Dysbiosis in the intestinal microflora can affect the gut production of microbial metabolites,and toxic substances can disrupt the barrier function of the intestinal wall,leading to the development of various diseases...Dysbiosis in the intestinal microflora can affect the gut production of microbial metabolites,and toxic substances can disrupt the barrier function of the intestinal wall,leading to the development of various diseases.Decreased levels of Clostridium subcluster XIVa(XIVa)are associated with the intestinal dysbiosis found in inflammatory bowel disease(IBD)and Clostridium difficile infection(CDI).Since XIVa is a bacterial group responsible for the conversion of primary bile acids(BAs)to secondary BAs,the proportion of intestinal XIVa can be predicted by determining the ratio of deoxycholic acid(DCA)/[DCA+cholic acid(CA)]in feces orserum.For example,serum DCA/(DCA+CA)was significantly lower in IBD patients than in healthy controls,even in the remission period.These results suggest that a low proportion of intestinal XIVa in IBD patients might be a precondition for IBD onset but not a consequence of intestinal inflammation.Another report showed that a reduced serum DCA/(DCA+CA)ratio could predict susceptibility to CDI.Thus,the BA profile,particularly the ratio of secondary to primary BAs,can serve as a surrogate marker of the intestinal dysbiosis caused by decreased XIVa.展开更多
Hybrid clustering combines partitional and hierarchical clustering for computational effectiveness and versatility in cluster shape. In such clustering, a dissimilarity measure plays a crucial role in the hierarchical...Hybrid clustering combines partitional and hierarchical clustering for computational effectiveness and versatility in cluster shape. In such clustering, a dissimilarity measure plays a crucial role in the hierarchical merging. The dissimilarity measure has great impact on the final clustering, and data-independent properties are needed to choose the right dissimilarity measure for the problem at hand. Properties for distance-based dissimilarity measures have been studied for decades, but properties for density-based dissimilarity measures have so far received little attention. Here, we propose six data-independent properties to evaluate density-based dissimilarity measures associated with hybrid clustering, regarding equality, orthogonality, symmetry, outlier and noise observations, and light-tailed models for heavy-tailed clusters. The significance of the properties is investigated, and we study some well-known dissimilarity measures based on Shannon entropy, misclassification rate, Bhattacharyya distance and Kullback-Leibler divergence with respect to the proposed properties. As none of them satisfy all the proposed properties, we introduce a new dissimilarity measure based on the Kullback-Leibler information and show that it satisfies all proposed properties. The effect of the proposed properties is also illustrated on several real and simulated data sets.展开更多
Tiny unicellular cyanobacteria or picocyanobacteria(0.5-3μm)are important due to their ecological significance.Chesa-peake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria.Studies of Ch...Tiny unicellular cyanobacteria or picocyanobacteria(0.5-3μm)are important due to their ecological significance.Chesa-peake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria.Studies of Chesapeake Bay picocy-anobacteria in the past 20 years led to the finding of new members of subcluster 5.2 Synechococcus.They laid the foundation for revealing the ecophysiology,biogeography,genomics,and molecular evolution of picocyanobacterial in the Chesapeake Bay and other coastal estuaries.The Bay picocyanobacteria are known to better tolerate the changes in temperature,salinity,and heavy metals compared to their coastal and open-ocean counterparts.Many picocyanobacteria isolated from the Bay contain rich toxin-antitoxin(TA)genes,suggesting that the TA system may provide them with a genetic advance to cope with variable estuarine environments.Distinct winter and summer picocyanobacteria are present in the Bay,suggesting a dynamic seasonal shift of the picocyanobacterial community in the temperate estuary.While the Bay contains subcluster 5.2 Synechococcus,it also contains freshwater Synechococcus,Cyanobium,and marine Synechococcus due to river influx and the ocean’s tidal influence.Some Chesapeake Bay picocyanobacterial clades were found in the Bering Sea and Chukchi Sea,showing a link between the Bay and polar picocyanobacteria.Genomic sequences of estuarine picocyanobacteria pro-vide new insight into the taxonomy and evolution of freshwater,estuarine,and marine unicellular cyanobacteria.Estuaries connect freshwater and marine ecosystems.This overview attempts to extend what we learned from Chesapeake Bay pico-cyanobacteria to picocyanobacteria in freshwater and marine waters.展开更多
文摘Dysbiosis in the intestinal microflora can affect the gut production of microbial metabolites,and toxic substances can disrupt the barrier function of the intestinal wall,leading to the development of various diseases.Decreased levels of Clostridium subcluster XIVa(XIVa)are associated with the intestinal dysbiosis found in inflammatory bowel disease(IBD)and Clostridium difficile infection(CDI).Since XIVa is a bacterial group responsible for the conversion of primary bile acids(BAs)to secondary BAs,the proportion of intestinal XIVa can be predicted by determining the ratio of deoxycholic acid(DCA)/[DCA+cholic acid(CA)]in feces orserum.For example,serum DCA/(DCA+CA)was significantly lower in IBD patients than in healthy controls,even in the remission period.These results suggest that a low proportion of intestinal XIVa in IBD patients might be a precondition for IBD onset but not a consequence of intestinal inflammation.Another report showed that a reduced serum DCA/(DCA+CA)ratio could predict susceptibility to CDI.Thus,the BA profile,particularly the ratio of secondary to primary BAs,can serve as a surrogate marker of the intestinal dysbiosis caused by decreased XIVa.
文摘Hybrid clustering combines partitional and hierarchical clustering for computational effectiveness and versatility in cluster shape. In such clustering, a dissimilarity measure plays a crucial role in the hierarchical merging. The dissimilarity measure has great impact on the final clustering, and data-independent properties are needed to choose the right dissimilarity measure for the problem at hand. Properties for distance-based dissimilarity measures have been studied for decades, but properties for density-based dissimilarity measures have so far received little attention. Here, we propose six data-independent properties to evaluate density-based dissimilarity measures associated with hybrid clustering, regarding equality, orthogonality, symmetry, outlier and noise observations, and light-tailed models for heavy-tailed clusters. The significance of the properties is investigated, and we study some well-known dissimilarity measures based on Shannon entropy, misclassification rate, Bhattacharyya distance and Kullback-Leibler divergence with respect to the proposed properties. As none of them satisfy all the proposed properties, we introduce a new dissimilarity measure based on the Kullback-Leibler information and show that it satisfies all proposed properties. The effect of the proposed properties is also illustrated on several real and simulated data sets.
基金The research grant awards(OCE-9730602,OCE-0049098,MCB-0132070,MCB-0537041,and 1829888)the U.S.National Science Foundation have greatly advanced our knowledge of the ecology of picocyanobacteria in the estuarine environment.
文摘Tiny unicellular cyanobacteria or picocyanobacteria(0.5-3μm)are important due to their ecological significance.Chesa-peake Bay is a temperate estuary that contains abundant and diverse picocyanobacteria.Studies of Chesapeake Bay picocy-anobacteria in the past 20 years led to the finding of new members of subcluster 5.2 Synechococcus.They laid the foundation for revealing the ecophysiology,biogeography,genomics,and molecular evolution of picocyanobacterial in the Chesapeake Bay and other coastal estuaries.The Bay picocyanobacteria are known to better tolerate the changes in temperature,salinity,and heavy metals compared to their coastal and open-ocean counterparts.Many picocyanobacteria isolated from the Bay contain rich toxin-antitoxin(TA)genes,suggesting that the TA system may provide them with a genetic advance to cope with variable estuarine environments.Distinct winter and summer picocyanobacteria are present in the Bay,suggesting a dynamic seasonal shift of the picocyanobacterial community in the temperate estuary.While the Bay contains subcluster 5.2 Synechococcus,it also contains freshwater Synechococcus,Cyanobium,and marine Synechococcus due to river influx and the ocean’s tidal influence.Some Chesapeake Bay picocyanobacterial clades were found in the Bering Sea and Chukchi Sea,showing a link between the Bay and polar picocyanobacteria.Genomic sequences of estuarine picocyanobacteria pro-vide new insight into the taxonomy and evolution of freshwater,estuarine,and marine unicellular cyanobacteria.Estuaries connect freshwater and marine ecosystems.This overview attempts to extend what we learned from Chesapeake Bay pico-cyanobacteria to picocyanobacteria in freshwater and marine waters.
