Complex mosaic structures of HIV-1 were found in the Democratic Republic of Congo (DRC). Currently, there is limited information on the circulating HIV-1 strains, the distribution of these strains ...and antiretroviral (ART) resistant viruses in different regions of the country, and the HIV-1 strains harbored by the high-risk groups like female sex workers (FSW) reported to be the source of recombinant and ART resistant viruses.
Dried Blood Spots (DBS), collected from 325 infected FSWs in ten cities from 2012 DRC HIV/STI Integrated Biological and Behavioral Surveillance Survey, were tested for HIV-1 genotypes and antiretroviral resistance mutations. Regional segregation of HIV-1 clades was detected using phylogenetics. The significance for differences in HIV-1 subtype and drug resistance mutations were evaluated using Chi-square tests.
There were 145 (env) and 93 (pol) sequences analyzed. Based on env sequences, the predominant subtype was A1 (44%), and recombinants as defined pol sequences comprised 35% of the total sample. Paired sequences of pol and env from DRC FSW revealed mosaic recombinant in 54% of the sequences. Distinct geographic distributions of different HIV-1 subtypes and recombinants were observed. Subtype A1 was prevalent (40%) in Goma located in the East and significantly higher than in Mbuji-Mayi (p<0.05) in the South-central region, or in Lubumbashi in the South. Antiretroviral resistance was detected in 21.5% of 93 pol sequences analyzed, with the M184I/V and K103N mutations that confer high-level resistance to NRTI and NNRTI, respectively, being the most frequent mutations. However, the K103N mutant viruses were found only in the East.
HIV-1 variants found in DRC FSW reflect those reported to circulate in the general population from the corresponding geographical locations. HIV-1 mosaic genetics were readily detected in FSW. Importantly, ART resistance mutations to NNRTI and NRTI were common in the DRC sex workers.
The advent of high-resolution spectrographs and detailed stellar atmosphere modelling has strengthened the need for accurate molecular data. Carbon-enhanced metal-poor (CEMP) stars spectra are ...interesting objects with which to study transitions from the CH molecule. We combine programs for spectral analysis of molecules and stellar-radiative transfer codes to build an extensive CH linelist, including predissociation broadening as well as newly identified levels. We show examples of strong predissociation CH lines in CEMP stars, and we stress the important role played by the CH features in the Bond-Neff feature depressing the spectra of barium stars by as much as 0.2 mag in the λ = 3000−5500 Å range. Because of the extreme thermodynamic conditions prevailing in stellar atmospheres (compared to the laboratory), molecular transitions with high energy levels can be observed. Stellar spectra can thus be used to constrain and improve molecular data.
Symbiotic associations with bacteria have facilitated important evolutionary transitions in insects and resulted in long‐term obligate interactions. Recent evidence suggests that these associations ...are not always evolutionarily stable and that symbiont replacement, and/or supplementation of an obligate symbiosis by an additional bacterium, has occurred during the history of many insect groups. Yet, the factors favouring one symbiont over another in this evolutionary dynamic are not well understood; progress has been hindered by our incomplete understanding of the distribution of symbionts across phylogenetic and ecological contexts. While many aphids are engaged into an obligate symbiosis with a single Gammaproteobacterium, Buchnera aphidicola, in species of the Lachninae subfamily, this relationship has evolved into a ‘ménage à trois’, in which Buchnera is complemented by a cosymbiont, usually Serratia symbiotica. Using deep sequencing of 16S rRNA bacterial genes from 128 species of Cinara (the most diverse Lachninae genus), we reveal a highly dynamic dual symbiotic system in this aphid lineage. Most species host both Serratia and Buchnera but, in several clades, endosymbionts related to Sodalis, Erwinia or an unnamed member of the Enterobacteriaceae have replaced Serratia. Endosymbiont genome sequences from four aphid species confirm that these coresident symbionts fulfil essential metabolic functions not ensured by Buchnera. We further demonstrate through comparative phylogenetic analyses that cosymbiont replacement is not associated with the adaptation of aphids to new ecological conditions. We propose that symbiont succession was driven by factors intrinsic to the phenomenon of endosymbiosis, such as rapid genome deterioration or competitive interactions between bacteria with similar metabolic capabilities.
see also the Perspective by Russell et al
We use the multiconfiguration Dirac-Hartree-Fock (MCDHF) method combined with the relativistic configuration interaction approach (GRASP2K) to provide a consistent set of transition energies and ...radiative transition data for the lower n = 3 states in all Cl-like ions of astrophysical importance, from Cr viii to Zn xiv. We also provide excitation energies calculated for Fe x using the many-body perturbation theory (MBPT, implemented within FAC). The comparison of the present MCDHF results with MBPT and with the available experimental energies indicates that the theoretical excitation energies are highly accurate, with uncertainties of only a few hundred cm−1. Detailed comparisons for Fe x and Ni xii highlight discrepancies in the experimental energies found in the literature. Several new identifications are proposed.
Predicting shifts in the distribution and abundance of pest organisms relies on an accurate forecasting of their response to climate change. The oak processionary moth (OPM)
Thaumetopoea processionea
...causes serious damages to oak trees in forest, urban and other landscapes as well as severe allergic reactions to humans and animals. In the 1990’s and 2000’s, the OPM extended its range from mainland Europe and the Middle East into northern Europe. In 2005, it was also accidentally introduced in the United Kingdom. Moreover, the intensity and the frequency of OPM outbreaks are thought to have recently increased in several countries of Europe including Belgium, the Netherlands, Germany and Austria. In the present study, we aimed at forecasting the potential distribution of the OPM in Europe under current and future climate conditions. We thoroughly compiled available records of established populations all across Europe and fitted MaxEnt and BIOCLIM models to infer bioclimatic requirements for this species. Both models showed good predictive performance under current climate conditions. In particular, the surroundings of London where the OPM recently got established were predicted as highly climatically suitable. Models also predicted that many parts of northern Europe where the OPM currently does not occur (e.g. central UK, Wales, Ireland, southern Scotland, Denmark, southern part of the Scandinavian Peninsula, etc.) might become climatically suitable by 2050. Our predictions warrant the need for proper communication and management planning around the risks associated with the potential expansion of the OPM in Europe.
Spectral lines from different isotopes display a small separation in energy, commonly referred to as the line isotope shift. The program ris 4 (Relativistic Isotope Shift) calculates normal and ...specific mass shift parameters as well as field shift electronic factors from relativistic multiconfiguration Dirac–Hartree–Fock wave functions. These quantities, together with available nuclear data, determine isotope-dependent energy shifts. Using a reformulation of the field shift, it is possible to study, in a model-independent way, the atomic energy shifts arising from changes in nuclear charge distributions, e.g. deformations.
Program title: ris 4
Program Files doi: http://dx.doi.org/10.17632/8vjpf69zch.1
Licensing provisions: MIT
Programming language: Fortran 77 and Fortran 90
Journal reference of previous version: Comput. Phys. Comm. 184 (2013) 2187
Does the new version supersede the previous version?: Yes
Subprograms used: grasp 2K VERSION 1_1
Nature of problem: Prediction of level and transition isotope shifts in atoms using four-component relativistic wave functions.
Solution method: The nuclear mass shifts and field shifts are treated using first order perturbation theory. The electron density and the normal and specific mass shift parameters can be expressed as ∑μ,νcμcν〈Φ(γμPJMJ)|Vˆ|Φ(γνPJMJ)〉, where Vˆ is the relevant operator and Ψ(γPJMJ)=∑ν=1McνΦ(γνPJMJ) is the configuration state expansion, where P, J and MJ are the parity and angular quantum numbers, respectively. The matrix elements, in turn, can be decomposed as sums over radial integrals multiplied by angular coefficients. The angular coefficients are calculated using routines from the grasp2K version 1_1 package 1.
Reasons for new version: This new version calculates field shift electronic factors resulting from non-constant (varying) electron densities inside the nucleus.
Summary of revisions: This new version uses an expression of the field shift that through a polynomial expansion of the electron density contains higher order radial moments and thus takes the varying electron density within the nuclear volume into account.
Restrictions: The complexity of the cases that can be handled is entirely determined by the grasp2K package 1 used for the generation of the electronic wave functions.
Unusual features: Using a reformulation of the field shift, it is possible to study the atomic energy shifts arising from changes in nuclear charge distributions, e.g. deformations.
References:
1 P. Jönsson, G. Gaigalas, J. Bieroń, C. Froese Fischer, I.P. Grant, New version: Grasp2K relativistic atomic structure package, Comput. Phys. Commun. 184 (9) (2013) 2197–2203.
ABSTRACT
In this work, we report a list of 91 strong Th ii spectral lines in the visible wavelength region that could be used as cosmochronometers in future investigations to determine stellar ages ...from thorium radioactive decay. This list was established on the basis of a pseudo-relativistic Hartree–Fock model including core-polarization corrections (HFR+CPOL) allowing us to compute the corresponding radiative decay parameters, the latter being found to be in good overall agreement with the most accurate experimental data when available. Besides this semi-empirical approach, the fully relativistic ab initio multiconfiguration Dirac–Hartree–Fock (MCDHF) method was attempted, showing large discrepancies with both the present HFR+CPOL and the most recent experimental oscillator strengths, although the calculated wavelengths from theoretical energy levels agreed with observed spectral line wavelengths within 2.4 per cent.
We solve the entanglement classification under stochastic local operations and classical communication (SLOCC) for all multipartite symmetric states in the general N-qubit case. For this purpose, we ...introduce 2 parameters playing a crucial role, namely, the diversity degree and the degeneracy configuration of a symmetric state. Those parameters give rise to a simple method of identifying operational families of SLOCC entanglement classes of all symmetric N-qubit states, where the number of families grows as the partition function of the number of qubits.
ABSTRACT
Even though the electromagnetic counterpart AT2017gfo to the binary neutron star merger GW170817 is powered by the radioactive decay of r-process nuclei, only few tentative identifications ...of light r-process elements have been made so far. One of the major limitations for the identification of heavy nuclei is incomplete or missing atomic data. While substantial progress has been made on lanthanide atomic data over the last few years, for actinides there has been less emphasis, with the first complete set of opacity data only recently published. We perform atomic structure calculations of neodymium (Z = 60) as well as the corresponding actinide uranium (Z = 92). Using two different codes flexible atomic code (fac) and hartree–fock-relativistic (hfr) for the calculation of the atomic data, we investigate the accuracy of the calculated data (energy levels and electric dipole transitions) and their effect on kilonova opacities. For the fac calculations, we optimize the local central potential and the number of included configurations and use a dedicated calibration technique to improve the agreement between theoretical and available experimental atomic energy levels (AELs). For ions with vast amounts of experimental data available, the presented opacities agree quite well with previous estimations. On the other hand, the optimization and calibration method cannot be used for ions with only few available AELs. For these cases, where no experimental nor benchmarked calculations are available, a large spread in the opacities estimated from the atomic data obtained with the various atomic structure codes is observed. We find that the opacity of uranium is almost double the neodymium opacity.
The bacterium
Xylella fastidiosa
(
Xf
) is an invasive insect-borne pathogen, which causes lethal diseases to important crops including olives, citrus, almonds and grapes as well as numerous forest, ...ornamental, and uncultivated plants. Outbreaks of
Xf
-related plant diseases are currently occurring in the Mediterranean region, causing substantial losses to various agricultural sectors. Several models have recently been published to identify which regions are at highest risk in Europe; however, such models did not consider the insect vectors, which constitute the key driver of short-range
Xf
spread. We fitted bioclimatic species distribution models to depict the macroclimatic preferences of the meadow spittlebug
Philaenus spumarius
L. (1978) (Hemiptera: Aphrophoridae), the major epidemiologically relevant vector currently responsible for
Xf
spread in the Europe. Many regions of Western Europe and Mediterranean basin are predicted by models as highly climatically suitable for this vector, including all regions where severe
Xf
have occurred so far. Conversely, the driest and warmest areas of the Mediterranean basin are predicted as little suitable for
P. spumarius
. Models forecast that agricultural-important parts of the southern Mediterranean area might experience a substantial decrease in climatic suitability for
P. spumarius
by the period 2040–2060. Areas predicted as highly suitable just for the bacterium but not optimal for this vector are apparently still free of severe
Xf
outbreaks, suggesting that climate tolerances of
P. spumarius
might partly explain the current spatial pattern of
Xf
outbreaks in Europe and should always be considered in further risk assessments.
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