The molecular epidemiology of human immunodeficiency virus type 1 in six cities in Britain and Ireland

The authors sequenced the p17 coding regions of the gag gene from 211 patients infected either through injecting drug use (IDU) or by sexual intercourse between men from six cities in Scotland, N. England, N. Ireland, and the Republic of Ireland. All sequences were of subtype 5. Phylogenetic analysis revealed substantial heterogeneity in the sequences from homosexual men. In contrast, sequence from over 80% of IDUs formed a relatively tight cluster, distinct both from those of published isolates and of the gay men. There was no large-scale clustering of sequences by city in either risk group, although a number of close associations between pairs of individuals were observed. From the known date of the HIV-1 epidemic among IDUs in Edinburgh, the rate of sequence divergence at synonymous sites is estimated to be about 0.8%. On this basis it has been estimated that the date of divergence of the sequences among homosexual men to be about 1975, which may correspond to the origin of the B subtype epidemic

Leaf-inhabiting genera of the Gnomoniaceae, Diaporthales

The Gnomoniaceae are characterised by ascomata that are generally immersed, solitary, without a stroma, or aggregated with a rudimentary stroma, in herbaceous plant material especially in leaves, twigs or stems, but also in bark or wood. The ascomata are black, soft-textured, thin-walled, and pseudoparenchymatous with one or more central or eccentric necks. The asci usually have a distinct apical ring. The Gnomoniaceae includes species having ascospores that are small, mostly less than 25 μm long, although some are longer, and range in septation from non-septate to one-septate, rarely multi-septate. Molecular studies of the Gnomoniaceae suggest that the traditional classification of genera based on characteristics of the ascomata such as position of the neck and ascospores such as septation have resulted in genera that are not monophyletic. In this paper the concepts of the leaf-inhabiting genera in the Gnomoniaceae are reevaluated using multiple genes, specifically nrLSU, translation elongation factor 1-alpha (tef1-α), and RNA polymerase II second largest subunit (rpb2) for 64 isolates. ITS sequences were generated for 322 isolates. Six genera of leaf-inhabiting Gnomoniaceae are defined based on placement of their type species within the multigene phylogeny. The new monotypic genus Ambarignomonia is established for an unusual species, A. petiolorum. A key to 59 species of leaf-inhabiting Gnomoniaceae is presented and 22 species of Gnomoniaceae are described and illustrated

Enumerating unlabeled and root labeled trees for causal model acquisition

To specify a Bayes net (BN), a conditional probability table (CPT), often of an effect conditioned on its n causes, needs to be assessed for each node. It generally has the complexity exponential on n. The non-impeding noisy-AND (NIN-AND) tree is a recently developed causal model that reduces the complexity to linear, while modeling both reinforcing and undermining interactions among causes. Acquisition of an NIN-AND tree model involves elicitation of a linear number of probability parameters and a tree structure. Instead of asking the human expert to describe the structure from scratch, in this work, we develop a two-step menu selection technique that aids structure acquisition

Towards effective elicitation of NIN-AND tree causal models

Abstract. To specify a Bayes net (BN), a conditional probability table (CPT), often of an effect conditioned on its n causes, needs assessed for each node. It generally has the complexity exponential on n. Noisy-OR reduces the complexity to linear, but can only represent reinforcing causal interactions. The non-impeding noisy-AND (NIN-AND) tree is the first causal model that explicitly expresses reinforcement, undermining, and their mixture. It has linear complexity, but requires elicitation of a tree topology for types of causal interactions. We study their topology space and develop two novel techniques for more effective elicitation.