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Creators/Authors contains: "Tsuji, Kaoru"

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  1. The genus Rosenbergiella is one of the most frequent bacterial inhabitants of flowers and a usual member of the insect microbiota worldwide. To date, there is only one publicly available Rosenbergiella genome, corresponding to the type strain of Rosenbergiella nectarea (8N4 T ), which precludes a detailed analysis of intra-genus phylogenetic relationships. In this study, we obtained draft genomes of the type strains of the other Rosenbergiella species validly published to date ( R. australiborealis , R. collisarenosi and R. epipactidis ) and 23 additional isolates of flower and insect origin. Isolate S61 T , retrieved from the nectar of an Antirrhinum sp. flower collected in southern Spain, displayed low average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values when compared with other Rosenbergiella members (≤86.5 and ≤29.8 %, respectively). Similarly, isolate JB07 T , which was obtained from the floral nectar of Metrosideros polymorpha plants in Hawaii (USA) had ≤95.7 % ANI and ≤64.1 % isDDH with other Rosenbergiella isolates. Therefore, our results support the description of two new Rosenbergiella species for which we propose the names Rosenbergiella gaditana sp. nov. (type strain: S61 T =NCCB 100789 T =DSM 111181 T ) and Rosenbergiella metrosideri sp. nov. (JB07 T =NCCB 100888 T =LMG 32616 T ). Additionally, some R. epipactidis and R. nectarea isolates showed isDDH values<79 % with other conspecific isolates, which suggests that these species include subspecies for which we propose the names Rosenbergiella epipactidis subsp. epipactidis subsp. nov. (S256 T =CECT 8502 T =LMG 27956 T ), Rosenbergiella epipactidis subsp. californiensis subsp. nov. (FR72 T =NCCB 100898 T =LMG 32786 T ), Rosenbergiella epipactidis subsp. japonicus subsp. nov. (K24 T =NCCB 100924 T =LMG 32785 T ), Rosenbergiella nectarea subsp. nectarea subsp. nov. (8N4 T = DSM 24150 T = LMG 26121 T ) and Rosenbergiella nectarea subsp. apis subsp. nov. (B1A T =NCCB 100810 T = DSM 111763 T ), respectively. Finally, we present the first phylogenomic analysis of the genus Rosenbergiella and update the formal description of the species R. australiborealis , R. collisarenosi , R. epipactidis and R. nectarea based on new genomic and phenotypic information. 
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  2. A common problem practitioners face is to select rare events in a large dataset. Unfortunately, standard techniques ranging from pre-trained models to active learning do not leverage proximity structure present in many datasets and can lead to worse-than-random results. To address this, we propose EZMODE, an algorithm for iterative selection of rare events in large, unlabeled datasets. EZMODE leverages active learning to iteratively train classifiers, but chooses the easiest positive examples to label in contrast to standard uncertainty techniques. EZMODE also leverages proximity structure (e.g., temporal sampling) to find difficult positive examples. We show that EZMODE can outperform baselines by up to 130× on a novel, real-world, 9,000 GB video dataset. 
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  3. null (Ed.)
    A detailed evaluation of eight bacterial isolates from floral nectar and animal visitors to flowers shows evidence that they represent three novel species in the genus Acinetobacter . Phylogenomic analysis shows the closest relatives of these new isolates are Acinetobacter apis , Acinetobacter boissieri and Acinetobacter nectaris , previously described species associated with floral nectar and bees, but high genome-wide sequence divergence defines these isolates as novel species. Pairwise comparisons of the average nucleotide identity of the new isolates compared to known species is extremely low (<83 %), thus confirming that these samples are representative of three novel Acinetobacter species, for which the names Acinetobacter pollinis sp. nov., Acinetobacter baretiae sp. nov. and Acinetobacter rathckeae sp. nov. are proposed. The respective type strains are SCC477 T (=TSD-214 T =LMG 31655 T ), B10A T (=TSD-213 T =LMG 31702 T ) and EC24 T (=TSD-215 T =LMG 31703 T =DSM 111781 T ). 
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  4. null (Ed.)
    Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar. 
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