Mammalian natural resistance-associated macrophage protein (Nramp) homologues are important determinants of susceptibility to infection by diverse intracellular pathogens including mycobacteria. Eukaryotic Nramp homologues transport divalent cations such as Fe(2+), Mn(2+), Zn(2+), and Cu(2+). Mycobacterium tuberculosis and Mycobacterium bovis (bacillus Calmette-Guérin [BCG]) also encode an Nram...

Despite being the standard loss function to train multi-class neural networks, the log-softmax has two potential limitations. First, it involves computations that scale linearly with the number of output classes, which can restrict the size of problems that we are able to tackle with current hardware. Second, it remains unclear how close it matches the task loss such as the top-k error rate or ...

Strain JLT2015(T) was isolated from the southeastern Pacific, as a representative of a new genus of the family Sphingomonadaceae of the Alphaproteobacteria. Here, we present the draft genome sequence of strain JLT2015(T), which provides insight into the oligotrophic strategy of this organism.

Bacteriophage (phage) therapy is expected to become an alternative therapy for Pseudomonas aeruginosa infections. P. aeruginosa phage KPP23 is a newly isolated phage belonging to the family Siphoviridae and may be a therapeutic phage candidate. We report its complete genome, which comprises 62,774 bp of double-stranded DNA containing 95 open reading frames.

We cloned a gene, abeM, for a multidrug efflux pump from Acinetobacter baumannii using Escherichia coli as the host. Sequence analysis revealed that AbeM is a member of the MATE family of pumps. AbeM was found to be an H(+)-coupled multidrug efflux pump and a unique member of the MATE family.

Intracellular bacteria have been found previously in one isolate of the arbuscular mycorrhizal (AM) fungus Gigaspora margarita BEG 34. In this study, we extended our investigation to 11 fungal isolates obtained from different geographic areas and belonging to six different species of the family Gigasporaceae. With the exception of Gigaspora rosea, isolates of all of the AM species harbored bact...

In the remodeling pathway for the synthesis of phosphatidylcholine (PC), acyl-CoA-dependent lysophosphatidylcholine (lysoPC) acyltransferase (LPCAT) catalyzes the reacylation of lysoPC. A number of genes encoding LPCATs have been cloned and characterized from several plants in recent years. Using Arabidopsis and other plant LPCAT sequences to screen the genome database of Nicotiana benthamiana,...

An investigation was undertaken of primate pol gene sequences from a novel endogenous retrovirus family, ERV-W, related to a new human endogenous retrovirus family (HERV-W) that includes multiple sclerosis-associated retrovirus (MSRV) sequences identified in particles recovered from monocyte cultures from patients with multiple sclerosis. The pol gene sequences of the ERV-W family were detected...

In a multi-class classification problem, it is standard to model the output of a neural network as a categorical distribution conditioned on the inputs. The output must therefore be positive and sum to one, which is traditionally enforced by a softmax. This probabilistic mapping allows to use the maximum likelihood principle, which leads to the well-known log-softmax loss. However the choice of...