Gag-Protease Sequence Evolution Following Protease Inhibitor Monotherapy Treatment Failure in HIV-1 Viruses Circulating in East Africa.

Around 2.5 million HIV-infected individuals failing first-line therapy qualify for boosted protease inhibitor (bPI)-based second-line therapy globally. Major resistance mutations are rarely present at treatment failure in patients receiving bPI and the determinants of failure in these patients remain unknown. There is evidence that Gag can impact PI susceptibility. Here, we have sequenced Gag-Protease before and following failure in 23 patients in the SARA trial infected with subtypes A, C, and D viruses. Before bPI, significant variation in Protease and Gag was observed at positions previously associated with PI exposure and resistance including Gag mutations L449P, S451N, and L453P and Protease K20I and L63P. Following PI failure, previously described mutations in Protease and Gag were observed, including those at the cleavage sites such as R361K and P453L. However, the emergence of clear genetic determinants of therapy failure across patients was not observed. Larger Gag sequence datasets will be required to comprehensively identify mutational correlates of bPI failure across subtypes

Extracting Spatial Information from Noise Measurements of Multi-Spatial-Mode Quantum States

We show that it is possible to use the spatial quantum correlations present in twin beams to extract information about the shape of a mask in the path of one of the beams. The scheme, based on noise measurements through homodyne detection, is useful in the regime where the number of photons is low enough that direct detection with a photodiode is difficult but high enough that photon counting is not an option. We find that under some conditions the use of quantum states of light leads to an enhancement of the sensitivity in the estimation of the shape of the mask over what can be achieved with a classical state with equivalent properties (mean photon flux and noise properties). In addition, we show that the level of enhancement that is obtained is a result of the quantum correlations and cannot be explained with only classical correlations

Effect of selective removal of badgers (Meles meles) on ranging behaviour during a ‘Test and Vaccinate or Remove’ intervention in Northern Ireland

Publication history: Accepted - 23 April 2021; Published online - 7 May 2021The role of the Eurasian badger (Meles meles) as a wildlife host has complicated the management of bovine tuberculosis (bTB) in cattle. Badger ranging behaviour has previously been found to be altered by culling of badgers and has been suggested to increase the transmission of bTB either among badgers or between badgers and cattle. In 2014, a five-year bTB intervention research project in a 100 km2 area in Northern Ireland was initiated involving selective removal of dual path platform (DPP) VetTB (immunoassay) test positive badgers and vaccination followed by release of DPP test negative badgers (‘Test and Vaccinate or Remove’). Home range sizes, based on position data obtained from global positioning system collared badgers, were compared between the first year of the project, where no DPP test positive badgers were removed, and follow-up years 2–4 when DPP test positive badgers were removed. A total of 105 individual badgers were followed over 21 200 collar tracking nights. Using multivariable analyses, neither annual nor monthly home ranges differed significantly in size between years, suggesting they were not significantly altered by the bTB intervention that was applied in the study area.This research was funded by the Department of Agriculture, Environment and Rural Affairs for Northern Ireland

Virtual Compton Scattering and Neutral Pion Electroproduction in the Resonance Region up to the Deep Inelastic Region at Backward Angles

We have made the first measurements of the virtual Compton scattering (VCS) process via the H$(e,e'p)\gamma$ exclusive reaction in the nucleon resonance region, at backward angles. Results are presented for the $W$-dependence at fixed $Q^2=1$ GeV$^2$, and for the $Q^2$-dependence at fixed $W$ near 1.5 GeV. The VCS data show resonant structures in the first and second resonance regions. The observed $Q^2$-dependence is smooth. The measured ratio of H$(e,e'p)\gamma$ to H$(e,e'p)\pi^0$ cross sections emphasizes the different sensitivity of these two reactions to the various nucleon resonances. Finally, when compared to Real Compton Scattering (RCS) at high energy and large angles, our VCS data at the highest $W$ (1.8-1.9 GeV) show a striking $Q^2$- independence, which may suggest a transition to a perturbative scattering mechanism at the quark level.Comment: 20 pages, 8 figures. To appear in Phys.Rev.

Nuclear transparency with the γn⃗π-p process in 4He

We have measured the nuclear transparency of the fundamental process γn⃗π-p in 4He. These measurements were performed at Jefferson Lab in the photon energy range of 1.6–4.5 GeV and at θcmπ=70° and 90°. These measurements are the first of their kind in the study of nuclear transparency in photoreactions. They also provide a benchmark test of Glauber calculations based on traditional models of nuclear physics. The transparency results suggest deviations from the traditional nuclear physics picture. The momentum transfer dependence of the measured nuclear transparency is consistent with Glauber calculations that include the quantum chromodynamics phenomenon of color transparency

Plane-wave impulse approximation extraction of the neutron magnetic form factor from quasielastic 3He(e,e′) at Q2=0.3 to 0.6 (GeV/c)2

A high precision measurement of the transverse spin-dependent asymmetry AT′ in 3He(e,e′) quasielastic scattering was performed in Hall A at Jefferson Lab at values of the squared four-momentum transfer, Q2, between 0.1 and 0.6 (GeV/c)2. AT′ is sensitive to the neutron magnetic form factor, GMn. Values of GMn at Q2=0.1 and 0.2 (GeV/c)2, extracted using Faddeev calculations, were reported previously. Here, we report the extraction of GMn for the remaining Q2 values in the range from 0.3 to 0.6 (GeV/c)2 using a plane-wave impulse approximation calculation. The results are in good agreement with recent precision data from experiments using a deuterium target

Plane-wave impulse approximation extraction of the neutron magnetic form factor from quasielastic 3He(e,e′) at Q2=0.3 to 0.6 (GeV/c)2

A high precision measurement of the transverse spin-dependent asymmetry AT′ in 3He(e,e′) quasielastic scattering was performed in Hall A at Jefferson Lab at values of the squared four-momentum transfer, Q2, between 0.1 and 0.6 (GeV/c)2. AT′ is sensitive to the neutron magnetic form factor, GMn. Values of GMn at Q2=0.1 and 0.2 (GeV/c)2, extracted using Faddeev calculations, were reported previously. Here, we report the extraction of GMn for the remaining Q2 values in the range from 0.3 to 0.6 (GeV/c)2 using a plane-wave impulse approximation calculation. The results are in good agreement with recent precision data from experiments using a deuterium target

Extraction of the Neutron Magnetic Form Factor from Quasi-Elastic 3He(pol)(e(pol),e') at Q^2 = 0.1 - 0.6 (GeV/c)^2

We have measured the spin-dependent transverse asymmetry, A_T', in quasi-elastic inclusive electron scattering from polarized 3He with high precision at Q^2 = 0.1 to 0.6 (GeV/c)^2. The neutron magnetic form factor, GMn, was extracted at Q^2 = 0.1 and 0.2 (GeV/c)^2 using a non-relativistic Faddeev calculation that includes both final-state interactions (FSI) and meson-exchange currents (MEC). In addition, GMn was extracted at Q^2 = 0.3 to 0.6 (GeV/c)^2 using a Plane Wave Impulse Approximation calculation. The accuracy of the modeling of FSI and MEC effects was tested and confirmed with a precision measurement of the spin-dependent asymmetry in the breakup threshold region of the 3He(pol)(e(pol),e') reaction. The total relative uncertainty of the extracted GMn data is approximately 3%. Close agreement was found with other recent high-precision GMn data in this Q^2 range.Comment: Archival paper, 17 pages, 10 figures, 5 tables, submitted to Physical Review C. v2: shortened considerably, updated comparison to theor

Dynamics of the 16^{16}O(e,e'p) cross section at high missing energies

We measured the cross section and response functions (R_L, R_T, and R_LT) for the 16O(e,e'p) reaction in quasielastic kinematics for missing energies 25 60 MeV and P_miss > 200 MeV/c, the cross section is relatively constant. Calculations which include contributions from pion exchange currents, isobar currents and short-range correlations account for the shape and the transversity but only for half of the magnitude of the measured cross section

Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option availabl