Inversion tillage with straw incorporation affects the patterns of soil microbial co-occurrence and multi-nutrient cycling in a Hapli-Udic Cambisol

Inversion tillage with straw amendment is widely applied in northeastern China, and it can substantially increase the storage of carbon and improve multiple subsoil functions. Soil microorganisms are believed to be the key to this process,but research into their role in subsoil amelioration is limited. Therefore, a field experiment was conducted in 2018 in a region in northeastern China with Hapli-Udic Cambisol using four treatments: conventional tillage(CT, tillage to a depth of 15 cm with no straw incorporation), straw incorporation with conventional tillage(SCT, tillage to a depth of 15 cm),inversion tillage(IT, tillage to a depth of 35 cm) and straw incorporation with inversion tillage(SIT, tillage to a depth of 35 cm). The soils were managed by inversion to a depth of 15 or 35 cm every year after harvest. The results indicated that SIT improved soil multi-nutrient cycling variables and increased the availability of key nutrients such as soil organic carbon, total nitrogen, available nitrogen, available phosphorus and available potassium in both the topsoil and subsoil.In contrast to CT and SCT, SIT created a looser microbial network structure but with highly centralized clusters by reducing the topological properties of average connectivity and node number, and by increasing the average path length and the modularity. A Random Forest analysis found that the average path length and the clustering coefficient were the main determinants of soil multi-nutrient cycling. These findings suggested that SIT can be an effective option for improving soil multi-nutrient cycling and the structure of microbial networks, and they provide crucial information about the microbial strategies that drive the decomposition of straw in Hapli-Udic Cambisol.

Temporal characteristics of algae-denitrifying bacteria co-occurrence patterns and denitrifier assembly in epiphytic biofilms on submerged macrophytes in Caohai Lake,SW China

Denitrifying bacteria in epiphytic biofilms play a crucial role in nitrogen cycle in aquatic habitats.However,little is known about the connection between algae and denitrifying bacteria and their assembly processes in epiphytic biofilms.Epiphytic biofilms were collected from submerged macrophytes(Patamogeton lucens and Najas marina L.)in the Caohai Lake,Guizhou,SW China,from July to November 2020 to:(1)investigate the impact of abiotic and biotic variables on denitrifying bacterial communities;(2)investigate the temporal variation of the algae-denitrifying bacteria co-occurrence networks;and(3)determine the contribution of deterministic and stochastic processes to the formation of denitrifying bacterial communities.Abiotic and biotic factors influenced the variation in the denitrifying bacterial community,as shown in the Mantel test.The co-occurrence network analysis unveiled intricate interactions among algae to denitrifying bacteria.Denitrifying bacterial community co-occurrence network complexity(larger average degrees representing stronger network complexity)increased continuously from July to September and decreased in October before increasing in November.The co-occurrence network complexity of the algae and nirS-encoding denitrifying bacteria tended to increase from July to November.The co-occurrence network complexity of the algal and denitrifying bacterial communities was modified by ammonia nitrogen(NH_(4)^(+)-N)and total phosphorus(TP),pH,and water temperature(WT),according to the ordinary least-squares(OLS)model.The modified stochasticity ratio(MST)results reveal that deterministic selection dominated the assembly of denitrifying bacterial communities.The influence of environmental variables to denitrifying bacterial communities,as well as characteristics of algal-bacterial co-occurrence networks and the assembly process of denitrifying bacterial communities,were discovered in epiphytic biofilms in this study.The findings could aid in the appropriate understanding and use of epiphytic biofilms denitrification function,as well as the enhancement of water quality.

Environment drives the co-occurrence of bacteria and microeukaryotes in a typical subtropical bay

The co-occurrence of bacteria and microeukaryote species is a ubiquitous ecological phenomenon,but there is limited cross-domain research in aquatic environments.We conducted a network statistical analysis and visualization of microbial cross-domain co-occurrence patterns based on DNA sampling of a typical subtropical bay during four seasons,using high-throughput sequencing of both 18S rRNA and 16S rRNA genes.First,we found obvious relationships between network stability and network complexity indices.For example,increased cooperation and modularity were found to weaken the stability of cross-domain networks.Secondly,we found that bacterial operational taxonomic units(OTUs)were the most important contributors to network complexity and stability as they occupied more nodes,constituted more keystone OTUs,built more connections,more importantly,ignoring bacteria led to greater variation in network robustness.Gammaproteobacteria,Alphaproteobacteria,Bacteroidetes,and Actinobacteria were the most ecologically important groups.Finally,we found that the environmental drivers most associated with cross-domain networks varied across seasons(in detail,the network in January was primarily constrained by temperature and salinity,the network in April was primarily constrained by depth and temperature,the network in July was mainly affected by depth,temperature,and salinity,depth was the most important factor affecting the network in October)and that environmental influence was stronger on bacteria than on microeukaryotes.

Community composition,co-occurrence,and environmental drivers of bacterioplankton community in surface and 50-m water layers in the subarctic North Pacific

The Western Subarctic Gyre(WSG)is one of the two gyre-systems in the subarctic North Pacific known for high nutrient and low-chlorophyll waters.However,the bacterioplankton in marine water of this area,either in terms of the taxonomic composition or functional structure,remains relatively unexplored.A total of 22 sampling sites from two water layers(surface water,SW and 50-m layer water,FW)were collected in this area.The physiochemical parameters of waters,Synechococcus,and bacterial density,as well as the bacterioplankton community composition and distribution pattern,were analyzed.The nutrient concentrations of DIN,DIP,and DSi,Chl-a concentration,and the average abundance of heterobacteria in FW were higher than those in SW.However,temperature and the average abundance of Synechococcus and pico-eukaryotes were higher in SW.A total of 3269 OTUs were assigned,and 2123OTUs were commonly shared;moreover,similar alpha diversity patterns were observed in both SW and FW.The bacterioplankton community showed significantly obvious correlation with salinity,DIP,DIN,and Chl a in both SW and FW.Proteobacteria,Cyanobacteria,Bacteroidota,Actinobacteriota,and Firmicutes were the main phyla while Synechococcus_CC9902,Psychrobacter,and Sulfitobacter were the dominant genera in each sampling site.Most correlations that happened between the OTUs in the cooccurrence network were positive and inter-module.Higher edges and graph density were found in SW,indicating that more correlations occurred,and the community was more complex in SW.This study provided novel knowledge on the bacterioplankton community structure and the correlation characteristics in WSG.

A Metric Approach to Hot Topics in Biomedicine via Keyword Co-occurrence

Purpose:To reveal the research hotpots and relationship among three research hot topics in b iomedicine,namely CRISPR,iPS(induced Pluripotent Stem)cell and Synthetic biology.Design/methodology/approach:We set up their keyword co-occurrence networks with using three indicators and information visualization for metric analysis.Findings:The results reveal the main research hotspots in the three topics are different,but the overlapping keywords in the three topics indicate that they are mutually integrated and interacted each other.Research limitations:All analyses use keywords,without any other forms.Practical implications:We try to find the information distribution and structure of these three hot topics for revealing their research status and interactions,and for promoting biomedical developments.Originality/value:We chose the core keywords in three research hot topics in biomedicine by using h-index.

Keyword Co-occurrence Analysis of Research on Innovation Ecosystem Studies

The aim of the paper is to identify and explore leading thematic areas within the research field related to innovation ecosystem.Based on data from the Web of Science database,the keywords frequency and its co-occurrence frequency pair were analyzed,and the theory of mapping knowledge domains was used to visualize the keywords co-occurrence network in innovation ecosystem to make further research of the heated issues.The findings indicate that the research scope involved in innovation ecosystem research is broad,and research content focus on micro and macro levels.According to the results of keywords co-occurrence analysis of different stages,innovation,network,knowledge,strategy,open innovation,value creation are the most important issues to innovation ecosystem research,given their position and role in the research network.The paper generates the added value mainly from the point of view of theory development.

基于co-occurrence相似度的聚类集成方法

首先提出了一种基于属性值的co-occurrence相似度概念,通过对其进一步的研究,提出了3个等价性表述;然后对属性值之间的co-occurrence相似度进行引申,给出了数据对象之间co-occurrence相似度的定义,并将其成功应用到聚类集成方法中。利用co-occurrence相似度在计算某个初始聚类结果中数据对象之间的相似度时,充分考虑了其他初始聚类结果和该初始聚类结果之间的相互影响和联系。实验表明,基于co-occurrence相似度的聚类集成(CSCE)方法能有效识别数据之间的细微结构,有助于提高聚类集成的效果。

基于加权co-occurrence矩阵的聚类集成算法

聚类集成是数据挖掘研究的一个热点。它是利用同一数据集的多个聚类划分集成在一起,以提高聚类分析的性能。当前相关研究大多没有考虑进行集成的聚类成员的质量,因此较差的成员会对集成结果产生不良影响。文中提出了一种基于加权co-occurrence矩阵的聚类集成算法(WCSCE)。该方法首先计算出聚类成员基于属性值的co-occurrence矩阵,然后对聚类成员的质量进行简单评价并赋予权重,生成加权co-occurrence矩阵,进而产生集成结果。最后通过实验验证了该算法的有效性,并提高了聚类质量。

WoS题录Keywords字段关键词频度统计程序设计与实现

使用Visual Basic编程,采用正则表达式批量提取由Web of Science导出的Bib Tex题录中所有Keywords字段关键词,按需合并所得关键词的同义词、近义词及词形变化词,然后将出现频度的统计数据写入Excel表,并编制Excel宏自动生成折线图,实现关键词分布的简单可视化。情报工作者后续可借助Excel功能对该程序生成的Excel表执行复杂的数据组合分析,以提高工作效率。

Artificial intelligence on diabetic retinopathy diagnosis: an automatic classification method based on grey level co-occurrence matrix and naive Bayesian model

AIM: To develop an automatic tool on screening diabetic retinopathy(DR) from diabetic patients.METHODS: We extracted textures from eye fundus images of each diabetes subject using grey level co-occurrence matrix method and trained a Bayesian model based on these textures. The receiver operating characteristic(ROC) curve was used to estimate the sensitivity and specificity of the Bayesian model.RESULTS: A total of 1000 eyes fundus images from diabetic patients in which 298 eyes were diagnosed as DR by two ophthalmologists. The Bayesian model was trained using four extracted textures including contrast, entropy, angular second moment and correlation using a training dataset. The Bayesian model achieved a sensitivity of 0.949 and a specificity of 0.928 in the validation dataset. The area under the ROC curve was 0.938, and the 10-fold cross validation method showed that the average accuracy rate is 93.5%.CONCLUSION: Textures extracted by grey level cooccurrence can be useful information for DR diagnosis, and a trained Bayesian model based on these textures can be an effective tool for DR screening among diabetic patients.

Combined effects of habitat and interspec ificinteraction define co-occurrence patterns of sympatric Galliformes

Background:Disentangling the relative importance of environmental variables and interspecific interaction in modulating co-occurrence patterns of sympatric species is essential for understanding the mechanisms of community assembly and biodiversity. For the two sympatric Galliformes, Silver Pheasants (Lophura nycthemera) and Whitenecklaced Partridges (Arborophila gingica), we know little about the role of habitat use and interspecific interactions in modulating their coexistence. Methods:We adopted a probabilistic approach incorporating habitat preference and interspecific interaction using occupancy model to account for imperfect detection,and used daily activity pattern analysis to investigate the cooccurrence pattern of these two sympatric Galliformes in wet and dry seasons. Results: We found that the detection probability of Silver Pheasant and White-necklaced Partridge were related to habitat variables and interspecific interaction. The presence of Silver Pheasant increases the detection probability of White-necklaced Partridge in both the wet and dry season. However, the presence of White-necklaced Partridges increases the detection probability of Silver Pheasants in the wet season, but decreases the probability in the dry season. Further, Silver Pheasants were detected frequently in the sites of high values of enhanced vegetable index (EVI) in both the wet and dry season, and in sites away from human residential settlement in the wet season. Whitenecklaced partridges were mainly detected in low EVI sites. The site use probabilities of two Galliformes were best explained by habitat variables, Silver Pheasants and White-necklaced Partridges preferred steeper areas during the wet and dry season. Both species mainly occurred in low EVI areas during the wet season and occupied sites away from the resident settlement during the dry season. Moreover, the site use probabilities of two species had opposite relationships with forest canopy coverage. Silver Pheasants preferred areas with high forest canopy coverage whereas White-necklaced Partridges preferred low forest canopy coverage in the dry season, and vice versa in the wet season. Species interaction factor (SIF)corroborated weak evidence of the dependence of the site use of one species on that of the other in the either dry or wet season.Temporally, high overlapping of daily activity pattern indicated no significantly temporal niche differentiation between sympatric Galliformes in both wet and dry seasons. Conclusions:Our results demonstrated that the presence of two species influenced the detection probability interactively and there was no temporal partitioning in activity time between Silver Pheasants and White-necklaced Partridges in the wet and dry seasons.The site use probability of two Galliformes was best explained by habitat variables, especially the forest canopy coverage.Therefore, environmental variables and interspecific interaction are the leading drivers regulating the detection and site use probability and promoting co-occurrence of Silver Pheasants and White-necklaced Partridges.

Assembly and co-occurrence patterns of rare and abundant bacterial sub-communities in rice rhizosphere soil under short-term nitrogen deep placement

Nitrogen(N)deep placement has been found to reduce N leaching and increase N use efficiency in paddy fields.However,relatively little is known how bacterial consortia,especially abundant and rare taxa,respond to N deep placement,which is critical for understanding the biodiversity and function of agricultural ecosystem.In this study,lllumina sequencing and ecological models were conducted to examine the diversity patterns and underlying assembly mechanisms of abundant and rare taxa in rice rhizosphere soil under different N fertilization regimes at four rice growth stages in paddy fields.The results showed that abundant and rare bacteria had distinct distribution patterns in rhizosphere samples.Abundant bacteria showed ubiquitous distribution;while rare taxa exhibited uneven distribution across all samples.Stochastic processes dominated community assembly of both abundant and rare bacteria,with dispersal limitation playing a more vital role in abundant bacteria,and undominated processes playing a more important role in rare bacteria.The N deep placement was associated with a greater influence of dispersal limitation than the broadcast N fertilizer(BN)and no N fertilizer(NN)treatments in abundant and rare taxa of rhizosphere soil;while greater contributions from homogenizing dispersal were observed for BN and NN in rare taxa.Network analysis indicated that abundant taxa with closer relationships were usually more likely to occupy the central position of the network than rare taxa.Nevertheless,most of the keystone species were rare taxa and might have played essential roles in maintaining the network stability.Overall,these findings highlighted that the ecological mechanisms and co-occurrence patterns of abundant and rare bacteria in rhizosphere soil under N deep placement.

An improved algorithm for weighting keywords in web documents

In this paper, an improved algorithm, web-based keyword weight algorithm （WKWA）, is presented to weight keywords in web documents. WKWA takes into account representation features of web documents and advantages of the TF＊IDF, TFC and ITC algorithms in order to make it more appropriate for web documents. Meanwhile, the presented algorithm is applied to improved vector space model （IVSM）. A real system has been implemented for calculating semantic similarities of web documents. Four experiments have been carried out. They are keyword weight calculation, feature item selection, semantic similarity calculation, and WKWA time performance. The results demonstrate accuracy of keyword weight, and semantic similarity is improved.

Co-occurrence of IPMN and malignant IPNB complicated by a pancreatobiliary fistula: A case report and review of the literature

BACKGROUND Intraductal papillary neoplasm of the bile duct(IPNB) is pathologically similar to intraductal papillary mucinous neoplasm(IPMN). However, there are several significant differences between them. The rate of IPMN associated with extrapancreatic malignancies has been reported to range from 10%-40%, and it may occasionally be complicated with the presence of fistulas. IPMN associated with malignant IPNB is extremely rare and only nine cases have been reported in the literature.CASE SUMMARY We report a 52-year-old man who presented with recurrent cholangitis for nine months. Computed tomography and magnetic resonance cholangiopancreatography showed the common bile duct stricture with dilated pancreatobiliary duct without other abnormal findings. The underlying pathogenesis could not be identified based on the radiologic images. Endoscopic retrograde cholangiopancreatography revealed a pancreatobiliary fistula with dilated main pancreatic duct, biliary stricture with dilated biliary tree, and mucus discharge from the enlarged orifice of the major papilla. The patient underwent SpyGlass cholangiopancreatoscopy due to a suspected mucin-producing biliary neoplasm and indeterminate main pancreatic duct dilatation. Multiple papillary growing neoplasms with vascular images, with the extent of lesions spreading in the biliopancreatic ductal lumens, were identified by SpyGlass. In addition, the presence of a pancreatobiliary fistula was also identified. The patient was diagnosed as having benign IPMN and malignant IPNB with focal invasion by postoperative pathology. Furthermore, varying histological subtypes were present in both IPMN and IPNB. Pylorus-preserving pancreaticoduodenectomy was performed on the patient with excellent results during the 52 month followup period.CONCLUSION We deemed that pancreatography and SpyGlass allowed for an efficient diagnosis of IPMN with pancreatobiliary fistula, whereas the etiology could not be identified by radiologic imaging.

Binary Image Steganalysis Based on Distortion Level Co-Occurrence Matrix

In recent years,binary image steganography has developed so rapidly that the research of binary image steganalysis becomes more important for information security.In most state-of-the-art binary image steganographic schemes,they always find out the flippable pixels to minimize the embedding distortions.For this reason,the stego images generated by the previous schemes maintain visual quality and it is hard for steganalyzer to capture the embedding trace in spacial domain.However,the distortion maps can be calculated for cover and stego images and the difference between them is significant.In this paper,a novel binary image steganalytic scheme is proposed,which is based on distortion level co-occurrence matrix.The proposed scheme first generates the corresponding distortion maps for cover and stego images.Then the co-occurrence matrix is constructed on the distortion level maps to represent the features of cover and stego images.Finally,support vector machine,based on the gaussian kernel,is used to classify the features.Compared with the prior steganalytic methods,experimental results demonstrate that the proposed scheme can effectively detect stego images.

Seasonal co-occurrence patterns of bacteria and eukaryotic phytoplankton and the ecological response in urban aquatic ecosystem

Microorganisms play a key role in aquatic ecosystems.Recent studies show that keystone taxa in microbial community could change the community structure and function.However,most previous studies focus on abundant taxa but neglected low abundant ones.To clarify the seasonal variation of bacterial and microalgal communities and understand their synergistic adaptation to diff erent environmental factors,we studied the bacterial and eukaryotic phytoplankton communities in Fenhe River that runs through Taiyuan City,central China,and their seasonal co-occurrence patterns using 16S and 18S rDNA sequencing.Results indicate that positive interaction of eukaryotic phytoplankton network was more active than negative one except winter,indicating that the cooperation(symbiotic phenomenon in which phytoplankton are interdependent and mutually benefi cial)among them could improve the adaption of microbial community to the local environmental changes and maintain the stability of microbial network.The main genera that identifi ed as keystone taxa in bacterial network were Salinivibrio and Sphingopyxis of Proteobacteria and they could respond to the variation of nitrite and make use of it,while those that identifi ed as keystone taxa in eukaryotic phytoplankton network were Pseudoschroederia and Nannochloris,and they were more susceptible to nitrate and phosphate.Mychonastes and Cryptomonas were closely related to water temperature.However,the loss of the co-occurrence by environmental factor changes aff ected the stability of network structure.This study provided a reference for analyzing relationship between bacteria and eukaryotic phytoplankton and revealing potential importance of keystone taxa in similar ecological domains in carbon,nitrogen,and phosphorus dynamics.

Lattice-Based Searchable Encryption Scheme against Inside Keywords Guessing Attack

To save the local storage,users store the data on the cloud server who offers convenient internet services.To guarantee the data privacy,users encrypt the data before uploading them into the cloud server.Since encryption can reduce the data availability,public-key encryption with keyword search(PEKS)is developed to achieve the retrieval of the encrypted data without decrypting them.However,most PEKS schemes cannot resist quantum computing attack,because the corresponding hardness assumptions are some number theory problems that can be solved efficiently under quantum computers.Besides,the traditional PEKS schemes have an inherent security issue that they cannot resist inside keywords guessing attack(KGA).In this attack,a malicious server can guess the keywords encapsulated in the search token by computing the ciphertext of keywords exhaustively and performing the test between the token and the ciphertext of keywords.In the paper,we propose a lattice-based PEKS scheme that can resist quantum computing attacks.To resist inside KGA,this scheme adopts a lattice-based signature technique into the encryption of keywords to prevent the malicious server from forging a valid ciphertext.Finally,some simulation experiments are conducted to demonstrate the performance of the proposed scheme and some comparison results are further shown with respect to other searchable schemes.

3D Gray Level Co-Occurrence Matrix Based Classification of Favor Benign and Borderline Types in Follicular Neoplasm Images

Since the efficiency of treatment of thyroid disorder depends on the risk of malignancy, indeterminate follicular neoplasm (FN) images should be classified. The diagnosis process has been done by visual interpretation of experienced pathologists. However, it is difficult to separate the favor benign from borderline types. Thus, this paper presents a classification approach based on 3D nuclei model to classify favor benign and borderline types of follicular thyroid adenoma (FTA) in cytological specimens. The proposed method utilized 3D gray level co-occurrence matrix (GLCM) and random forest classifier. It was applied to 22 data sets of FN images. Furthermore, the use of 3D GLCM was compared with 2D GLCM to evaluate the classification results. From experimental results, the proposed system achieved 95.45% of the classification. The use of 3D GLCM was better than 2D GLCM according to the accuracy of classification. Consequently, the proposed method probably helps a pathologist as a prescreening tool.

The reflection of hierarchical cluster analysis of co-occurrence matrices in SPSS

Purpose： To discuss the problems arising from hierarchical cluster analysis of co-occurrence matrices in SPSS, and the corresponding solutions. Design/methodology/approach： We design different methods of using the SPSS hierarchical clustering module for co-occurrence matrices in order to compare these methods. We offer the correct syntax to deactivate the similarity algorithm for clustering analysis within the hierarchical clustering module of SPSS. Findings： When one inputs co-occurrence matrices into the data editor of the SPSS hierarchical clustering module without deactivating the embedded similarity algorithm, the program calculates similarity twice, and thus distorts and overestimates the degree of similarity. Practical implications： We offer the correct syntax to block the similarity algorithm for clustering analysis in the SPSS hierarchical clustering module in the case of co-occurrence matrices. This syntax enables researchers to avoid obtaining incorrect results. Originality/value： This paper presents a method of editing syntax to prevent the default use of a similarity algorithm for SPSS＇s hierarchical clustering module. This will help researchers, especially those from China, to properly implement the co-occurrence matrix when using SPSS for hierarchical cluster analysis, in order to provide more scientific and rational results.

A knowledge discovery method based on analysis of multiple co-occurrence relationships in collections of journal papers

Purpose: This paper explores a method of knowledge discovery by visualizing and analyzing co-occurrence relations among three or more entities in collections of journal articles.Design/methodology/approach: A variety of methods such as the model construction,system analysis and experiments are used. The author has improved Morris' crossmapping technique and developed a technique for directly describing,visualizing and analyzing co-occurrence relations among three or more entities in collections of journal articles.Findings: The visualization tools and the knowledge discovery method can efficiently reveal the multiple co-occurrence relations among three entities in collections of journal papers. It can reveal more and in-depth information than analyzing co-occurrence relations between two entities. Therefore,this method can be used for mapping knowledge domain that is manifested in association with the entities from multi-dimensional perspectives and in an all-round way.Research limitations: The technique could only be used to analyze co-occurrence relations of less than three entities at present.Practical implications: This research has expanded the study scope of co-occurrence analysis.The research result has provided a theoretical support for co-occurrence analysis.Originality/value: There has not been a systematic study on co-occurrence relations among multiple entities in collections of journal articles. This research defines multiple co-occurrence and the research scope,develops the visualization analysis tool and designs the analysis model of the knowledge discovery method.