Good and bad dispositions between archaea and bacteria in the human gut:New insights from metagenomic survey and co-occurrence analysis

Archaea are an understudied component of the human microbiome.In this study,the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing.Archaea were ubiquitously found in a wide range of abundances,reaching up to 7.2%.The dominant archaeal phylum was Methanobacteriota,specifically the family Methanobacteriaceae,encompassing more than 50%of Archaea in 50 samples.The previously underestimated Thermoplasmatota,mostly composed of Methanomassiliicoccaceae,dominated in 10 subjects(>50%)and was present in all others except one.Halobacteriota,the sole other archaeal phylum,occurred in negligible concentration,except for two samples(4.6-4.8%).This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway:i)hydrogenotrophic reduction of CO_(2) is the predominant,being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples;ii)the second pathway,that involved Methanomassiliicoccales,was the hydrogenotrophic reduction of methyl-compounds;iii)dismutation of acetate or methyl-compounds seemed to be absent.Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community,allowing to depict a clearer picture of the human gut archaeome.

Effect of land use on soil nematode community composition and co-occurrence network relationship

Land use influences soil biota community composition and diversity,and then belowground ecosystem processes and functions.To characterize the effect of land use on soil biota,soil nematode communities in crop land,forest land and fallow land were investigated in six regions of northern China.Generic richness,diversity,abundance and biomass of soil nematodes was the lowest in crop land.The richness and diversity of soil nematodes were 28.8and 15.1%higher in fallow land than in crop land,respectively.No significant differences in soil nematode indices were found between forest land and fallow land,but their network keystone genera composition was different.Among the keystone genera,50%of forest land genera were omnivores-predators and 36%of fallow land genera were bacterivores.The proportion of fungivores in forest land was 20.8%lower than in fallow land.The network complexity and the stability were lower in crop land than forest land and fallow land.Soil pH,NH_(4)^(+)-N and NO_(3)^(–)-N were the major factors influencing the soil nematode community in crop land while soil organic carbon and moisture were the major factors in forest land.Soil nematode communities in crop land influenced by artificial management practices were more dependent on the soil environment than communities in forest land and fallow land.Land use induced soil environment variation and altered network relationships by influencing trophic group proportions among keystone nematode genera.

Machine learning prediction model for gray-level co-occurrence matrix features of synchronous liver metastasis in colorectal cancer

BACKGROUND Synchronous liver metastasis(SLM)is a significant contributor to morbidity in colorectal cancer(CRC).There are no effective predictive device integration algorithms to predict adverse SLM events during the diagnosis of CRC.AIM To explore the risk factors for SLM in CRC and construct a visual prediction model based on gray-level co-occurrence matrix(GLCM)features collected from magnetic resonance imaging(MRI).METHODS Our study retrospectively enrolled 392 patients with CRC from Yichang Central People’s Hospital from January 2015 to May 2023.Patients were randomly divided into a training and validation group(3:7).The clinical parameters and GLCM features extracted from MRI were included as candidate variables.The prediction model was constructed using a generalized linear regression model,random forest model(RFM),and artificial neural network model.Receiver operating characteristic curves and decision curves were used to evaluate the prediction model.RESULTS Among the 392 patients,48 had SLM(12.24%).We obtained fourteen GLCM imaging data for variable screening of SLM prediction models.Inverse difference,mean sum,sum entropy,sum variance,sum of squares,energy,and difference variance were listed as candidate variables,and the prediction efficiency(area under the curve)of the subsequent RFM in the training set and internal validation set was 0.917[95%confidence interval(95%CI):0.866-0.968]and 0.09(95%CI:0.858-0.960),respectively.CONCLUSION A predictive model combining GLCM image features with machine learning can predict SLM in CRC.This model can assist clinicians in making timely and personalized clinical decisions.

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.

Development and interpretation of ISO 13205:2024,Marine technology-Seawater desalination-Vocabulary

Vocabulary is the most basic subject of standardization.Despite that individual terms related to seawater desalination have been mentioned in some standards and technical documents of ISO,WHO,and ASTM,the inconsistent expression might still induce ambiguity in communications among the participators in this area.Moreover,terms in these documents are not comprehensive.Consequently,ISO 13205:2024 is developed to eliminate the misunderstanding in both the academic and commercial communications.This paper expounds on the specific progress of the research in three aspects:background,drafting of ISO 13205:2024,and interpretation of ISO 13205:2024.The significance of the standard is also discussed.

Training Low-Achiever EFL Learners with Metacognitive Strategy Training for Effective Vocabulary Retention

There is ample research on the vocabulary learning strategies used by EFL and ESL learners.Moreover,many researchers have attempted to discern the effectiveness of teaching vocabulary learning strategies instruction.However,the impact of using metacognitive strategies along with vocabulary learning strategies on weak language learners has not been researched.The aim of this paper is to report on the effects of training low-achiever English as a foreign language learners with vocabulary learning strategies along with metacognitive strategies on vocabulary acquisition.Two B1 level groups of students were assigned as treatment and control groups at a university in Istanbul,Turkey.A Vocabulary Strategy Use Survey was given to identify the vocabulary strategy use of the subjects at the outset of the study.The treatment group was trained on vocabulary learning strategies combined with metacognitive strategy training.The control group studied the same words without any training.A vocabulary test was administered to both groups as a post-test and the results were compared.The findings of the Post-Test demonstrated that training weak language learners with vocabulary learning strategies along with metacognitive strategies has a positive impact on helping these learners increase their lexical knowledge,as the experimental group scored higher on the post-test compared to the control group.

通用学术词表Academic Vocabulary List(AVL)修订述略

学术英语词汇是学术英语教学的重点和难点,不同时代和学科曾编写过各类学术词表。加德纳和戴维斯(2014)基于学术语料容量达1.2亿的COCA语料库推出学术词表Academic Vocabulary List(AVL),该词表在学术英语教学和研究中得到广泛应用。然而实践表明,AVL词表收录的3015个词元存在词汇重复、以词元为单位排列的词表和以词族为单位排列的词表不相吻合等问题。本研究尝试以科学性原则、适切性原则、时效性原则为指导,基于AVL词表原有的比率、分布、离散度、学科指数四条选词标准,增加最低频次和经验判断两条新标准对AVL词表予以完善和修订。完善修订后的AVL词表由先前的1991个词族、3015个词元缩减至709个词族1715个词元,较修订前更具简洁性和高效性。希望依据3项原则和6项标准所做的修订为学术英语教与学以及学术英语教材编写和选用带来新的参考。

A Study of the Use and Translation of Archaic Functional Vocabulary in the Berne Convention

The archaic functional vocabulary is highly with the legal features of formality and conservativeness and still holding a place in legal English.The Berne Convention is a good example to study the use and translation of the archaic functional vocabulary.By studying what archaic functional words or phrases are used in the Berne Convention,their meanings and the different use frequencies of them between the Berne Convention and the Copy Right Law of PRC,it has been found that arhcaic adverbs are used of low frequency,while some adjectives or adjectival groups as well as some prepositions or prepositional phrases are used of high frequencies.The use frequencies of the archaic functional vocabulary is higher in the Berne Convention than those in the Copy Right law of PRC.Some suggestions can be put forward to help improve translating Chinese legal documents into English or writing English legal documents.

A Study on Effective Methods of English Vocabulary Learning

English is a key subject in high school that troubles many students,especially in the aspect of vocabulary learning.Only by laying a good vocabulary foundation can students better complete the learning tasks such as reading,writing,listening,and speaking training.This paper aims to explain the importance of improving the efficiency of English vocabulary learning and discuss the effective methods of English vocabulary learning in high school,in order to help more students find their own learning methods,improve vocabulary memory and application skills,and lay a solid foundation for follow-up learning,examination,and even work.

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。

Co-occurrence Patterns of Above-ground and Below-ground Mite Communities in Farmland of Sanjiang Plain, Northeast China

One of the fundamental questions in community ecology is whether communities are random or formed by deterministic mechanisms. Although many efforts have been made to verify non-randomness in community structure, little is known with regard to co-occurrence patterns in above-ground and below-ground communities. In this paper, we used a null model to test non-randomness in the structure of the above-ground and below-ground mite communities in farmland of the Sanjiang Plain, Northeast China. Then, we used four tests for non-randomness to recognize species pairs that would be demonstrated as significantly aggregated or segregated co-occurrences of the above-ground and below-ground mite communities. The pattern of the above-ground mite commu- nity was significantly non-random in October, suggesting species segregation and hence interspecific competition. Additionally, species co-occurrence patterns did not differ from randomness in the above-ground mite community in August or in below-ground mite com- munities in August and October. Only one significant species pair was detected in the above-ground mite community in August, while no significant species pairs were recognized in the above-ground mite community in October or in the below-ground mite communities in August and October. The results indicate that non-randomness and significant species pairs may not be the general rule in the above-ground and below-ground mite communities in farmland of the Sanjiang Plain at the fine scale.

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.

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.

An Efficient Algorithm for Discovering Co-occurrence Concepts Through Pathfinder Paradigm

The Pathfinder paradigm has been used in generating and analyzing graph models that support clustering similar concepts and minimum-cost paths to provide an associative network structure within a domain. The co-occurrence pathfinder network （ CPFN ） extends the traditional pathfinder paradigm so that co-occurring concepts can be calculated at each sampling time. Existing algorithms take O（n（s）） time to calculate the pathfinder network （PFN） at each sampling time for a non-completed input graph of a CPFN （r = ∞, q = n - 1）, where n is the number of nodes in the input graph, r is the Minkowski exponent and q is the maximum number of links considered in finding a minimum cost path between vertices. To reduce the complexity of calculating the CPFN, we propose a greedy based algorithm, MEC（G） algorithm, which takes shortcuts to avoid unnecessary steps in the existing algorithms, to correctly calculate a CPFN （r = ∞, q= n - 1） in O（klogk） time where k is the number of edges of the input graph. Our example demonstrates the efficiency and correctness of the proposed MEC（G） algorithm, confirming our mathematic analysis on this algorithm.