Analytical theory of forced rotating sheared turbulence: The perpendicular case

Rotation and shear flows are ubiquitous features of many astrophysical and geophysical bodies. To understand their origin and effect on turbulent transport in these systems, we consider a forced turbulence and investigate the combined effect of rotation and shear flow on the turbulence properties. Specifically, we study how rotation and flow shear influence the generation of shear flow (e.g., the direction of energy cascade), turbulence level, transport of particles and momentum, and the anisotropy in these quantities. In all the cases considered, turbulence amplitude is always quenched due to strong shear (ξ=νky2/A⪡1, where A is the shearing rate, ν is the molecular viscosity, and ky is a characteristic wave number of small-scale turbulence), with stronger reduction in the direction of the shear than those in the perpendicular directions. Specifically, in the large rotation limit (Ω⪢A), they scale as A−1 and A−1|ln ξ|, respectively, while in the weak rotation limit (Ω⪡A), they scale as A−1 and A−2/3, respectively. Thus, flow shear always leads to weak turbulence with an effectively stronger turbulence in the plane perpendicular to shear than in the shear direction, regardless of rotation rate. The anisotropy in turbulence amplitude is, however, weaker by a factor of ξ1/3|ln ξ| (∝A−1/3|ln ξ|) in the rapid rotation limit (Ω⪢A) than that in the weak rotation limit (Ω⪡A) since rotation favors almost-isotropic turbulence. Compared to turbulence amplitude, particle transport is found to crucially depend on whether rotation is stronger or weaker than flow shear. When rotation is stronger than flow shear (Ω⪢A), the transport is inhibited by inertial waves, being quenched inversely proportional to the rotation rate (i.e., ∝Ω−1) while in the opposite case, it is reduced by shearing as A−1. Furthermore, the anisotropy is found to be very weak in the strong rotation limit (by a factor of 2) while significant in the strong shear limit. The turbulent viscosity is found to be negative with inverse cascade of energy as long as rotation is sufficiently strong compared to flow shear (Ω⪢A) while positive in the opposite limit of weak rotation (Ω⪡A). Even if the eddy viscosity is negative for strong rotation (Ω⪢A), flow shear, which transfers energy to small scales, has an interesting effect by slowing down the rate of inverse cascade with the value of negative eddy viscosity decreasing as |νT|∝A−2 for strong shear. Furthermore, the interaction between the shear and the rotation is shown to give rise to a nondiffusive flux of angular momentum (Λ effect), even in the absence of external sources of anisotropy. This effect provides a mechanism for the existence of shearing structures in astrophysical and geophysical systems

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to 'subgroup a' of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.We would like to gratefully acknowledge the help of Christine Munk and Megan Lu for finishing the genome sequence (both at JGI). The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, and was also supported by grants CW-TOP 700.55.343 and ALW 819.02.014 of the Netherlands Science Foundation (NWO) and grant 323009 of the European Research Council

Trabectedin plus pegylated liposomal doxorubicin in relapsed ovarian cancer delays third-line chemotherapy and prolongs the platinum-free interval

Background: OVA-301 is a large randomized trial that showed superiority of trabectedin plus pegylated liposomal doxorubicin (PLD; CentoCor Ortho Biotech Products L.P., Raritan, NJ, USA). over single-agent PLD in 672 patients with relapsed ovarian cancer, particularly in the partially platinum-sensitive subgroup [platinum-free interval (PFI) of 6–12 months]. This superiority has been suggested to be due to the differential impact of subsequent (platinum) therapy

Trabectedin plus pegylated liposomal doxorubicin in relapsed ovarian cancer: outcomes in the partially platinum-sensitive (platinum-free interval 6–12 months) subpopulation of OVA-301 phase III randomized trial

Background: OVA-301 is a large randomized trial that showed superiority of trabectedin plus pegylated liposomal doxorubicin (PLD) over PLD alone in relapsed ovarian cancer. The optimal management of patients with partially platinum-sensitive relapse [6–12 months platinum-free interval (PFI)] is unclear

Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota

The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. OS and MSG were supported by the Russian Science Foundation (RSF, grant 14-24-00155). EB-O and SG were supported by the RSF grant 14-24-00165. IK, NC, AL, and MM were supported by the Russian Foundation for Basic Research grant 14-04-00503.http://www.frontiersin.orgam2017Biochemistr