Monomorphic trypanozoon:Towards reconciling phylogeny and pathologies

Trypanosoma brucei evansi and T. brucei equiperdum are animal infective trypanosomes conventionally classified by their clinical disease presentation, mode of transmission, host range, kinetoplast DNA (kDNA) composition and geographical distribution. Unlike other members of the subgenus Trypanozoon, they are non-tsetse transmitted and predominantly morphologically uniform (monomorphic) in their mammalian host. Their classification as independent species or subspecies has been long debated and genomic studies have found that isolates within T. brucei evansi and T. brucei equiperdum have polyphyletic origins. Since current taxonomy does not fully acknowledge these polyphyletic relationships, we re-analysed publicly available genomic data to carefully define each clade of monomorphic trypanosome. This allowed us to identify, and account for, lineage-specific variation. We included a recently published isolate, IVM-t1, which was originally isolated from the genital mucosa of a horse with dourine and typed as T. equiperdum. Our analyses corroborate previous studies in identifying at least four distinct monomorphic T. brucei clades. We also found clear lineage-specific variation in the selection efficacy and heterozygosity of the monomorphic lineages, supporting their distinct evolutionary histories. The inferred evolutionary position of IVM-t1 suggests its reassignment to the T. brucei evansi type B clade, challenging the relationship between the Trypanozoon species, the infected host, mode of transmission and the associated pathological phenotype. The analysis of IVM-t1 also provides, to our knowledge, the first evidence of the expansion of T. brucei evansi type B, or a fifth monomorphic lineage represented by IVM-t1, outside of Africa, with important possible implications for disease diagnosis

Cohesive and mixed sediment in the Regional Ocean Modeling System (ROMS v3.6) implemented in the Coupled Ocean-Atmosphere-Wave-Sediment Transport Modeling System (COAWST r1234)

We describe and demonstrate algorithms for treating cohesive and mixed sediment that have been added to the Regional Ocean Modeling System (ROMS version 3.6), as implemented in the Coupled Ocean-Atmosphere-Wave- Sediment Transport Modeling System (COAWST Subversion repository revision 1234). These include the following: floc dynamics (aggregation and disaggregation in the water column); changes in floc characteristics in the seabed; erosion and deposition of cohesive and mixed (combination of cohesive and non-cohesive) sediment; and biodiffusive mixing of bed sediment. These routines supplement existing noncohesive sediment modules, thereby increasing our ability to model fine-grained and mixed-sediment environments. Additionally, we describe changes to the sediment bed layering scheme that improve the fidelity of the modeled stratigraphic record. Finally, we provide examples of these modules implemented in idealized test cases and a realistic application

High-spin states with seniority v=4,4,6 in 119-126Sn

The 119-126Sn nuclei have been produced as fission fragments in two reactions induced by heavy ions: 12C+238U at 90 MeV bombarding energy, 18O+208Pb at 85 MeV. Their level schemes have been built from gamma rays detected using the Euroball array. High-spin states located above the long-lived isomeric states of the even- and odd-A 120-126Sn nuclei have been identified. Moreover isomeric states lying around 4.5 MeV have been established in 120,122,124,126Sn from the delayed coincidences between the fission fragment detector SAPhIR and the Euroball array. The states located above 3-MeV excitation energy are ascribed to several broken pairs of neutrons occupying the nu h11/2 orbit. The maximum value of angular momentum available in such a high-j shell, i.e. for mid-occupation and the breaking of the three neutron pairs, has been identified. This process is observed for the first time in spherical nuclei.Comment: 20 pages, 22 figures, 12 tables, accepted for publication in Physical Review

Particle-core coupling in S 37

R. Chapman et al. ; 8 págs.; 6 figs.; 2 tabs.Excited states of the neutron-rich N=21 S37 nucleus have been studied using binary grazing reactions produced by the interaction of a 215-MeV beam of S36 ions with a thin Pb208 target. The magnetic spectrometer, PRISMA, and the γ-ray array, CLARA, were used in the measurements. The level scheme of S37 was established to an excitation energy of 4196 keV and a number of new transitions were observed, in particular that corresponding to the decay of the proposed Jπ=(11/2-) level at an excitation energy of 2776 keV. The structure of the state is discussed within the context of state-of-the-art shell-model calculations using the SDPF-U effective interaction; the main component of the wave function corresponds to the coupling of the odd 1f7/2 neutron to the first 2+ state of the S36 core. The electromagnetic decay properties of the state are discussed within the context of a particle-core coupling model and the shell model. The other members of the multiplet of states are also discussed. ©2016 American Physical SocietyWe would like to thank the technical staff of the INFN Legnaro National Laboratory for their support during this experiment. This work was supported by the EPSRC (U.K). Four of us (A.H,M.B, K.L.K., and A.P.) would like to acknowledge the receipt of financial support from EPSRC during the course of this work. A.J. would like to acknowledge support from the Spanish Ministerio de Economía y Competitividad under Contract No. FPA2014-57196-C5-4-P. Z.D. acknowledges financial support from OTKA Grant No. K100835.Peer Reviewe

First in-beam γ -ray study of the level structure of neutron-rich S 39

R. Chapman et al. ; 8 págs.; 6 figs.; 1 tab.The neutron-rich S39 nucleus has been studied using binary grazing reactions produced by the interaction of a 215-MeV beam of S36 ions with a thin Pb208 target. The magnetic spectrometer, PRISMA, and the γ-ray array, CLARA, were used in the measurements. Gamma-ray transitions of the following energies were observed: 339, 398, 466, 705, 1517, 1656, and 1724 keV. Five of the observed transitions have been tentatively assigned to the decay of excited states with spins up to (11/2-). The results of a state-of-the-art shell-model calculation of the level scheme of S39 using the SDPF-U effective interaction are also presented. The systematic behavior of the excitation energy of the first 11/2- states in the odd-A isotopes of sulfur and argon is discussed in relation to the excitation energy of the first excited 2+ states of the adjacent even-A isotopes. The states of S39 that have the components in their wave functions corresponding to three neutrons in the 1f7/2 orbital outside the N=20 core have also been discussed within the context of the 0 ω shell-model calculations presented here. ©2016 American Physical SocietyThis work was supported in part by the EPSRC (UK) and by the European Union under Contract No. RII3-CT- 2004-506065. Five of us (D.O., M.B., A.H., K.K., and A.P.) acknowledge financial support from the EPSRC. Z.M.W. acknowledges support from ORSAS and from the University of the West of Scotland. A.N.D. acknowledges support from the STFC. A.J. acknowledges financial support from the Spanish Ministerio de Ciencia e Innovación under Contracts No. FPA2007-66069 and No. FPA2009-13377-C02-02. Zs.D. acknowledges financial support from OTKA under Project No. K100835. S.S. acknowledges support from the Croatian Science Foundation under Project No. 7194. The contribution of the accelerator and target-fabrication staff at the INFN Legnaro National Laboratory is gratefully acknowledged.Peer Reviewe

Modeling the bremsstrahlung emission from converters

The bremsstrahlung angular and energy theoretical distributions delivered from W and UCx thick converters are reported. This study is focussed on initial kinetic energies of the electron beam included in the range 30-60 MeV, suitable for the production of large radiative yields able to induce the $^{238}$U fission. These results offer the possibility to evaluate the required shielding for a neutron rich nuclei source