Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing act...Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing activity and thus play signifi cant roles in organic carbon remineralization,benthic geochemical action,and plant-microbe interactions.Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors.Therefore,in this study,functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China:Zostera japonica and Scirpus mariqueter.To this end,some physicochemical characteristics of the sediments as well as the phylogenetic structure,community composition,diversity,and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed.The Z.japonic a meadow had a higher dissimilatory sulfate reduction capability than the S.mariqueter-comprising saltmarsh,owing to its larger proportion of SRB in the microbial community,larger proportions of functional genes involved in dissimilatory sulfate reduction,and the stronger ability of the SRB to degrade organic substrates completely.This study confi rmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB,which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.展开更多
This study investigated the effects of planting duration(1,5,10 and 15 years)on soil properties,bacterial community diversity,and function in the rhizosphere of Zanthoxylum bungeanum.We employed Illumina highthroughpu...This study investigated the effects of planting duration(1,5,10 and 15 years)on soil properties,bacterial community diversity,and function in the rhizosphere of Zanthoxylum bungeanum.We employed Illumina highthroughput sequencing and PICRUSt2 functional prediction to analyze the structure and functional potential of rhizosphere soil bacterial communities.The Mantel test and redundancy analysis were used to identify physicochemical factors influencing bacterial community structure and function.The results indicated significant differences in rhizosphere soil physicochemical properties across planting years:the content of organic matter,alkaline hydrolyzable nitrogen in the soil,as well as the activity of invertase,urease,and alkaline phosphatase initially increased and then decreased,while available potassium,Olsen-phosphorus content,and peroxidase activity continued to increase.However,bacterial alpha diversity(Chao1 and Shannon indices)and the number of amplicon sequence variants increased continuously with planting duration.Principal coordinate analysis and Adonis tests revealed that the planting year significantly influenced the bacterial community structure(p<0.05).The phyla Proteobacteria,Actinobacteria,Acidobacteriota and Chloroflexi collectively constituted 56.7%to 71.2%of the relative abundance,representing the dominant taxa.PICRUSt2 predictions indicated key functional categories(cellular processes,metabolism,genetic information processing,and environmental information processing)each exceeding 10%relative abundance.BugBase analysis revealed a progressive increase in aerobic and oxidative stress-tolerant bacteria and a decrease in anaerobic and potentially pathogenic bacteria.Differential indicator species analysis identified Firmicutes,Planctomycetes,Methylomirabilota and Actinobacteriota as key discriminators for the 1-,5-,10-and 15-year stages,respectively.Organic matter,alkaline phosphatase,soil pH,and available phosphorus were the primary physicochemical drivers of bacterial communities.Notably,soil organic matter significantly influenced both the community structure(p<0.05)and predictedmetabolic functions(p<0.05).In conclusion,prolonged planting duration significantly enhanced rhizosphere microbial diversity and functional gene abundance in Z.bungeanumwhile driving the structural succession of bacterial communities dominated by Proteobacteria,Actinobacteria,Acidobacteriota,and Chloroflexi.This ecological shift,characterized by increased aerobic/oxidative-stress taxa and decreased anaerobic/pathogenic bacteria,was primarily regulated by soil organic matter,a key driver shaping both community structure and metabolic functions,ultimately improving soil microecological health.展开更多
Diversity of soil microorganisms in different habitats of arid and semi-arid areas plays an important role in the soil texture and nutrient,promoting the growth of vegetation in those areas.To clarify the response of ...Diversity of soil microorganisms in different habitats of arid and semi-arid areas plays an important role in the soil texture and nutrient,promoting the growth of vegetation in those areas.To clarify the response of soil bacterial community diversity to the changes of environmental factors in different habitats,this study collected soil samples under the canopies of Tamarix ramosissima Ledeb.in oasis,transition zone,and desert habitats in the upper reaches of the Tarim River,Northwest China.High-throughput sequencing technology and PICRUSt2 software were used to explore the composition and function of soil bacterial communities in different habitats of T.ramosissima.The results showed that:(1)soil environmental factors under the canopy of T.ramosissima in the three habitats differed significantly,with soil moisture and nutrient conditions being better in the oasis;(2)Proteobacteria,Bacteroidetes,Firmicutes,Actinobacteria,and Gemmatimonadetes were the major bacterial communities in the three habitats;(3)soil bacterial community composition under the canopy of T.ramosissima varied greatly,and the richness was significantly different among the three habitats;(4)redundancy analysis indicated that soil water content and available phosphorous were the most important environmental factors influencing the composition of soil bacterial community;and(5)6 primary functions and 21 secondary functions were obtained by PICRUSt2 function prediction,with metabolism being the most dominant function.This study revealed the response of soil bacterial community composition to habitat changes and their driving factors in the upper reaches of the Tarim River,which could improve the understanding of ecological sensitivity of soil microorganisms in arid and semi-arid areas,and provide a theoretical foundation for improving soil quality and ecological protection.展开更多
Microbial corrosion of hydraulic concrete structures(HCSs)has received increasing research concerns.However,knowledge on the morphology of attached biofilms,as well as the community structures and functions cultivated...Microbial corrosion of hydraulic concrete structures(HCSs)has received increasing research concerns.However,knowledge on the morphology of attached biofilms,as well as the community structures and functions cultivated under variable nutrient levels is lacking.Here,biofilm colonization patterns and community structures responding to variable levels of ammonia and sulfate were explored.From field sampling,NH_(4)^(+)-N was proven key factor governing community structure in attached biofilms,verifying the reliability of selecting target nutrient species in batch experiments.Biofilms exhibited significant compositional differences in field sampling and incubation experiments.As the nutrient increased in batch experiments,the growth of biofilms gradually slowed down and uneven distribution was detected.The proportions of proteins and β-d-glucose polysaccharides in biofilms experienced a decrease in response to elevated levels of nutrients.With the increased of nutrients,themass losses of concretes exhibited an increase,reaching a highest value of 2.37%in the presence of 20 mg/L of ammonia.Microbial communities underwent a significant transition in structure and metabolic functions to ammonia gradient.The highest activity of nitrification was observed in biofilms colonized in the presence of 20 mg/L of ammonia.While the communities and their functions remained relativelymore stable responding to sulfate gradient.Our research provides novel insights into the structures of biofilms attached on HCSs and the metabolic functions in the presence of high level of nutrients,which is of significance for the operation and maintenance of hydraulic engineering structures.展开更多
The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how...The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.展开更多
Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investig...Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation.Within the context of protein research,an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings.Due to the exorbitant costs and limited throughput inherent in experimental investigations,computational models offer a promising alternative to accelerate protein function annotation.In recent years,protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks.This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction.In this review,we elucidate the historical evolution and research paradigms of computational methods for predicting protein function.Subsequently,we summarize the progress in protein and molecule representation as well as feature extraction techniques.Furthermore,we assess the performance of machine learning-based algorithms across various objectives in protein function prediction,thereby offering a comprehensive perspective on the progress within this field.展开更多
For autonomous vehicles and driver assist systems,path planning and collision avoidance algorithms benefit from accurate predictions of future location of other vehicles and intent of their drivers.In the literature,t...For autonomous vehicles and driver assist systems,path planning and collision avoidance algorithms benefit from accurate predictions of future location of other vehicles and intent of their drivers.In the literature,the algorithms that provide driver intent belong to two categories:those that use physics based models with some type of filtering,and machine learning based approaches.In this paper we employ barrier functions(BF)to decide driver intent.BFs are typically used to prove safety by establishing forward invariance of an admissible set.Here,we decide if the“target”vehicle is violating one or more possibly fictitious(i.e.,non-physical)barrier constraints determined based on the context provided by the road geometry.The algorithm has a very small computational footprint and better false positive and negative rates than some of the alternatives.The predicted intent is then used by a control barrier function(CBF)based collision avoidance system to prevent unnecessary interventions,for either an autonomous or human-driven vehicle.展开更多
[Objective] The study was to analyze the structure and function of HpaGXoo and the relationship between the two.[Method] Some related bioinformatics analysis software on internet such as NPSA,Swiss-Model,SAPS and Inte...[Objective] The study was to analyze the structure and function of HpaGXoo and the relationship between the two.[Method] Some related bioinformatics analysis software on internet such as NPSA,Swiss-Model,SAPS and InterPro Scan were adopted to analyze the structure and predict its function.[Result] HpaGXoo consists of 139 amino acids,and has many alpha-helical and coiled structure,no signal peptide on N-terminal and no transmembrane structure.It locates in bacterial cytoplasm.[Conclusion] The study will lay ...展开更多
Background:Bacillus amyloliquefaciens(BA)and Bacillus subtilis(BS)are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals.However,few research have reported the effects of...Background:Bacillus amyloliquefaciens(BA)and Bacillus subtilis(BS)are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals.However,few research have reported the effects of BA and BS on fermentation characteristics and bacterial community successions of whole-plant corn silage during ensiling.If the BA and BS inoculants have positive effects on silages,then they could not only improve fermentation characteristics,but also deliver BA or BS viable cells to ruminants,which would play its probiotic effect.Therefore,the objectives of this study were to investigate the effects of BA and BS on the fermentation,chemical characteristics,bacterial community and their metabolic pathway of whole-plant corn silage.Results:Freshly chopped whole-plant corn was inoculated without or with BA and BS,respectively,and ensiled for1,3,7,14 and 60 d.Results showed that BA and BS inoculations increased lactic acid concentrations of whole-plant corn silages compared with control,and BA inoculation decreased acetic acid concentrations,whereas BS inoculation decreased fiber contents and increased crude protein(CP)content.Higher water-soluble carbohydrate contents and lower starch contents were observed in BA-and BS-inoculated silages compared with that in control.The decreased CP content and increased non-protein nitrogen content were observed in BA-inoculated silage,which was consistent with the higher amino acid metabolism abundances observed in BA-inoculated silage.In addition,it was noteworthy that BA and BS inoculations increased the metabolism of cofactors and vitamins,and decreased the relative abundances of drug resistance:antimicrobial pathways.We also found that the bacterial metabolism pathways were clearly separated into three clusters based on the ensiling times of whole-plant corn silage in the present study.There were no significant differences in bacterial community compositions among the three groups during ensiling.However,BA and BS inoculations decreased the relative abundances of undesirable bacteria such as Acetobacter and Acinetobacter.Conclusion:Our findings suggested that the BS strain was more suitable as silage inoculants than the BA strain in whole-plant corn silage in this study.展开更多
The general regression neural network(GRNN) model was proposed to model and predict the length of day(LOD) change, which has very complicated time-varying characteristics. Meanwhile, considering that the axial atmosph...The general regression neural network(GRNN) model was proposed to model and predict the length of day(LOD) change, which has very complicated time-varying characteristics. Meanwhile, considering that the axial atmospheric angular momentum(AAM) function is tightly correlated with the LOD changes, it was introduced into the GRNN prediction model to further improve the accuracy of prediction. Experiments with the observational data of LOD changes show that the prediction accuracy of the GRNN model is 6.1% higher than that of BP network, and after introducing AAM function, the improvement of prediction accuracy further increases to 14.7%. The results show that the GRNN with AAM function is an effective prediction method for LOD changes.展开更多
The random delays in a networked control system (NCS) degrade control performance and can even destabilize the control system.To deal with this problem,the time-stamped predictive functional control (PFC) algorithm is...The random delays in a networked control system (NCS) degrade control performance and can even destabilize the control system.To deal with this problem,the time-stamped predictive functional control (PFC) algorithm is proposed,which generalizes the standard PFC algorithm to networked control systems with random delays.The algorithm uses the time-stamp method to estimate the control delay,predicts the future outputs based on a discrete time delay state space model,and drives the control law that applies to an NCS from the idea of a PFC algorithm.A networked control system was constructed based on TrueTime simulator,with which the time-stamped PFC algorithm was compared with the standard PFC algorithm.The response curves show that the proposed algorithm has better control performance.展开更多
The rhizosphere bacteria play crucial roles in plant health and growth as they are involved in assimilating nutrients and resisting adverse conditions such as nutrient stress,drought,and wind erosion.Agriophyllum squa...The rhizosphere bacteria play crucial roles in plant health and growth as they are involved in assimilating nutrients and resisting adverse conditions such as nutrient stress,drought,and wind erosion.Agriophyllum squarrosum(L.)Moq.is a pioneer plant used in sand fixation due to its strong resistance to drought and wind erosion.However,the bacterial community characteristics and ecological function in the rhizosphere of A.squarrosum are poorly understood.In this study,soil samples were collected from different developmental stages(seedling stage,vegetative stage,reproductive stage,and withering stage)of A.squarrosum.Illumina Miseq sequencing was used to detect differences in soil bacterial abundance.The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States(PICRUSt)program was used to predict bacterial functions,and the relationships among bacteria,functional populations,and soil nutrients were examined using a heatmap analysis.The results showed that the Shannon and Sobs indices of rhizosphere bacteria were significantly higher during the reproductive stage than during the other stages.Pantoea sp.(7.03%)was the dominant genus during the seedling stage;Arthrobacter sp.was the dominant genus during the vegetative(13.94%),reproductive(7.57%),and withering(12.30%)stages.The relative abundances of Chloroflexi,Acidobacteria,and Gemmatimonadetes were significantly high during the reproductive stage.According to the PICRUSt analysis,membrane transport,signal transduction,and environmental adaptation of the bacterial functional population occurred during the seedling stage.Carbohydrate metabolism increased during the vegetative stage,while energy metabolism,lipid metabolism,and biosynthesis of other secondary metabolites of the bacterial functional population significantly increased during the reproductive stage.The abundances of bacterial communities,functional genes,and soil nutrients were synergistically altered during various developmental stages.Our findings suggest that the developmental stages of A.squarrosum play a significant role in defining the composition and structure of bacterial communities in the rhizosphere.The results will provide a basis for better prediction and understanding of soil bacterial metabolic potential and functions of A.squarrosum rhizosphere in sandy areas.展开更多
The Qinghai-Xizang Plateau presents an extreme environment characterized by high altitude,low oxygen availability,and harsh living conditions.High-altitude-residing amphibians,such as Rana kukunoris,have evolved speci...The Qinghai-Xizang Plateau presents an extreme environment characterized by high altitude,low oxygen availability,and harsh living conditions.High-altitude-residing amphibians,such as Rana kukunoris,have evolved specific physiological adaptations to survive in these habitats.However,the composition and functional significance of their gut microbiota with regard to these adaptations remain poorly explored.This study utilized 16S rR NA gene sequencing to characterize and compare the gut microbiota of Rana kukunoris with that of two low-altitude frogs,Rana amurensis and Rana dybowskii,to investigate potential microbial contributions to high-altitude adaptation.Results revealed significant differences in gut microbiota diversity and composition between high-and lowaltitude frogs.Notably,Akkermansia muciniphila and Desulfovibrio species were significantly enriched in Rana kukunoris.Functional predictions indicated significant enrichment of arginine biosynthesis pathways and associated metabolic processes in the high-altitude frog,which may enhance oxygen utilization and vascular homeostasis under hypoxic conditions.These findings provide insights into the gut microbiota of Rana kukunoris and suggest a potential crucial role in facilitating physiological adaptations to extreme environments through enhanced metabolic flexibility and stress resistance.展开更多
A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology (GO) annotations together. The operation system was based on Debian Linux 3.1, with Apache as the web server and Mysql ...A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology (GO) annotations together. The operation system was based on Debian Linux 3.1, with Apache as the web server and Mysql database as the data storage system. FASTA files with GO annotations were taken as the sequence source for blast alignment, which were formatted by wu-formatdb program. The GoBlast system includes three Bioperl modules in Perl:a data input module, a data process module and a data output module. A GoBlast query starts with an amino acid or nucleotide sequence. It ends with an output in an html page, presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts. A simple click on a GO term leads to the detailed explanation of the specific gene function. This avails gene function prediction by Blast. GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.展开更多
In heating, ventilating and air-conditioning （HVAC） systems, there exist severe nonlinearity, time-varying nature, disturbances and uncertainties. A new predictive functional control based on Takagi-Sugeno （T-S） f...In heating, ventilating and air-conditioning （HVAC） systems, there exist severe nonlinearity, time-varying nature, disturbances and uncertainties. A new predictive functional control based on Takagi-Sugeno （T-S） fuzzy model was proposed to control HVAC systems. The T-S fuzzy model of stabilized controlled process was obtained using the least squares method, then on the basis of global linear predictive model from T-S fuzzy model, the process was controlled by the predictive functional controller. Especially the feedback regulation part was developed to compensate uncertainties of fuzzy predictive model. Finally simulation test results in HVAC systems control applications showed that the proposed fuzzy model predictive functional control improves tracking effect and robustness. Compared with the conventional PID controller, this control strategy has the advantages of less overshoot and shorter setting time, etc.展开更多
The control of gas fractionation unit(GFU) in petroleum industry is very difficult due to multivariable characteristics and a large time delay.PID controllers are still applied in most industry processes.However,the t...The control of gas fractionation unit(GFU) in petroleum industry is very difficult due to multivariable characteristics and a large time delay.PID controllers are still applied in most industry processes.However,the traditional PID control has been proven not sufficient and capable for this particular petro-chemical process.In this work,an incremental multivariable predictive functional control(IMPFC) algorithm was proposed with less online computation,great precision and fast response.An incremental transfer function matrix model was set up through the step-response data,and predictive outputs were deduced with the theory of single-value optimization.The results show that the method can optimize the incremental control variable and reject the constraint of the incremental control variable with the positional predictive functional control algorithm,and thereby making the control variable smoother.The predictive output error and future set-point were approximated by a polynomial,which can overcome the problem under the model mismatch and make the predictive outputs track the reference trajectory.Then,the design of incremental multivariable predictive functional control was studied.Simulation and application results show that the proposed control strategy is effective and feasible to improve control performance and robustness of process.展开更多
In order to obtain accurate prediction model and compensate for the influence of model mismatch on the control performance of the system and avoid solving nonlinear programming problem,an adaptive fuzzy predictive fun...In order to obtain accurate prediction model and compensate for the influence of model mismatch on the control performance of the system and avoid solving nonlinear programming problem,an adaptive fuzzy predictive functional control(AFPFC) scheme for multivariable nonlinear systems was proposed.Firstly,multivariable nonlinear systems were described based on Takagi-Sugeno(T-S) fuzzy models;assuming that the antecedent parameters of T-S models were kept,the consequent parameters were identified on-line by using the weighted recursive least square(WRLS) method.Secondly,the identified T-S models were linearized to be time-varying state space model at each sampling instant.Finally,by using linear predictive control technique the analysis solution of the optimal control law of AFPFC was established.The application results for pH neutralization process show that the absolute error between the identified T-S model output and the process output is smaller than 0.015;the tracking ability of the proposed AFPFC is superior to that of non-AFPFC(NAFPFC) for pH process without disturbances,the overshoot of the effluent pH value of AFPFC with disturbances is decreased by 50% compared with that of NAFPFC;when the process parameters of AFPFC vary with time the integrated absolute error(IAE) performance index still retains to be less than 200 compared with that of NAFPFC.展开更多
The predictive model is built according to the characteristics of the impulse response of integrating process. In order to eliminate the permanent offset between the setpoint and the process output in the presence of ...The predictive model is built according to the characteristics of the impulse response of integrating process. In order to eliminate the permanent offset between the setpoint and the process output in the presence of the load disturbance, a novel error compensation method is proposed. Then predictive functional control of integrating process is designed. The method given generates a simple control structure, which can significandy reduce online computation. Furthermore, the tuning of the controller is fairly straightforward. Simulation results indicate that the designed control system is relatively robust to the parameters variation of the process.展开更多
The surface subsidence is a common environmental hazard in mined-out area. Based on careful analysis of the regularity of surface subsidence in mined-out area, we proposed a new time function based on Harris curve mod...The surface subsidence is a common environmental hazard in mined-out area. Based on careful analysis of the regularity of surface subsidence in mined-out area, we proposed a new time function based on Harris curve model in consideration of the shortage of current surface subsidence time functions. By analyzing the characteristics of the new time function, we found that it could meet the dynamic process, the velocity change process and the acceleration change process during surface subsidence. Then its rationality had been verified through project cases. The results show that the proposed time function model can give a good reflection of the regularity of surface subsidence in mined-out area and can accurately predict surface subsidence. And the prediction data of the model are a little greater than measured data on condition of proper measured data quantity, which is safety in the engineering. This model provides a new method for the analysis of surface subsidence in mined-out area and reference for future prediction, and it is valuable to engineering application.展开更多
Reaction control system(RCS) is a powerful and efficient actuator for space vehicles attitude control, which is typically characterized as a pulsed unilateral effector only with two states(off/on). Along with inevitab...Reaction control system(RCS) is a powerful and efficient actuator for space vehicles attitude control, which is typically characterized as a pulsed unilateral effector only with two states(off/on). Along with inevitable internal uncertainties and external disturbances in practice, this inherent nonlinear character always hinders space vehicles autopilot from pursuing precise tracking performance. Compared to most of pre-existing methodologies that passively suppress the uncertainties and disturbances, a design based on predictive functional control(PFC) and generalized extended state observer(GESO) is firstly proposed for three-axis RCS control system to actively reject that with no requirement for additional fuel consumption. To obtain a high fidelity predictive model on which the performance of PFC greatly depends, the nonlinear coupling multiple-input multiple-output(MIMO) flight dynamics model is parameterized as a state-dependent coefficient form. And based on that, a MIMO PFC algorithm in state space domain for a plant of arbitrary orders is deduced in this paper.The internal uncertainties and external disturbances are lumped as a total disturbance, which is estimated and cancelled timely to further enhance the robustness. The continuous control command synthesised by above controller-rejector tandem is finally modulated by pulse width pulse frequency modulator(PWPF) to on-off signals to meet RCS requirement. The robustness and feasibility of the proposed design are validated by a series of performance comparison simulations with some prominent methods in the presence of significant perturbations and disturbances, as well as measurement noise.展开更多
基金Supported by the Scientifi c Research Fund of the Second Institute of Oceanography,Ministry of Natural Resources(MNR)(Nos.JB1906,JG1616,JG1910)the Zhejiang Qingshan Lake Innovation Platform for Marine Science and Technology(No.2017E80001)+4 种基金the Key Projects of Philosophy and Social Sciences Research,Ministry of Education(No.18JZD059)the National Key Technology Research and Development Program of the Ministry of Science and Technology of the China(No.2015BAD08B01)the State Key Laboratory of Satellite Ocean Environment Dynamics(No.SOEDZZ1902)the National Natural Science Foundation of China(No.41806136)the Project of Long Term Observation and Research Plan in the Changjiang Estuary and the Adjacent East China Sea(LORCE,14282)。
文摘Sulfate-reducing bacteria(SRB)are ubiquitous anaerobic microorganisms that play signifi cant roles in the global biogeochemical cycle.Coastal wetlands,one of the major habitats of SRB,exhibit high sulfate-reducing activity and thus play signifi cant roles in organic carbon remineralization,benthic geochemical action,and plant-microbe interactions.Recent studies have provided credible evidence that the functional rather than the taxonomic composition of microbes responds more closely to environmental factors.Therefore,in this study,functional gene prediction based on PacBio single molecular real-time sequencing of 16S rDNA was applied to determine the sulfate-reducing and organic substrate-decomposing activities of SRB in the rhizospheres of two typical coastal wetland plants in North and South China:Zostera japonica and Scirpus mariqueter.To this end,some physicochemical characteristics of the sediments as well as the phylogenetic structure,community composition,diversity,and proportions of several functional genes of the SRB in the two plant rhizospheres were analyzed.The Z.japonic a meadow had a higher dissimilatory sulfate reduction capability than the S.mariqueter-comprising saltmarsh,owing to its larger proportion of SRB in the microbial community,larger proportions of functional genes involved in dissimilatory sulfate reduction,and the stronger ability of the SRB to degrade organic substrates completely.This study confi rmed the feasibility of applying microbial community function prediction in research on the metabolic features of SRB,which will be helpful for gaining new knowledge of the biogeochemical and ecological roles of these bacteria in coastal wetlands.
基金supported by Forestry and Grassland Science and Technology Innovation Project(LCKJCX2022001)from Forestry and Grassland Bureau of Gansu Province’s.
文摘This study investigated the effects of planting duration(1,5,10 and 15 years)on soil properties,bacterial community diversity,and function in the rhizosphere of Zanthoxylum bungeanum.We employed Illumina highthroughput sequencing and PICRUSt2 functional prediction to analyze the structure and functional potential of rhizosphere soil bacterial communities.The Mantel test and redundancy analysis were used to identify physicochemical factors influencing bacterial community structure and function.The results indicated significant differences in rhizosphere soil physicochemical properties across planting years:the content of organic matter,alkaline hydrolyzable nitrogen in the soil,as well as the activity of invertase,urease,and alkaline phosphatase initially increased and then decreased,while available potassium,Olsen-phosphorus content,and peroxidase activity continued to increase.However,bacterial alpha diversity(Chao1 and Shannon indices)and the number of amplicon sequence variants increased continuously with planting duration.Principal coordinate analysis and Adonis tests revealed that the planting year significantly influenced the bacterial community structure(p<0.05).The phyla Proteobacteria,Actinobacteria,Acidobacteriota and Chloroflexi collectively constituted 56.7%to 71.2%of the relative abundance,representing the dominant taxa.PICRUSt2 predictions indicated key functional categories(cellular processes,metabolism,genetic information processing,and environmental information processing)each exceeding 10%relative abundance.BugBase analysis revealed a progressive increase in aerobic and oxidative stress-tolerant bacteria and a decrease in anaerobic and potentially pathogenic bacteria.Differential indicator species analysis identified Firmicutes,Planctomycetes,Methylomirabilota and Actinobacteriota as key discriminators for the 1-,5-,10-and 15-year stages,respectively.Organic matter,alkaline phosphatase,soil pH,and available phosphorus were the primary physicochemical drivers of bacterial communities.Notably,soil organic matter significantly influenced both the community structure(p<0.05)and predictedmetabolic functions(p<0.05).In conclusion,prolonged planting duration significantly enhanced rhizosphere microbial diversity and functional gene abundance in Z.bungeanumwhile driving the structural succession of bacterial communities dominated by Proteobacteria,Actinobacteria,Acidobacteriota,and Chloroflexi.This ecological shift,characterized by increased aerobic/oxidative-stress taxa and decreased anaerobic/pathogenic bacteria,was primarily regulated by soil organic matter,a key driver shaping both community structure and metabolic functions,ultimately improving soil microecological health.
基金supported by the Sciences Foundation of Xinjiang Uygur Autonomous Region(2024D01C32)the Xinjiang Uygur Autonomous Region Education Department Basic Scientific Project(XJEDU2023P005)+1 种基金the National Natural Science Foundation of China(32001145)the 2024 Xinjiang Uygur Autonomous Region Postdoctoral Funding Project.
文摘Diversity of soil microorganisms in different habitats of arid and semi-arid areas plays an important role in the soil texture and nutrient,promoting the growth of vegetation in those areas.To clarify the response of soil bacterial community diversity to the changes of environmental factors in different habitats,this study collected soil samples under the canopies of Tamarix ramosissima Ledeb.in oasis,transition zone,and desert habitats in the upper reaches of the Tarim River,Northwest China.High-throughput sequencing technology and PICRUSt2 software were used to explore the composition and function of soil bacterial communities in different habitats of T.ramosissima.The results showed that:(1)soil environmental factors under the canopy of T.ramosissima in the three habitats differed significantly,with soil moisture and nutrient conditions being better in the oasis;(2)Proteobacteria,Bacteroidetes,Firmicutes,Actinobacteria,and Gemmatimonadetes were the major bacterial communities in the three habitats;(3)soil bacterial community composition under the canopy of T.ramosissima varied greatly,and the richness was significantly different among the three habitats;(4)redundancy analysis indicated that soil water content and available phosphorous were the most important environmental factors influencing the composition of soil bacterial community;and(5)6 primary functions and 21 secondary functions were obtained by PICRUSt2 function prediction,with metabolism being the most dominant function.This study revealed the response of soil bacterial community composition to habitat changes and their driving factors in the upper reaches of the Tarim River,which could improve the understanding of ecological sensitivity of soil microorganisms in arid and semi-arid areas,and provide a theoretical foundation for improving soil quality and ecological protection.
基金supported by the National Key Research and Development Project of China(No.2021YFB2600200)the National Natural Science Foundation of China(Nos.52470185 and 52170159)the Open Research Fund of National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety,the Fund of National Key Laboratory of Water Disaster Prevention and Key Research and Development Program of Jiangsu Province(No.BE2022601).
文摘Microbial corrosion of hydraulic concrete structures(HCSs)has received increasing research concerns.However,knowledge on the morphology of attached biofilms,as well as the community structures and functions cultivated under variable nutrient levels is lacking.Here,biofilm colonization patterns and community structures responding to variable levels of ammonia and sulfate were explored.From field sampling,NH_(4)^(+)-N was proven key factor governing community structure in attached biofilms,verifying the reliability of selecting target nutrient species in batch experiments.Biofilms exhibited significant compositional differences in field sampling and incubation experiments.As the nutrient increased in batch experiments,the growth of biofilms gradually slowed down and uneven distribution was detected.The proportions of proteins and β-d-glucose polysaccharides in biofilms experienced a decrease in response to elevated levels of nutrients.With the increased of nutrients,themass losses of concretes exhibited an increase,reaching a highest value of 2.37%in the presence of 20 mg/L of ammonia.Microbial communities underwent a significant transition in structure and metabolic functions to ammonia gradient.The highest activity of nitrification was observed in biofilms colonized in the presence of 20 mg/L of ammonia.While the communities and their functions remained relativelymore stable responding to sulfate gradient.Our research provides novel insights into the structures of biofilms attached on HCSs and the metabolic functions in the presence of high level of nutrients,which is of significance for the operation and maintenance of hydraulic engineering structures.
基金supported by the King Abdullah University of Science and Technology(KAUST)Office of Sponsored Research(OSR)(Grant Nos.URF/1/1976-04,URF/1/1976-06)。
文摘The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.
基金supported in part by the National Natural Science Foundation of China(22033001)the National Key R&D Program of China(2022YFA1303700)the Chinese Academy of Medical Sciences(2021-I2M-5-014).
文摘Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation.Within the context of protein research,an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings.Due to the exorbitant costs and limited throughput inherent in experimental investigations,computational models offer a promising alternative to accelerate protein function annotation.In recent years,protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks.This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction.In this review,we elucidate the historical evolution and research paradigms of computational methods for predicting protein function.Subsequently,we summarize the progress in protein and molecule representation as well as feature extraction techniques.Furthermore,we assess the performance of machine learning-based algorithms across various objectives in protein function prediction,thereby offering a comprehensive perspective on the progress within this field.
文摘For autonomous vehicles and driver assist systems,path planning and collision avoidance algorithms benefit from accurate predictions of future location of other vehicles and intent of their drivers.In the literature,the algorithms that provide driver intent belong to two categories:those that use physics based models with some type of filtering,and machine learning based approaches.In this paper we employ barrier functions(BF)to decide driver intent.BFs are typically used to prove safety by establishing forward invariance of an admissible set.Here,we decide if the“target”vehicle is violating one or more possibly fictitious(i.e.,non-physical)barrier constraints determined based on the context provided by the road geometry.The algorithm has a very small computational footprint and better false positive and negative rates than some of the alternatives.The predicted intent is then used by a control barrier function(CBF)based collision avoidance system to prevent unnecessary interventions,for either an autonomous or human-driven vehicle.
基金Supported by Langfang Teachers College Research Grant(LSZB200803)~~
文摘[Objective] The study was to analyze the structure and function of HpaGXoo and the relationship between the two.[Method] Some related bioinformatics analysis software on internet such as NPSA,Swiss-Model,SAPS and InterPro Scan were adopted to analyze the structure and predict its function.[Result] HpaGXoo consists of 139 amino acids,and has many alpha-helical and coiled structure,no signal peptide on N-terminal and no transmembrane structure.It locates in bacterial cytoplasm.[Conclusion] The study will lay ...
基金funded by National Natural Science Foundation of China(project no.31872417)。
文摘Background:Bacillus amyloliquefaciens(BA)and Bacillus subtilis(BS)are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals.However,few research have reported the effects of BA and BS on fermentation characteristics and bacterial community successions of whole-plant corn silage during ensiling.If the BA and BS inoculants have positive effects on silages,then they could not only improve fermentation characteristics,but also deliver BA or BS viable cells to ruminants,which would play its probiotic effect.Therefore,the objectives of this study were to investigate the effects of BA and BS on the fermentation,chemical characteristics,bacterial community and their metabolic pathway of whole-plant corn silage.Results:Freshly chopped whole-plant corn was inoculated without or with BA and BS,respectively,and ensiled for1,3,7,14 and 60 d.Results showed that BA and BS inoculations increased lactic acid concentrations of whole-plant corn silages compared with control,and BA inoculation decreased acetic acid concentrations,whereas BS inoculation decreased fiber contents and increased crude protein(CP)content.Higher water-soluble carbohydrate contents and lower starch contents were observed in BA-and BS-inoculated silages compared with that in control.The decreased CP content and increased non-protein nitrogen content were observed in BA-inoculated silage,which was consistent with the higher amino acid metabolism abundances observed in BA-inoculated silage.In addition,it was noteworthy that BA and BS inoculations increased the metabolism of cofactors and vitamins,and decreased the relative abundances of drug resistance:antimicrobial pathways.We also found that the bacterial metabolism pathways were clearly separated into three clusters based on the ensiling times of whole-plant corn silage in the present study.There were no significant differences in bacterial community compositions among the three groups during ensiling.However,BA and BS inoculations decreased the relative abundances of undesirable bacteria such as Acetobacter and Acinetobacter.Conclusion:Our findings suggested that the BS strain was more suitable as silage inoculants than the BA strain in whole-plant corn silage in this study.
基金Projects(U1231105,10878026)supported by the National Natural Science Foundation of China
文摘The general regression neural network(GRNN) model was proposed to model and predict the length of day(LOD) change, which has very complicated time-varying characteristics. Meanwhile, considering that the axial atmospheric angular momentum(AAM) function is tightly correlated with the LOD changes, it was introduced into the GRNN prediction model to further improve the accuracy of prediction. Experiments with the observational data of LOD changes show that the prediction accuracy of the GRNN model is 6.1% higher than that of BP network, and after introducing AAM function, the improvement of prediction accuracy further increases to 14.7%. The results show that the GRNN with AAM function is an effective prediction method for LOD changes.
文摘The random delays in a networked control system (NCS) degrade control performance and can even destabilize the control system.To deal with this problem,the time-stamped predictive functional control (PFC) algorithm is proposed,which generalizes the standard PFC algorithm to networked control systems with random delays.The algorithm uses the time-stamp method to estimate the control delay,predicts the future outputs based on a discrete time delay state space model,and drives the control law that applies to an NCS from the idea of a PFC algorithm.A networked control system was constructed based on TrueTime simulator,with which the time-stamped PFC algorithm was compared with the standard PFC algorithm.The response curves show that the proposed algorithm has better control performance.
基金supported by the Natural Science Foundation Project of Inner Mongolia Autonomous Region(2024LHMS03017)Research Capacity Enhancement“Unveiling and Leading”Project of Inner Mongolia Forestry Science Research Institute(2024NLTS03).
文摘The rhizosphere bacteria play crucial roles in plant health and growth as they are involved in assimilating nutrients and resisting adverse conditions such as nutrient stress,drought,and wind erosion.Agriophyllum squarrosum(L.)Moq.is a pioneer plant used in sand fixation due to its strong resistance to drought and wind erosion.However,the bacterial community characteristics and ecological function in the rhizosphere of A.squarrosum are poorly understood.In this study,soil samples were collected from different developmental stages(seedling stage,vegetative stage,reproductive stage,and withering stage)of A.squarrosum.Illumina Miseq sequencing was used to detect differences in soil bacterial abundance.The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States(PICRUSt)program was used to predict bacterial functions,and the relationships among bacteria,functional populations,and soil nutrients were examined using a heatmap analysis.The results showed that the Shannon and Sobs indices of rhizosphere bacteria were significantly higher during the reproductive stage than during the other stages.Pantoea sp.(7.03%)was the dominant genus during the seedling stage;Arthrobacter sp.was the dominant genus during the vegetative(13.94%),reproductive(7.57%),and withering(12.30%)stages.The relative abundances of Chloroflexi,Acidobacteria,and Gemmatimonadetes were significantly high during the reproductive stage.According to the PICRUSt analysis,membrane transport,signal transduction,and environmental adaptation of the bacterial functional population occurred during the seedling stage.Carbohydrate metabolism increased during the vegetative stage,while energy metabolism,lipid metabolism,and biosynthesis of other secondary metabolites of the bacterial functional population significantly increased during the reproductive stage.The abundances of bacterial communities,functional genes,and soil nutrients were synergistically altered during various developmental stages.Our findings suggest that the developmental stages of A.squarrosum play a significant role in defining the composition and structure of bacterial communities in the rhizosphere.The results will provide a basis for better prediction and understanding of soil bacterial metabolic potential and functions of A.squarrosum rhizosphere in sandy areas.
基金supported by the Open Project Funding of the Key Laboratory of Southwest China Wildlife Resource Conservation (Ministry of Education) (XNYB24-02)。
文摘The Qinghai-Xizang Plateau presents an extreme environment characterized by high altitude,low oxygen availability,and harsh living conditions.High-altitude-residing amphibians,such as Rana kukunoris,have evolved specific physiological adaptations to survive in these habitats.However,the composition and functional significance of their gut microbiota with regard to these adaptations remain poorly explored.This study utilized 16S rR NA gene sequencing to characterize and compare the gut microbiota of Rana kukunoris with that of two low-altitude frogs,Rana amurensis and Rana dybowskii,to investigate potential microbial contributions to high-altitude adaptation.Results revealed significant differences in gut microbiota diversity and composition between high-and lowaltitude frogs.Notably,Akkermansia muciniphila and Desulfovibrio species were significantly enriched in Rana kukunoris.Functional predictions indicated significant enrichment of arginine biosynthesis pathways and associated metabolic processes in the high-altitude frog,which may enhance oxygen utilization and vascular homeostasis under hypoxic conditions.These findings provide insights into the gut microbiota of Rana kukunoris and suggest a potential crucial role in facilitating physiological adaptations to extreme environments through enhanced metabolic flexibility and stress resistance.
文摘A GoBlast system was built to predict gene function by integrating Blast search and Gene Ontology (GO) annotations together. The operation system was based on Debian Linux 3.1, with Apache as the web server and Mysql database as the data storage system. FASTA files with GO annotations were taken as the sequence source for blast alignment, which were formatted by wu-formatdb program. The GoBlast system includes three Bioperl modules in Perl:a data input module, a data process module and a data output module. A GoBlast query starts with an amino acid or nucleotide sequence. It ends with an output in an html page, presenting high scoring gene products which are of a high homology to the queried sequence and listing associated GO terms beside respective gene poducts. A simple click on a GO term leads to the detailed explanation of the specific gene function. This avails gene function prediction by Blast. GoBlast can be a very useful tool for functional genome research and is available for free at http://bioq.org/goblast.
基金This work was supported by Young Scientists Fundamental Research Program of Shandong Province of China (No. 031B5147).
文摘In heating, ventilating and air-conditioning （HVAC） systems, there exist severe nonlinearity, time-varying nature, disturbances and uncertainties. A new predictive functional control based on Takagi-Sugeno （T-S） fuzzy model was proposed to control HVAC systems. The T-S fuzzy model of stabilized controlled process was obtained using the least squares method, then on the basis of global linear predictive model from T-S fuzzy model, the process was controlled by the predictive functional controller. Especially the feedback regulation part was developed to compensate uncertainties of fuzzy predictive model. Finally simulation test results in HVAC systems control applications showed that the proposed fuzzy model predictive functional control improves tracking effect and robustness. Compared with the conventional PID controller, this control strategy has the advantages of less overshoot and shorter setting time, etc.
基金Project(61203021)supported by the National Natural Science Foundation of ChinaProject(2011216011)supported by the Scientific and Technological Program of Liaoning Province,China+2 种基金Project(2013020024)supported by the Natural Science Foundation of Liaoning Province,ChinaProject(2012BAF05B00)supported by the National Science and Technology Support Program,ChinaProject(LJQ2015061)supported by the Program for Liaoning Excellent Talents in Universities,China
文摘The control of gas fractionation unit(GFU) in petroleum industry is very difficult due to multivariable characteristics and a large time delay.PID controllers are still applied in most industry processes.However,the traditional PID control has been proven not sufficient and capable for this particular petro-chemical process.In this work,an incremental multivariable predictive functional control(IMPFC) algorithm was proposed with less online computation,great precision and fast response.An incremental transfer function matrix model was set up through the step-response data,and predictive outputs were deduced with the theory of single-value optimization.The results show that the method can optimize the incremental control variable and reject the constraint of the incremental control variable with the positional predictive functional control algorithm,and thereby making the control variable smoother.The predictive output error and future set-point were approximated by a polynomial,which can overcome the problem under the model mismatch and make the predictive outputs track the reference trajectory.Then,the design of incremental multivariable predictive functional control was studied.Simulation and application results show that the proposed control strategy is effective and feasible to improve control performance and robustness of process.
基金Project(2007AA04Z162) supported by the National High-Tech Research and Development Program of ChinaProjects(2006T089, 2009T062) supported by the University Innovation Team in the Educational Department of Liaoning Province, China
文摘In order to obtain accurate prediction model and compensate for the influence of model mismatch on the control performance of the system and avoid solving nonlinear programming problem,an adaptive fuzzy predictive functional control(AFPFC) scheme for multivariable nonlinear systems was proposed.Firstly,multivariable nonlinear systems were described based on Takagi-Sugeno(T-S) fuzzy models;assuming that the antecedent parameters of T-S models were kept,the consequent parameters were identified on-line by using the weighted recursive least square(WRLS) method.Secondly,the identified T-S models were linearized to be time-varying state space model at each sampling instant.Finally,by using linear predictive control technique the analysis solution of the optimal control law of AFPFC was established.The application results for pH neutralization process show that the absolute error between the identified T-S model output and the process output is smaller than 0.015;the tracking ability of the proposed AFPFC is superior to that of non-AFPFC(NAFPFC) for pH process without disturbances,the overshoot of the effluent pH value of AFPFC with disturbances is decreased by 50% compared with that of NAFPFC;when the process parameters of AFPFC vary with time the integrated absolute error(IAE) performance index still retains to be less than 200 compared with that of NAFPFC.
基金This work was supported by National Science Fundation of China (No.60274032)Specialized Research Fund for the Doctoral Program of Higher Education (SRFDP) (No.20030248040)and Alexander von Humboldt Research Fellowship
文摘The predictive model is built according to the characteristics of the impulse response of integrating process. In order to eliminate the permanent offset between the setpoint and the process output in the presence of the load disturbance, a novel error compensation method is proposed. Then predictive functional control of integrating process is designed. The method given generates a simple control structure, which can significandy reduce online computation. Furthermore, the tuning of the controller is fairly straightforward. Simulation results indicate that the designed control system is relatively robust to the parameters variation of the process.
基金supported by the Key Program of the National Natural Science Foundation of China (No. 50334060)
文摘The surface subsidence is a common environmental hazard in mined-out area. Based on careful analysis of the regularity of surface subsidence in mined-out area, we proposed a new time function based on Harris curve model in consideration of the shortage of current surface subsidence time functions. By analyzing the characteristics of the new time function, we found that it could meet the dynamic process, the velocity change process and the acceleration change process during surface subsidence. Then its rationality had been verified through project cases. The results show that the proposed time function model can give a good reflection of the regularity of surface subsidence in mined-out area and can accurately predict surface subsidence. And the prediction data of the model are a little greater than measured data on condition of proper measured data quantity, which is safety in the engineering. This model provides a new method for the analysis of surface subsidence in mined-out area and reference for future prediction, and it is valuable to engineering application.
文摘Reaction control system(RCS) is a powerful and efficient actuator for space vehicles attitude control, which is typically characterized as a pulsed unilateral effector only with two states(off/on). Along with inevitable internal uncertainties and external disturbances in practice, this inherent nonlinear character always hinders space vehicles autopilot from pursuing precise tracking performance. Compared to most of pre-existing methodologies that passively suppress the uncertainties and disturbances, a design based on predictive functional control(PFC) and generalized extended state observer(GESO) is firstly proposed for three-axis RCS control system to actively reject that with no requirement for additional fuel consumption. To obtain a high fidelity predictive model on which the performance of PFC greatly depends, the nonlinear coupling multiple-input multiple-output(MIMO) flight dynamics model is parameterized as a state-dependent coefficient form. And based on that, a MIMO PFC algorithm in state space domain for a plant of arbitrary orders is deduced in this paper.The internal uncertainties and external disturbances are lumped as a total disturbance, which is estimated and cancelled timely to further enhance the robustness. The continuous control command synthesised by above controller-rejector tandem is finally modulated by pulse width pulse frequency modulator(PWPF) to on-off signals to meet RCS requirement. The robustness and feasibility of the proposed design are validated by a series of performance comparison simulations with some prominent methods in the presence of significant perturbations and disturbances, as well as measurement noise.
