PubMed · 8272657
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L I Kheifets. 1993. Cluster analysis: a perspective.. https://doi.org/10.1002/sim.4780121903
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MOTIVATION: Combining omics and images can lead to a more comprehensive clustering of individuals than classic single-view approaches. Among the various approaches for multi-view clustering, nonnegative matrix tri-factorization (NMTF) and nonnegative Tucker decomposition (NTD) are advantageous in learning low-rank embeddings with promising interpretability. Besides, there is a need to handle unwanted drivers of clusterings (i.e. confounders). RESULTS: In this work, we introduce a novel multi-view clustering method based on NMTF and NTD, named INMTD, which integrates omics and 3D imaging data to derive unconfounded subgroups of individuals. According to the adjusted Rand index, INMTD outperformed other clustering methods on a synthetic dataset with known clusters. In the application to real-life facial-genomic data, INMTD generated biologically relevant embeddings for individuals, genetics, and facial morphology. By removing confounded embedding vectors, we derived an unconfounded clustering with better internal and external quality; the genetic and facial annotations of each derived subgroup highlighted distinctive characteristics. In conclusion, INMTD can effectively integrate omics data and 3D images for unconfounded clustering with biologically meaningful interpretation. AVAILABILITY AND IMPLEMENTATION: INMTD is freely available at https://github.com/ZuqiLi/INMTD.
BACKGROUND: It is a matter of ongoing debate whether a universal species concept is possible for bacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form discrete genotypic clusters that can be assigned as species. The most challenging test of whether species can be clearly delineated is provided by analysis of large populations of closely-related, highly recombinogenic, bacteria that colonise the same body site. We have used concatenated sequences of seven house-keeping loci from 770 strains of 11 named Neisseria species, and phylogenetic trees, to investigate whether genotypic clusters can be resolved among these recombinogenic bacteria and, if so, the extent to which they correspond to named species. RESULTS: Alleles at individual loci were widely distributed among the named species but this distorting effect of recombination was largely buffered by using concatenated sequences, which resolved clusters corresponding to the three species most numerous in the sample, N. meningitidis, N. lactamica and N. gonorrhoeae. A few isolates arose from the branch that separated N. meningitidis from N. lactamica leading us to describe these species as 'fuzzy'. CONCLUSION: A multilocus approach using large samples of closely related isolates delineates species even in the highly recombinogenic human Neisseria where individual loci are inadequate for the task. This approach should be applied by taxonomists to large samples of other groups of closely-related bacteria, and especially to those where species delineation has historically been difficult, to determine whether genotypic clusters can be delineated, and to guide the definition of species.
Monkeypox is an orthopoxvirus with enzootic circulation in rainforests of central and western Africa; the virus can be transmitted to humans and cause a syndrome clinically similar to smallpox (e.g., pustular rash, fever, respiratory symptoms, and in some cases, death). From February through August 1996, a total of 71 clinical cases of monkeypox, including six deaths, occurred in 13 villages in Africa in the Katako-Kombe health zone (1996 combined population: 15,698), Sankuru subregion, Kasai Oriental, Zaire. During the initial investigation of this cluster of human cases, specimens of serum and/or crusted scab or fluid from vesicles were collected from 11 patients, and monkeypox virus infection was confirmed in all 11 patients by the World Health Organization (WHO) Collaborating Center for Smallpox and Other Poxvirus Infections at CDC. Preliminary DNA phylogenetic studies of this strain of virus indicated only minor genetic variation compared with other strains of monkeypox virus from Zaire collected during 1970-1979. Because of reports by local public health officials of ongoing disease transmission, the Zaire Ministry of Health and WHO organized a follow-up investigation in February 1997 to characterize the magnitude of the outbreak. This report summarizes the preliminary results of the ongoing multidisciplinary investigation, which suggest that person-to-person transmission accounted for most monkeypox cases investigated in 1996 and 1997; in contrast, during previous years, reports were primarily for sporadic cases that resulted from animal-to-human transmission.