift toward more comprehensive and collaborative research methods marks a significant step in addressing GN risks.CONCLUSION This study underscores advancements in GN risk assessment through genetic analyses and machine learning and reveals significant geographical disparities in research emphasis.This calls for enhanced global collaboration and integration of artificial intelligence to improve cancer prevention and treatment accuracy,ultimately enhancing worldwide patient care. 展开更多
关键词 Gastrointestinal neoplasms Bibliometric analysis Risk assessment Network analysis Research trends
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Intertwined depressive and cognitive trajectories and the risk of dementia and death in older adults:a competing risk analysis
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作者 Ziyang Ren Lirong Nie +1 位作者 Yushan Du Jufen Liu 《General Psychiatry》 CSCD 2024年第2期207-215,共9页
Background Depressive symptoms and cognitive impairment often interact,rendering their associations controversial.To date,their joint trajectories and associations with dementia and death remain underexplored.Aims To ... Background Depressive symptoms and cognitive impairment often interact,rendering their associations controversial.To date,their joint trajectories and associations with dementia and death remain underexplored.Aims To explore the interactions between depressive symptoms and cognitive function,their developmental trajectories and the associations with all-cause dementia,Alzheimer’s disease(AD)and all-cause death in older adults.Methods Data were from the Health and Retirement Study.Depressive symptoms and cognitive function were measured using the 8-item Centre for Epidemiologic Studies Depression Scale and the Telephone Interview of Cognitive Status,respectively.All-cause dementia and AD were defined by self-reported or proxy-reported physician diagnoses.All-cause death was determined by interviews.The restricted cubic spline,group-based trajectory modelling and subdistribution hazard regression were used.Results Significant interactions between depressive symptoms and cognitive function in 2010 in their association with new-onset all-cause dementia and AD from 2010 to 2020 were found,especially in women(p for interaction<0.05).Independent trajectory analysis showed that emerging or high(vs no)depressive trajectories and poor or rapidly decreased cognitive trajectories(vs very good)from 1996 to 2010 were at significantly higher risk of subsequent all-cause dementia,AD and all-cause death.15 joint trajectories of depressive symptoms and cognitive function from 1996 to 2010 were determined,where rapidly decreased cognitive function was more common in those with no depressive symptoms.Compared with older adults with the trajectory of no depressive symptoms and very good cognitive function,those with the trajectory of no depressive symptoms but rapidly decreased cognitive function were much more likely to develop new-onset all-cause dementia and death,with subdistribution hazard ratios(95%confidence intervals)of 4.47(2.99 to 6.67)and 1.84(1.43 to 2.36),especially in women.Conclusions To effectively mitigate the risk of dementia and death,it is crucial to acknowledge the importance of preventing cognitive decline in older adults without depressive symptoms,particularly in women. 展开更多
关键词 DEATH analysis RENDERING
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Social-ecological perspective on the suicidal behaviour factors of early adolescents in China:a network analysis
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作者 Yuan Li Peiying Li +5 位作者 Mengyuan Yuan Yonghan Li Xueying Zhang Juan Chen Gengfu Wang Puyu Su 《General Psychiatry》 CSCD 2024年第1期143-150,共8页
Background In early adolescence,youth are highly prone to suicidal behaviours.Identifying modifiable risk factors during this critical phase is a priority to inform effective suicide prevention strategies.Aims To expl... Background In early adolescence,youth are highly prone to suicidal behaviours.Identifying modifiable risk factors during this critical phase is a priority to inform effective suicide prevention strategies.Aims To explore the risk and protective factors of suicidal behaviours(ie,suicidal ideation,plans and attempts)in early adolescence in China using a social-ecological perspective.Methods Using data from the cross-sectional project‘Healthy and Risky Behaviours Among Middle School Students in Anhui Province,China',stratified random cluster sampling was used to select 5724 middle school students who had completed self-report questionnaires in November 2020.Network analysis was employed to examine the correlates of suicidal ideation,plans and attempts at four levels,namely individual(sex,academic performance,serious physical llness/disability,history of self-harm,depression,impulsivity,sleep problems,resilience),family(family economic status,relationship with mother,relationship with father,family violence,childhood abuse,parental mental illness),school(relationship with teachers,relationship with classmates,school-bullying victimisation and perpetration)and social(social support,satisfaction with society).Results In total,37.9%,19.0%and 5.5%of the students reported suicidal ideation,plans and attempts in the past 6 months,respectively.The estimated network revealed that suicidal ideation,plans and attempts were collectively associated with a history of self-harm,sleep problems,childhood abuse,school bullying and victimisation.Centrality analysis indicated that the most influential nodes in the network were history of self-harm and childhood abuse.Notably,the network also showed unique correlates of suicidal ideation(sex,weight=0.60;impulsivity,weight=0.24;family violence,weight=0.17;relationship with teachers,weight=-0.03;school-bullying perpetration,weight=0.22),suicidal plans(social support,weight=-0.15)and suicidal attempts(relationship with mother,weight=-0.10;parental mental llness,weight=0.61).Conclusions This study identified the correlates of suicidal ideation,plans and attempts,and provided practical implications for suicide prevention for young adolescents in China.Firstly,this study highlighted the importance of joint interventions across multiple departments.Secondly,the common risk factors of suicidal ideation,plans and attempts were elucidated.Thirdly,this study proposed target interventions to address the unique influencing factors of suicidal ideation,plans and attempts. 展开更多
关键词 NETWORK analysis PREVENTION
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