Environmental trade-offs of meeting nutritional requirements with a lower share of animal protein for adult subpopulations.

Decreasing the share of protein contributed by animal-based foods is recommended to move towards more sustainable and healthier diets. This study aimed to assess the potential environmental impacts of diets with a lower share of animal protein. The diets were modeled to include the minimum share of animal protein in total protein that met nutrient requirements and did not increase costs. The new diets also minimized the difference in the quantity of food from those of observed (OBS) diets. They were modeled for five adult subpopulations (defined by sex and age) using mathematical optimization. The model was created by combining the INCA2 database (to model OBS diets in the French population) and a database of 207 food items to adjust nutritional and price parameters. All modeled diets satisfied nutritional and cost constraints. A low-animal-protein (LAP) diet was identified for each subpopulation by progressively decreasing the share of animal protein by steps of 5% until the recommended quantity of protein and/or consumption constraints were no longer satisfied. Potential environmental impacts of the LAP diets in eight impact categories were calculated using life cycle assessment and life cycle inventories from Agribalyse® 3.0. A LAP diet for the entire population was calculated as a weighted mean of the subpopulations' LAP diets. The share of animal protein decreased from 70% in the OBS diet to 50% in the LAP diet. Compared to the OBS diet, the LAP diet decreased five environmental impacts: climate change (greenhouse gas emissions), acidification (emissions of acidifying compounds) and land occupation (all by more than 30%), cumulative energy demand (by 23%) and marine eutrophication (by 13%). Conversely, it increased three environmental impacts: freshwater eutrophication and water use (both by ca. 40%) and biodiversity damage potential (potential loss of species associated with land use) (by 66%). These results suggest that decreasing the share of animal protein to 50% is compatible with nutritional requirements, affordability and consumption constraints, but would have mixed effects on the environment.

Dynamics and durability of HIV-1 neutralization are determined by viral replication.

Human immunodeficiency virus type 1 (HIV-1)-neutralizing antibodies (nAbs) that prevent infection are the main goal of HIV vaccine discovery. But as no nAb-eliciting vaccines are yet available, only data from HIV-1 neutralizers-persons with HIV-1 who naturally develop broad and potent nAbs-can inform about the dynamics and durability of nAb responses in humans, knowledge which is crucial for the design of future HIV-1 vaccine regimens. To address this, we assessed HIV-1-neutralizing immunoglobulin G (IgG) from 2,354 persons with HIV-1 on or off antiretroviral therapy (ART). Infection with non-clade B viruses, CD4+ T cell counts <200 µl-1, being off ART and a longer time off ART were independent predictors of a more potent and broad neutralization. In longitudinal analyses, we found nAb half-lives of 9.3 and 16.9 years in individuals with no- or low-level viremia, respectively, and 4.0 years in persons who newly initiated ART. Finally, in a potent HIV-1 neutralizer, we identified lower fractions of serum nAbs and of nAb-encoding memory B cells after ART initiation, suggesting that a decreasing neutralizing serum activity after antigen withdrawal is due to lower levels of nAbs. These results collectively show that HIV-1-neutralizing responses can persist for several years, even at low antigen levels, suggesting that an HIV-1 vaccine may elicit a durable nAb response.

Avoidance behaviour of aquatic macroinvertebrates for real-time detection of micropollutant surge in wastewater effluents.

Micropollutants are regularly detected at the outlets of wastewater treatment plants (WWTPs). Across urban and industrial WWTPs, monitoring directives only require assessment for a handful of chemicals via sampling methods that fail to capture the temporal variability in micropollutant discharge. In this study, we develop a biotest for real-time on-line monitoring of micropollutant discharge dynamics in WWTPs effluents. The selected biomonitoring device ToxMate uses videotracking of invertebrate movement, which was used to deduce avoidance behaviour of the amphipod Gammarus fossarum. Organism conditioning was set up to induce a state of minimal locomotor activity in basal conditions to maximise avoidance signal sensitivity to micropollutant spikes. We showed that with a standardised protocol, it was possible to minimise both overall movement and sensitivity to physio-chemical variations typical to WWTP effluents, as well as capture the spikes of two micropollutants upon exposure (copper and methomyl). Spikes in avoidance behaviour were consistently seen for the two chemicals, as well as a strong correlation between avoidance intensity and spiked concentration. A two-year effluent monitoring case study also illustrates how this biomonitoring method is suitable for real-time on-site monitoring, and shows a promising non-targeted approach for characterising complex micropollutant discharge variability at WWTP effluents, which today remains poorly understood.

Magnetite nanoparticles as a kinetically favorable source of iron to enhance GBM response to chemoradiosensitization with pharmacological ascorbate.

Ferumoxytol (FMX) is an FDA-approved magnetite (Fe3O4) nanoparticle used to treat iron deficiency anemia that can also be used as an MR imaging agent in patients that can't receive gadolinium. Pharmacological ascorbate (P-AscH-; IV delivery; plasma levels ≈ 20 mM) has shown promise as an adjuvant to standard of care chemo-radiotherapy in glioblastoma (GBM). Since ascorbate toxicity mediated by H2O2 is enhanced by Fe redox cycling, the current study determined if ascorbate catalyzed the release of ferrous iron (Fe2+) from FMX for enhancing GBM responses to chemo-radiotherapy. Ascorbate interacted with Fe3O4 in FMX to produce redox-active Fe2+ while simultaneously generating increased H2O2 fluxes, that selectively enhanced GBM cell killing (relative to normal human astrocytes) as opposed to a more catalytically active Fe complex (EDTA-Fe3+) in an H2O2 - dependent manner. In vivo, FMX was able to improve GBM xenograft tumor control when combined with pharmacological ascorbate and chemoradiation in U251 tumors that were unresponsive to pharmacological ascorbate therapy. These data support the hypothesis that FMX combined with P-AscH- represents a novel combined modality therapeutic approach to enhance cancer cell selective chemoradiosentization in the management of glioblastoma.

Quantum chemical insight into the effects of the local electron environment on T2*-based MRI.

T2* relaxation is an intrinsic magnetic resonance imaging (MRI) parameter that is sensitive to local magnetic field inhomogeneities created by the deposition of endogenous paramagnetic material (e.g. iron). Recent studies suggest that T2* mapping is sensitive to iron oxidation state. In this study, we evaluate the spin state-dependence of T2* relaxation using T2* mapping. We experimentally tested this physical principle using a series of phantom experiments showing that T2* relaxation times are directly proportional to the spin magnetic moment of different transition metals along with their associated magnetic susceptibility. We previously showed that T2* relaxation time can detect the oxidation of Fe2+. In this paper, we demonstrate that T2* relaxation times are significantly longer for the diamagnetic, d10 metal Ga3+, compared to the paramagnetic, d5 metal Fe3+. We also show in a cell culture model that cells supplemented with Ga3+ (S = 0) have a significantly longer relaxation time compared to cells supplemented with Fe3+ (S = 5/2). These data support the hypothesis that dipole-dipole interactions between protons and electrons are driven by the strength of the electron spin magnetic moment in the surrounding environment giving rise to T2* relaxation.

Antiretroviral Imprints and Genomic Plasticity of HIV-1 pol in Non-clade B: Implications for Treatment.

Combinational antiretroviral therapy (cART) is the most effective tool to prevent and control HIV-1 infection without an effective vaccine. However, HIV-1 drug resistance mutations (DRMs) and naturally occurring polymorphisms (NOPs) can abrogate cART efficacy. Here, we aimed to characterize the HIV-1 pol mutation landscape in Cameroon, where highly diverse HIV clades circulate, and identify novel treatment-associated mutations that can potentially affect cART efficacy. More than 8,000 functional Cameroonian HIV-1 pol sequences from 1987 to 2020 were studied for DRMs and NOPs. Site-specific amino acid frequencies and quaternary structural features were determined and compared between periods before (≤2003) and after (2004-2020) regional implementation of cART. cART usage in Cameroon induced deep mutation imprints in reverse transcriptase (RT) and to a lower extent in protease (PR) and integrase (IN), according to their relative usage. In the predominant circulating recombinant form (CRF) 02_AG (CRF02_AG), 27 canonical DRMs and 29 NOPs significantly increased or decreased in RT during cART scale-up, whereas in IN, no DRM and only seven NOPs significantly changed. The profound genomic imprints and higher prevalence of DRMs in RT compared to PR and IN mirror the dominant use of reverse transcriptase inhibitors (RTIs) in sub-Saharan Africa and the predominantly integrase strand transfer inhibitor (InSTI)-naïve study population. Our results support the potential of InSTIs for antiretroviral treatment in Cameroon; however, close surveillance of IN mutations will be required to identify emerging resistance patterns, as observed in RT and PR. Population-wide genomic analyses help reveal the presence of selective pressures and viral adaptation processes to guide strategies to bypass resistance and reinstate effective treatment.

Feasibility of energy adaptive angular meshing for perpendicular and parallel magnetic fields in a grid based Boltzmann solver.

PURPOSE: To develop the enabling algorithmic techniques which allow forward-peaked adaptive angular meshing to be compatible with angular advection of magnetic fields within a deterministic Grid Based Boltzmann Solver (GBBS) for MRI-guided radiotherapy, and establish appropriate energy adaptive meshing schemes which minimize total numerical degrees of freedom while preserving high dosimetric accuracy for parallel and perpendicular magnetic fields. METHODS: A framework to independently adapt angular mesh resolution and basis function refinement of forward and backscattering hemispheres is developed, uniquely accommodating angular advection introduced by magnetic fields. Upwind stabilization techniques to accurately transfer fluence between hemispheres having different discretization are established. To facilitate oblique beam and magnetic field orientations, cardinal forward-peaked mesh orientations were devised to balance requirements for acyclic space-angle sweep ordering, while ensuring the beam predominantly overlaps the forward hemisphere. Energy-dependent fluence anisotropy is investigated, leading to adaptive angular meshing schemes for parallel and perpendicular magnetic fields. Calculated dose distributions were validated against GEANT4 Monte Carlo calculations on slab geometry and anthropomorphic phantoms. RESULTS: Forward-peaked and isotropic energy adaptive angular meshing schemes were developed for parallel and perpendicular magnetic fields respectively, which reduce the number of elements solved by 52.8% and 47.7% respectively compared to static discretization using 32 quadratic elements while retaining over 97% of points passing the gamma 1%/1 mm criterion against Monte Carlo. CONCLUSIONS: Techniques to preserve angular upwind-stabilization between hemispheres of a forward-peaked mesh and establish an acyclic directed space-angle sweep graph enabled energy-adaptive meshing schemes to be developed while accurately solving for magnetic fields. This substantially reduced the numerical degrees of freedom while retaining excellent dosimetric agreement with Monte Carlo. These algorithmic underpinnings contribute towards a fast deterministic GBBS for MRI-guided radiotherapy.

Near full genome characterization of HIV-1 unique recombinant forms in Cameroon reveals dominant CRF02_AG and F2 recombination patterns.

INTRODUCTION: In Cameroon, a manifold diversity of HIV strains exists with CRF02_AG and unique recombinant forms (URFs) being the predominant strains. In recent years, a steady increase in URFs and clade F2 viruses has been monitored through partial genome sequencing. There is an information gap in the characterization of emerging URFs along the full genome, which is needed to address the challenges URFs pose towards diagnosis, treatment and HIV-1 vaccine design. METHOD: Eighteen Cameroonian URFs from samples collected between the years 2000 and 2015 were studied using a newly developed near full genome sequencing (NFGS) protocol based on variable nested RT-PCRs with a versatile primer set. Near full genomes were characterized for recombination patterns and sequence signatures with possible impact on antiretroviral treatment or Env-directed immune responses. Third-generation sequencing (3GS) of near full or half genomes (HGs) gave insight into intra-patient URF diversity. RESULTS: The characterized URFs were composed of a broad variety of subtypes and recombinants including A, F, G, CRF01_AE, CRF02_AG and CRF22_01A1. Phylogenetic analysis unveiled dominant CRF02_AG and F2 recombination patterns. 3GS indicated a high intra-patient URF diversity with up to four distinct viral sub-populations present in plasma at the same time. URF pol genomic analysis revealed a number of accessory drug resistance mutations (DRMs) in the ART-naïve participants. Genotypic env analysis suggests CCR5 usage in 14/18 samples and identified deviations at residues, critical for gp120/gp41 interphase and CD4 binding site broadly neutralizing antibodies in more than half of the studied URFs. V1V2 sites of immune pressure in the human RV144 vaccine study varied in more than a third of URFs. CONCLUSIONS: This study identified novel mosaic patterns in URFs in Cameroon. In line with the regional predominance of CRF_02AG and the increased prevalence of clade F2, prominent CRF_02AG and F2 background patterns were observed underlying the URFs. In the context of the novel mosaic genomes, the impact of the identified accessory DRMs and Env epitope variations on treatment and immune control remains elusive. The evolving diversity of HIV-1 URFs in Cameroon requires continuous monitoring to respond to the increasing challenges for diagnosis, antiretroviral treatment and prevention.

A novel transport sweep architecture for efficient deterministic patient dose calculations in MRI-guided radiotherapy.

Accurate and efficient patient dose calculations are essential for treatment planning in magnetic resonance imaging guided radiotherapy (MRIgRT). Achieving reasonable performance for a space-angle discontinuous finite element method (DFEM) grid based Boltzmann solver (GBBS) with magnetic fields for clinical MRIgRT applications largely depends on how the transport sweep is orchestrated. Compared to classical Discrete Ordinates, DFEM in angle introduces increased angular degrees of freedom and eliminates ray-effect artifacts. However, the inclusion of magnetic fields introduces additional serial dependencies such that parallelization of the space-angle transport sweeps becomes more challenging. Novel techniques for the transport sweep and right-hand source assembly are developed, predicated on limiting the number of bulk material densities modeled in the transport sweep scatter calculations. Specifically, k-means clustering is used to assign sub-intervals of mass-density for each spatial element to execute the scatter-dose calculations using batched multiplication by pre-inverted transport sweep matrices. This is shown to be two orders of magnitude more efficient than solving each elemental system individually at runtime. Even with discrete material densities used in the transport sweep scatter calculations, accuracy is maintained by optimizing the material density assignments using k-means clustering, and by performing the primary photon fluence calculations (ray-tracing) using the underlying continuous density of the computed tomography (CT) image. In the presence of 0.5 T parallel and 1.5 T perpendicular magnetic fields, this approach demonstrates high levels of accuracy with gamma 1%/1 mm passing rates exceeding 94% across a range of anatomical sites compared to GEANT4 Monte Carlo dose calculations which used continuous densities. This deterministic GBBS approach maintains unconditional stability, produces no ray-effect artifacts, and has the benefit of no statistical uncertainty. Runtime on a non-parallelized Matlab implementation averaged 10 min per beam averaging 80 000 spatial elements, paving way for future development based on this algorithmically efficient paradigm.

Immune Correlates of Disease Progression in Linked HIV-1 Infection.

Genetic and immunologic analyses of epidemiologically-linked HIV transmission enable insights into the impact of immune responses on clinical outcomes. Human vaccine trials and animal studies of HIV-1 infection have suggested immune correlates of protection; however, their role in natural infection in terms of protection from disease progression is mostly unknown. Four HIV-1+ Cameroonian individuals, three of them epidemiologically-linked in a polygamous heterosexual relationship and one incidence-matched case, were studied over 15 years for heterologous and cross-neutralizing antibody responses, antibody binding, IgA/IgG levels, antibody-dependent cellular cytotoxicity (ADCC) against cells expressing wild-type or CD4-bound Env, viral evolution, Env epitopes, and host factors including HLA-I alleles. Despite viral infection with related strains, the members of the transmission cluster experienced contrasting clinical outcomes including cases of rapid progression and long-term non-progression in the absence of strongly protective HLA-I or CCR5Δ32 alleles. Slower progression and higher CD4/CD8 ratios were associated with enhanced IgG antibody binding to native Env and stronger V1V2 antibody binding responses in the presence of viruses with residue K169 in V2. ADCC against cells expressing Env in the CD4-bound conformation in combination with low Env-specific IgA/IgG ratios correlated with better clinical outcome. This data set highlights for the first time that V1V2-directed antibody responses and ADCC against cells expressing open, CD4-exposed Env, in the presence of low plasma IgA/IgG ratios, can correlate with clinical outcome in natural infection. These parameters are comparable to the major correlates of protection, identified post-hoc in the RV144 vaccine trial; thus, they may also modulate the rate of clinical progression once infected. The findings illustrate the potential of immune correlate analysis in natural infection to guide vaccine development.

Development of a Versatile, Near Full Genome Amplification and Sequencing Approach for a Broad Variety of HIV-1 Group M Variants.

Near full genome sequencing (NFGS) of HIV-1 is required to assess the genetic composition of HIV-1 strains comprehensively. Population-wide, it enables a determination of the heterogeneity of HIV-1 and the emergence of novel/recombinant strains, while for each individual it constitutes a diagnostic instrument to assist targeted therapeutic measures against viral components. There is still a lack of robust and adaptable techniques for efficient NFGS from miscellaneous HIV-1 subtypes. Using rational primer design, a broad primer set was developed for the amplification and sequencing of diverse HIV-1 group M variants from plasma. Using pure subtypes as well as diverse, unique recombinant forms (URF), variable amplicon approaches were developed for NFGS comprising all functional genes. Twenty-three different genomes composed of subtypes A (A1), B, F (F2), G, CRF01_AE, CRF02_AG, and CRF22_01A1 were successfully determined. The NFGS approach was robust irrespective of viral loads (≥306 copies/mL) and amplification method. Third-generation sequencing (TGS), single genome amplification (SGA), cloning, and bulk sequencing yielded similar outcomes concerning subtype composition and recombinant breakpoint patterns. The introduction of a simple and versatile near full genome amplification, sequencing, and cloning method enables broad application in phylogenetic studies of diverse HIV-1 subtypes and can contribute to personalized HIV therapy and diagnosis.

ERRα promotes breast cancer cell dissemination to bone by increasing RANK expression in primary breast tumors.

Bone is the most common metastatic site for breast cancer. Estrogen-related-receptor alpha (ERRα) has been implicated in cancer cell invasiveness. Here, we established that ERRα promotes spontaneous metastatic dissemination of breast cancer cells from primary mammary tumors to the skeleton. We carried out cohort studies, pharmacological inhibition, gain-of-function analyses in vivo and cellular and molecular studies in vitro to identify new biomarkers in breast cancer metastases. Meta-analysis of human primary breast tumors revealed that high ERRα expression levels were associated with bone but not lung metastases. ERRα expression was also detected in circulating tumor cells from metastatic breast cancer patients. ERRα overexpression in murine 4T1 breast cancer cells promoted spontaneous bone micro-metastases formation when tumor cells were inoculated orthotopically, whereas lung metastases occurred irrespective of ERRα expression level. In vivo, Rank was identified as a target for ERRα. That was confirmed in vitro in Rankl stimulated tumor cell invasion, in mTOR/pS6K phosphorylation, by transactivation assay, ChIP and bioinformatics analyses. Moreover, pharmacological inhibition of ERRα reduced primary tumor growth, bone micro-metastases formation and Rank expression in vitro and in vivo. Transcriptomic studies and meta-analysis confirmed a positive association between metastases and ERRα/RANK in breast cancer patients and also revealed a positive correlation between ERRα and BRCA1mut carriers. Taken together, our results reveal a novel ERRα/RANK axis by which ERRα in primary breast cancer promotes early dissemination of cancer cells to bone. These findings suggest that ERRα may be a useful therapeutic target to prevent bone metastases.

Monte Carlo determination of k Q and k Qmsr values for the exradin A26 ionisation chamber for the Varian TrueBeam.

We have calculated conversion factors, k Q for the A26 micro ionisation chamber along with machine specific reference beam quality factors, k Qmsr, for a number of field sizes and beam qualities for the Varian TrueBeam accelerator. The A12 ionisation chamber was simulated alongside the A26, so as to validate against known literature values. Both ionisation chambers were modelled from manufacturer data sheets and schematics. The egs_chamber Monte Carlo user code was used to simulate each absorbed dose relevant to the beam quality conversion factors k Q and k Qmsr. Tabulated spectra for beam energies of 4 through 25 MV were used in the k Q calculations for both investigated chambers. Varian TrueBeam phase space files for 6 MV flattened as well as 6 and 10 MV unflattened beams were used in the simulations of the A26 chamber in field sizes from 2 × 2 cm square to 20 × 20 cm square in order to determine k Qmsr values. The PDD(10)x values of the tabulated spectra were found to be within variation between studies, with an average deviance of 0.4% from one prior study. The simulated A12 k Q values matched the accepted literature values with an average variation of <0.1%. The A26 k Q values match the manufacturer provided values to within 0.5%. For all investigated field sizes the k Qmsr values are within 0.006 of unity. There is no published data for this chamber for a direct comparison, but there is similarity between these results and results from other chambers regularly used in similar circumstances. Furthermore, the agreement of the simulated k Q values to knowns, and the agreement of the PDD(10)x factors would suggest the correctness and accuracy of the study.

Next-generation sequencing provides an added value in determining drug resistance and viral tropism in Cameroonian HIV-1 vertically infected children.

With limited and low-genetic barrier drugs used for the prevention of mother-to-child transmission (PMTCT) of HIV in sub-Saharan Africa, vertically transmitted HIV-1 drug-resistance (HIVDR) is concerning and might prompt optimal pediatric strategies.The aim of this study was to ascertain HIVDR and viral-tropism in majority and minority populations among Cameroonian vertically infected children.A comparative analysis among 18 HIV-infected children (7 from PMTCT-exposed mothers and 11 from mothers without PMTCT-exposure) was performed. HIVDR and HIV-1 co-receptor usage was evaluated by analyzing sequences obtained by both Sanger sequencing and ultra-deep 454-pyrosequencing (UDPS), set at 1% threshold.Overall, median (interquartile range) age, viremia, and CD4 count were 6 (4-10) years, 5.5 (4.9-6.0) log10 copies/mL, and 526 (282-645) cells/mm, respectively. All children had wild-type viruses through both Sanger sequencing and UDPS, except for 1 PMTCT-exposed infant harboring minority K103N (8.31%), born to a mother exposed to AZT+3TC+NVP. X4-tropic viruses were found in 5 of 15 (33.3%) children (including 2 cases detected only by UDPS). Rate of X4-tropic viruses was 0% (0/6) below 5 years (also as minority species), and became relatively high above 5 years (55.6% [5/9], P = .040. X4-tropic viruses were higher with CD4 ≤15% (4/9 [44.4%]) versus CD4 >15% (1/6 [16.7%], P = .580); similarly for CD4 ≤200 (3/4 [75%]) versus CD4 >200 (2/11 [18.2%] cells/mm, P = .077.NGS has the ability of excluding NRTI- and NNRTI-mutations as minority species in all but 1 children, thus supporting the safe use of these drug-classes in those without such mutations, henceforth sparing ritonavir-boosted protease inhibitors or integrase inhibitors for the few remaining cases. In children under five years, X4-tropic variants would be rare, suggesting vertical-transmission with CCR5-tropic viruses and possible maraviroc usage at younger ages.

A novel upwind stabilized discontinuous finite element angular framework for deterministic dose calculations in magnetic fields.

Angular discretization impacts nearly every aspect of a deterministic solution to the linear Boltzmann transport equation, especially in the presence of magnetic fields, as modeled by a streaming operator in angle. In this work a novel stabilization treatment of the magnetic field term is developed for an angular finite element discretization on the unit sphere, specifically involving piecewise partitioning of path integrals along curved element edges into uninterrupted segments of incoming and outgoing flux, with outgoing components updated iteratively. Correct order-of-accuracy for this angular framework is verified using the method of manufactured solutions for linear, quadratic, and cubic basis functions in angle. Higher order basis functions were found to reduce the error especially in strong magnetic fields and low density media. We combine an angular finite element mesh respecting octant boundaries on the unit sphere to spatial Cartesian voxel elements to guarantee an unambiguous transport sweep ordering in space. Accuracy for a dosimetrically challenging scenario involving bone and air in the presence of a 1.5 T parallel magnetic field is validated against the Monte Carlo package GEANT4. Accuracy and relative computational efficiency were investigated for various angular discretization parameters. 32 angular elements with quadratic basis functions yielded a reasonable compromise, with gamma passing rates of 99.96% (96.22%) for a 2%/2 mm (1%/1 mm) criterion. A rotational transformation of the spatial calculation geometry is performed to orient an arbitrary magnetic field vector to be along the z-axis, a requirement for a constant azimuthal angular sweep ordering. Working on the unit sphere, we apply the same rotational transformation to the angular domain to align its octants with the rotated Cartesian mesh. Simulating an oblique 1.5 T magnetic field against GEANT4 yielded gamma passing rates of 99.42% (95.45%) for a 2%/2 mm (1%/1 mm) criterion.

Stability analysis of a deterministic dose calculation for MRI-guided radiotherapy.

Modern effort in radiotherapy to address the challenges of tumor localization and motion has led to the development of MRI guided radiotherapy technologies. Accurate dose calculations must properly account for the effects of the MRI magnetic fields. Previous work has investigated the accuracy of a deterministic linear Boltzmann transport equation (LBTE) solver that includes magnetic field, but not the stability of the iterative solution method. In this work, we perform a stability analysis of this deterministic algorithm including an investigation of the convergence rate dependencies on the magnetic field, material density, energy, and anisotropy expansion. The iterative convergence rate of the continuous and discretized LBTE including magnetic fields is determined by analyzing the spectral radius using Fourier analysis for the stationary source iteration (SI) scheme. The spectral radius is calculated when the magnetic field is included (1) as a part of the iteration source, and (2) inside the streaming-collision operator. The non-stationary Krylov subspace solver GMRES is also investigated as a potential method to accelerate the iterative convergence, and an angular parallel computing methodology is investigated as a method to enhance the efficiency of the calculation. SI is found to be unstable when the magnetic field is part of the iteration source, but unconditionally stable when the magnetic field is included in the streaming-collision operator. The discretized LBTE with magnetic fields using a space-angle upwind stabilized discontinuous finite element method (DFEM) was also found to be unconditionally stable, but the spectral radius rapidly reaches unity for very low-density media and increasing magnetic field strengths indicating arbitrarily slow convergence rates. However, GMRES is shown to significantly accelerate the DFEM convergence rate showing only a weak dependence on the magnetic field. In addition, the use of an angular parallel computing strategy is shown to potentially increase the efficiency of the dose calculation.

Short Communication: False Recent Ratio of the Limiting-Antigen Avidity Assay and Viral Load Testing Algorithm Among Cameroonians with Long-Term HIV Infection.

Current serological assays that are used for cross-sectional HIV incidence estimation have been shown to misclassify individuals with chronic infection. Limited information exists on the performance of cross-sectional incidence assays in Central Africa. HIV-positive individuals from Cameroon who were infected for at least 1 or 2 years were evaluated to determine the false recent ratio (FRR) of a two-assay algorithm, which includes the Limiting Antigen Avidity (LAg-Avidity) assay (normalized optical density units, ODn <1.5) and HIV viral load (>1000 copies/ml). The subject-level FRR was 5.3% (95% confidence interval [CI], 2.1-10.5) for individuals infected for ≥1 year and 3.9% (95% CI, 0.8-11.0) for individuals infected for ≥2 years. These data suggest that the LAg-Avidity plus viral load incidence algorithm may overestimate HIV incidence rates in Central Africa.

Multimethod Longitudinal HIV Drug Resistance Analysis in Antiretroviral-Therapy-Naive Patients.

The global intensification of antiretroviral therapy (ART) can lead to increased rates of HIV drug resistance (HIVDR) mutations in treated and also in ART-naive patients. ART-naive HIV-1-infected patients from Cameroon were subjected to a multimethod HIVDR analysis using amplification-refractory mutation system (ARMS)-PCR, Sanger sequencing, and longitudinal next-generation sequencing (NGS) to determine their profiles for the mutations K103N, Y181C, K65R, M184V, and T215F/Y. We processed 66 ART-naive HIV-1-positive patients with highly diverse subtypes that underlined the predominance of CRF02_AG and the increasing rate of F2 and other recombinant forms in Cameroon. We compared three resistance testing methods for 5 major mutation sites. Using Sanger sequencing, the overall prevalence of HIVDR mutations was 7.6% (5/66) and included all studied mutations except K65R. Comparing ARMS-PCR with Sanger sequencing as a reference, we obtained a sensitivity of 100% (5/5) and a specificity of 95% (58/61), caused by three false-positive calls with ARMS-PCR. For 32/66 samples, we obtained NGS data and we observed two additional mismatches made up of minority variants (7% and 18%) that might not be clinically relevant. Longitudinal NGS analyses revealed changes in HIVDR mutations in all five positive subjects that could not be attributed to treatment. In one of these cases, superinfection led to the temporary masking of a resistant virus. HIVDR mutations can be sensitively detected by ARMS-PCR and sequencing methods with comparable performances. Longitudinal changes in HIVDR mutations have to be considered even in the absence of treatment.

Contrasting antibody responses to intrasubtype superinfection with CRF02_AG.

HIV superinfection describes the sequential infection of an individual with two or more unrelated HIV strains. Intersubtype superinfection has been shown to cause a broader and more potent heterologous neutralizing antibody response when compared to singly infected controls, yet the effects of intrasubtype superinfection remain controversial. Longitudinal samples were analyzed phylogenetically for pol and env regions using Next-Generation Sequencing and envelope cloning. The impact of CRF02_AG intrasubtype superinfection was assessed for heterologous neutralization and antibody binding responses. We compared two cases of CRF02_AG intrasubtype superinfection that revealed complete replacement of the initial virus by superinfecting CRF02_AG variants with signs of recombination. NYU6564, who became superinfected at an early time point, exhibited greater changes in antibody binding profiles and generated a more potent neutralizing antibody response post-superinfection compared to NYU6501. In contrast, superinfection occurred at a later time point in NYU6501 with strains harboring significantly longer V1V2 regions with no observable changes in neutralization patterns. Here we show that CRF02_AG intrasubtype superinfection can induce a cross-subtype neutralizing antibody response, and our data suggest timing and/or superinfecting viral envelope characteristics as contributing factors. These results highlight differential outcomes in intrasubtype superinfection and provide the first insight into cases with CRF02_AG, the fourth most prevalent HIV-1 strain worldwide.

Effect of production quotas on economic and environmental values of growth rate and feed efficiency in sea cage fish farming.

In sea cage fish farming, production quotas aim to constrain the impact of fish farming on the surrounding ecosystem. It is unknown how these quotas affect economic profitability and environmental impact of genetic improvement. We combined bioeconomic modelling with life cycle assessment (LCA) to calculate the economic (EV) and environmental (ENV) values of thermal growth coefficient (TGC) and feed conversion ratio (FCR) of sea bass reared in sea cages, given four types of quota commonly used in Europe: annual production (Qprod), annual feed distributed (Qannual_feed), standing stock (Qstock), and daily feed distributed (Qdaily_feed). ENV were calculated for LCA impact categories climate change, eutrophication and acidification. ENV were expressed per ton of fish produced per year (ENV(fish)) and per farm per year (ENV(farm)). Results show that irrespective of quota used, EV of FCR as well as ENV(fish) and ENV(farm) were always positive, meaning that improving FCR increased profit and decreased environmental impacts. However, the EV and the ENV(fish) of TGC were positive only when quota was Qstock or Qdaily_feed. Moreover, the ENV(farm) of TGC was negative in Qstock and Qdaily_feed quotas, meaning that improving TGC increased the environmental impact of the farm. We conclude that Qstock quota and Qdaily_feed quota are economically favorable to a genetic improvement of TGC, a major trait for farmers. However, improving TGC increases the environmental impact of the farm. Improving FCR represents a good opportunity to balance out this increase but more information on its genetic background is needed to develop breeding programs improving FCR.