Data clustering plays a vital role in object identification. In real life we mainly use the concept in biometric identification and object detection. In this paper we use Fuzzy Weighted Rules, Fuzzy Inference System (...Data clustering plays a vital role in object identification. In real life we mainly use the concept in biometric identification and object detection. In this paper we use Fuzzy Weighted Rules, Fuzzy Inference System (FIS), Fuzzy C-Mean clustering (FCM), Support Vector Machine (SVM) and Artificial Neural Network (ANN) to distinguish three types of Iris data called Iris-Setosa, Iris-Versicolor and Iris-Virginica. Each class in the data table is identified by four-dimensional vector, where vectors are used as the input variable called: Sepal Length (SL), Sepal Width (SW), Petal Length (PL) and Petal Width (PW). The combination of five machine learning methods provides above 98% accuracy of class identification.展开更多
During the early systemic infection of plant pathogens,individual cells can harbor pathogens at various stages of infection,ranging from absent to abundant.Consequently,gene expression levels within these cells in res...During the early systemic infection of plant pathogens,individual cells can harbor pathogens at various stages of infection,ranging from absent to abundant.Consequently,gene expression levels within these cells in response to the pathogens exhibit significant variability.These variations are pivotal in determining pathogenicity or susceptibility,yet they remain largely unexplored and poorly understood.Sugarcane mosaic virus(SCMV)is a representative member of the monocot-infecting potyviruses with a polyadeny-lated RNA genome,which can be captured by single-cell RNA sequencing(scRNA-seq).Here,we per-formed scRNA-seq on SCMV-infected maize leaves during early systemic infection(prior to symptom mani-festation)to investigate the co-variation patterns between viral accumulation and intracellular gene expression alterations.We identifiedfive cell types and found that mesophyll-4(MS4)cells exhibited the highest levels of viral accumulation in most cells.Early systemic infection of SCMV resulted in a greater up-regulation of differentially expressed genes,which were mainly enriched in biological processes related to translation,peptide biosynthesis,and metabolism.Co-variation analysis of the altered maize gene expres-sion and viral accumulation levels in MS1,2,and 4 revealed several patterns,and the co-expression rela-tionships between them were mainly positive.Furthermore,functional studies identified several potential anti-or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection.These results not only provide new insights into plant gene regulation during viral infection but also offer a foundation for future investigations of host–virus interactions across molecular,cellular,and physiolog-ical scales.展开更多
Transcription factors （TFs） are major modulators of transcription and subsequent cellular processes. The binding of TFs to specific regulatory elements is governed by their specificity. Considering the gap between k...Transcription factors （TFs） are major modulators of transcription and subsequent cellular processes. The binding of TFs to specific regulatory elements is governed by their specificity. Considering the gap between known TFs sequence and specificity, specificity prediction frameworks are highly desired. Key inputs to such frameworks are protein residues that modulate the specificity of TF under consideration. Simple measures like mutual information （MI） to delineate specificity influencing residues （SIRs） from alignment fail due to structural constraints imposed by the three-dimensional structure of protein. Structural restraints on the evolution of the amino-acid sequence lead to identification of false SIRs. In this manuscript we extended three methods （direct information, PSICOV and adjusted mutual information） that have been used to disentangle spurious indirect protein residue-residue contacts from direct contacts, to identify SIRs from joint alignments of amino-acids and specificity. We predicted SIRs for homeodomain （HI））, helix-loop-helix, LacI and GntR families of TFs using these methods and compared to MI. Using various measures, we show that the performance of these three methods is comparable but better than MI. Implication of these methods in specificity prediction framework is discussed. The methods are implemented as an R package and available along with the alignments at http：//stormo.wustl.edu/SpecPred.展开更多
Water and sediment transport from rivers to oceans is of primary importance in global geochemical cycle.Against the background of global change,this study examines the changes in water and sediment fluxes and their dr...Water and sediment transport from rivers to oceans is of primary importance in global geochemical cycle.Against the background of global change,this study examines the changes in water and sediment fluxes and their drivers for 4307 large rivers worldwide(basin area!1000 km2)based on the longest available records.Here we find that 24%of the world’s large rivers experienced significant changes in water flux and 40%in sediment flux,most notably declining trends in water and sediment fluxes in Asia’s large rivers and an increasing trend in suspended sediment concentrations in the Amazon River.In particular,nine binary patterns of changes in water-sediment fluxes are interpreted in terms of climate change and human impacts.The change of precipitation is found significantly correlated to the change of water flux in 71%of the world’s large rivers,while dam operation and irrigation rather control the change of sediment flux in intensively managed catchments.Globally,the annual water flux from rivers to sea of the recent years remained stable compared with the long-time average annual value,while the sediment flux has decreased by 20.8%.展开更多
The argument given by strong representationalists about phenomenal consciousness usually has two steps. The first is to identify all phenomenal consciousness with representation. The second is to identify all phenomen...The argument given by strong representationalists about phenomenal consciousness usually has two steps. The first is to identify all phenomenal consciousness with representation. The second is to identify all phenomenal aspects of phenomenal consciousness with certain representational content. Pain is often thought to be a counterexample torepresentationalism. However, current objections from this perspective mostly focus on the second step and try to show that pains have some special qualities that representational content cannot explain. This paper objects to representationalism with regard to pain （that pain is not representation） by way of a focus on the first step. First, it shows that by borrowing the notion of ＂representation＂ from the causal co-variation theory of representation, representationalists are not able to demonstrate that pain is representation. Second, by laying out some well-accepted criteria for what counts as representation, it argues that pains do not satisfy them. Thus, pain is not representation.展开更多
文摘Data clustering plays a vital role in object identification. In real life we mainly use the concept in biometric identification and object detection. In this paper we use Fuzzy Weighted Rules, Fuzzy Inference System (FIS), Fuzzy C-Mean clustering (FCM), Support Vector Machine (SVM) and Artificial Neural Network (ANN) to distinguish three types of Iris data called Iris-Setosa, Iris-Versicolor and Iris-Virginica. Each class in the data table is identified by four-dimensional vector, where vectors are used as the input variable called: Sepal Length (SL), Sepal Width (SW), Petal Length (PL) and Petal Width (PW). The combination of five machine learning methods provides above 98% accuracy of class identification.
基金supported by grants from the National Natural Science Foundation of China(grant 32072384,W2412104)the China Agriculture Research System of MOF and MARA(CARS-02)+2 种基金This study was also supported by the Ministry of Agriculture and Rural Affairs of China(NK2023070202)S.C.G.is supported by startup funds from the University of California,Riversideby a grant from the National Institute of General Medical Sciences of the National Institutes of Health(award no.R35GM151194).
文摘During the early systemic infection of plant pathogens,individual cells can harbor pathogens at various stages of infection,ranging from absent to abundant.Consequently,gene expression levels within these cells in response to the pathogens exhibit significant variability.These variations are pivotal in determining pathogenicity or susceptibility,yet they remain largely unexplored and poorly understood.Sugarcane mosaic virus(SCMV)is a representative member of the monocot-infecting potyviruses with a polyadeny-lated RNA genome,which can be captured by single-cell RNA sequencing(scRNA-seq).Here,we per-formed scRNA-seq on SCMV-infected maize leaves during early systemic infection(prior to symptom mani-festation)to investigate the co-variation patterns between viral accumulation and intracellular gene expression alterations.We identifiedfive cell types and found that mesophyll-4(MS4)cells exhibited the highest levels of viral accumulation in most cells.Early systemic infection of SCMV resulted in a greater up-regulation of differentially expressed genes,which were mainly enriched in biological processes related to translation,peptide biosynthesis,and metabolism.Co-variation analysis of the altered maize gene expres-sion and viral accumulation levels in MS1,2,and 4 revealed several patterns,and the co-expression rela-tionships between them were mainly positive.Furthermore,functional studies identified several potential anti-or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection.These results not only provide new insights into plant gene regulation during viral infection but also offer a foundation for future investigations of host–virus interactions across molecular,cellular,and physiolog-ical scales.
文摘Transcription factors （TFs） are major modulators of transcription and subsequent cellular processes. The binding of TFs to specific regulatory elements is governed by their specificity. Considering the gap between known TFs sequence and specificity, specificity prediction frameworks are highly desired. Key inputs to such frameworks are protein residues that modulate the specificity of TF under consideration. Simple measures like mutual information （MI） to delineate specificity influencing residues （SIRs） from alignment fail due to structural constraints imposed by the three-dimensional structure of protein. Structural restraints on the evolution of the amino-acid sequence lead to identification of false SIRs. In this manuscript we extended three methods （direct information, PSICOV and adjusted mutual information） that have been used to disentangle spurious indirect protein residue-residue contacts from direct contacts, to identify SIRs from joint alignments of amino-acids and specificity. We predicted SIRs for homeodomain （HI））, helix-loop-helix, LacI and GntR families of TFs using these methods and compared to MI. Using various measures, we show that the performance of these three methods is comparable but better than MI. Implication of these methods in specificity prediction framework is discussed. The methods are implemented as an R package and available along with the alignments at http：//stormo.wustl.edu/SpecPred.
基金supported by the National Natural Science Foundation of China (51721006 and 91647211)
文摘Water and sediment transport from rivers to oceans is of primary importance in global geochemical cycle.Against the background of global change,this study examines the changes in water and sediment fluxes and their drivers for 4307 large rivers worldwide(basin area!1000 km2)based on the longest available records.Here we find that 24%of the world’s large rivers experienced significant changes in water flux and 40%in sediment flux,most notably declining trends in water and sediment fluxes in Asia’s large rivers and an increasing trend in suspended sediment concentrations in the Amazon River.In particular,nine binary patterns of changes in water-sediment fluxes are interpreted in terms of climate change and human impacts.The change of precipitation is found significantly correlated to the change of water flux in 71%of the world’s large rivers,while dam operation and irrigation rather control the change of sediment flux in intensively managed catchments.Globally,the annual water flux from rivers to sea of the recent years remained stable compared with the long-time average annual value,while the sediment flux has decreased by 20.8%.
文摘The argument given by strong representationalists about phenomenal consciousness usually has two steps. The first is to identify all phenomenal consciousness with representation. The second is to identify all phenomenal aspects of phenomenal consciousness with certain representational content. Pain is often thought to be a counterexample torepresentationalism. However, current objections from this perspective mostly focus on the second step and try to show that pains have some special qualities that representational content cannot explain. This paper objects to representationalism with regard to pain （that pain is not representation） by way of a focus on the first step. First, it shows that by borrowing the notion of ＂representation＂ from the causal co-variation theory of representation, representationalists are not able to demonstrate that pain is representation. Second, by laying out some well-accepted criteria for what counts as representation, it argues that pains do not satisfy them. Thus, pain is not representation.
