PubMed · 1596058
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C M Grossman. 1992-07-01. Subgroup analyses.. https://doi.org/10.7326/0003-4819-117-1-93_2
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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.
The Small Area Health Statistics Unit (SAHSU) is a new independent facility for the investigation of disease near industrial installations in the UK. SAHSU analysed the incidence of cancers of the larynx and lung near the incinerator of waste solvents and oils at Charnock Richard, Coppull, Lancashire (which operated between 1972 and 1980) and nine other similar incinerators in Great Britain, after reports of a cluster of cases of cancer of the larynx near the Charnock Richard site. Postcoded cancer registration data were available for 1974-84 in England and Wales and 1975-87 in Scotland. Lag periods of 5 and 10 years were used between start-up (or first registration) of the incinerators and cancer incidence. Standardised observed/expected (O/E) ratios were assessed within 3 km and 3-10 km of each site and then aggregated over all sites. Expected values were based on national rates (regionally adjusted) with and without stratification by Carstairs' index, a measure of the socioeconomic profile of areas that uses census data for enumeration districts. Data were also assessed over a range of circles up to 10 km to test for trend in O/E ratios with distance. For Charnock Richard, none of the O/E ratios within 3 km or from 3-10 km differed significantly from unity, for either cancer or lag period. In the analysis of all sites with stratification by Carstairs' index, none of these O/E ratios differed significantly from unity for the two cancers. There was no evidence of decreasing risk with distance from the sites of either cancer. We conclude that the apparent cluster of cases of cancer of the larynx reported near Charnock Richard was unlikely to be due to its former incinerator.