X Chromosome Inactivation and Xist Evolution in a Rodent Lacking LINE-1 Activity

Dosage compensation in eutherian mammals occurs by inactivation of one X chromosome in females. Silencing of that X chromosome is initiated by Xist, a large non-coding RNA, whose coating of the chromosome extends in cis from the X inactivation center. LINE-1 (L1) retrotransposons have been implicated as possible players for propagation of the Xist signal, but it has remained unclear whether they are essential components. We previously identified a group of South American rodents in which L1 retrotransposition ceased over 8 million years ago and have now determined that at least one species of these rodents, Oryzomys palustris, still retains X inactivation. We have also isolated and analyzed the majority of the Xist RNA from O. palustris and a sister species retaining L1 activity, Sigmodon hispidus, to determine if evolution in these sequences has left signatures that might suggest a critical role for L1 elements in Xist function. Comparison of rates of Xist evolution in the two species fails to support L1 involvement, although other explanations are possible. Similarly, comparison of known repeats and potential RNA secondary structures reveals no major differences with the exception of a new repeat in O. palustris that has potential to form new secondary structures

Light scattering in a turbulent cloud: Simulations to explore cloud-chamber experiments

Radiative transfer through clouds can be impacted by variations in particle number size distribution, but also in particle spatial distribution. Due to turbulent mixing and inertial effects, spatial correlations often exist, even on scales reaching the cloud droplet separation distance. The resulting clusters and voids within the droplet field can lead to deviations from exponential extinction. Prior work has numerically investigated these departures from exponential attenuation in absorptive and scattering media; this work takes a step towards determining the feasibility of detecting departures from exponential behavior due to spatial correlation in turbulent clouds generated in a laboratory setting. Large Eddy Simulation (LES) is used to mimic turbulent mixing clouds generated in a laboratory convection cloud chamber. Light propagation through the resulting polydisperse and spatially correlated particle fields is explored via Monte Carlo ray tracing simulations. The key finding is that both mean radiative flux and standard deviation about the mean differ when correlations exist, suggesting that an experiment using a laboratory convection cloud chamber could be designed to investigate non-exponential behavior. Total forward flux is largely unchanged (due to scattering being highly forward-dominant for the size parameters considered), allowing it to be used for conditional sampling based on optical thickness. Direct and diffuse forward flux means are modified by approximately one standard deviation. Standard deviations of diffuse forward and backward fluxes are strongly enhanced, suggesting that fluctuations in the scattered light are a more sensitive metric to consider. The results also suggest the possibility that measurements of radiative transfer could be used to infer the strength and scales of correlations in a turbulent cloud, indicating entrainment and mixing effects

Atomic Oxygen Textured Polymers

Atomic oxygen can be used to microscopically alter the surface morphology of polymeric materials in space or in ground laboratory facilities. For polymeric materials whose sole oxidation products are volatile species, directed atomic oxygen reactions produce surfaces of microscopic cones. However, isotropic atomic oxygen exposure results in polymer surfaces covered with lower aspect ratio sharp-edged craters. Isotropic atomic oxygen plasma exposure of polymers typically causes a significant decrease in water contact angle as well as altered coefficient of static friction. Such surface alterations may be of benefit for industrial and biomedical applications. The results of atomic oxygen plasma exposure of thirty-three (33) different polymers are presented, including typical morphology changes, effects on water contact angle, and coefficient of static friction

Steady state free radical budgets and ozone photochemistry during TOPSE

A steady state model, constrained by a number of measured quantities, was used to derive peroxy radical levels for the conditions of the Tropospheric Ozone Production about the Spring Equinox (TOPSE) campaign. The analysis is made using data collected aboard the NCAR/NSF C-130 aircraft from February through May 2000 at latitudes from 40° to 85°N, and at altitudes from the surface to 7.6 km. HO2 + RO2 radical concentrations were measured during the experiment, which are compared with model results over the domain of the study showing good agreement on the average. Average measurement/model ratios are 1.04 (σ = 0.73) and 0.96 (σ = 0.52) for the MLB and HLB, respectively. Budgets of total peroxy radical levels as well as of individual free radical members were constructed, which reveal interesting differences compared to studies at lower latitudes. The midlatitude part of the study region is a significant net source of ozone, while the high latitudes constitute a small net sink leading to the hypothesis that transport from the middle latitudes can explain the observed increase in ozone in the high latitudes. Radical reservoir species concentrations are modeled and compared with the observations. For most conditions, the model does a good job of reproducing the formaldehyde observations, but the peroxide observations are significantly less than steady state for this study. Photostationary state (PSS) derived total peroxy radical levels and NO/NO2ratios are compared with the measurements and the model; PSS-derived results are higher than observations or the steady state model at low NO concentrations

Jnk2 Effects on Tumor Development, Genetic Instability and Replicative Stress in an Oncogene-Driven Mouse Mammary Tumor Model

Oncogenes induce cell proliferation leading to replicative stress, DNA damage and genomic instability. A wide variety of cellular stresses activate c-Jun N-terminal kinase (JNK) proteins, but few studies have directly addressed the roles of JNK isoforms in tumor development. Herein, we show that jnk2 knockout mice expressing the Polyoma Middle T Antigen transgene developed mammary tumors earlier and experienced higher tumor multiplicity compared to jnk2 wildtype mice. Lack of jnk2 expression was associated with higher tumor aneuploidy and reduced DNA damage response, as marked by fewer pH2AX and 53BP1 nuclear foci. Comparative genomic hybridization further confirmed increased genomic instability in PyV MT/jnk2−/− tumors. In vitro, PyV MT/jnk2−/− cells underwent replicative stress and cell death as evidenced by lower BrdU incorporation, and sustained chromatin licensing and DNA replication factor 1 (CDT1) and p21Waf1 protein expression, and phosphorylation of Chk1 after serum stimulation, but this response was not associated with phosphorylation of p53 Ser15. Adenoviral overexpression of CDT1 led to similar differences between jnk2 wildtype and knockout cells. In normal mammary cells undergoing UV induced single stranded DNA breaks, JNK2 localized to RPA (Replication Protein A) coated strands indicating that JNK2 responds early to single stranded DNA damage and is critical for subsequent recruitment of DNA repair proteins. Together, these data support that JNK2 prevents replicative stress by coordinating cell cycle progression and DNA damage repair mechanisms

Robust Single-view Cone-beam X-ray Pose Estimation with Neural Tuned Tomography (NeTT) and Masked Neural Radiance Fields (mNeRF)

Many tasks performed in image-guided, mini-invasive, medical procedures can be cast as pose estimation problems, where an X-ray projection is utilized to reach a target in 3D space. Expanding on recent advances in the differentiable rendering of optically reflective materials, we introduce new methods for pose estimation of radiolucent objects using X-ray projections, and we demonstrate the critical role of optimal view synthesis in performing this task. We first develop an algorithm (DiffDRR) that efficiently computes Digitally Reconstructed Radiographs (DRRs) and leverages automatic differentiation within TensorFlow. Pose estimation is performed by iterative gradient descent using a loss function that quantifies the similarity of the DRR synthesized from a randomly initialized pose and the true fluoroscopic image at the target pose. We propose two novel methods for high-fidelity view synthesis, Neural Tuned Tomography (NeTT) and masked Neural Radiance Fields (mNeRF). Both methods rely on classic Cone-Beam Computerized Tomography (CBCT); NeTT directly optimizes the CBCT densities, while the non-zero values of mNeRF are constrained by a 3D mask of the anatomic region segmented from CBCT. We demonstrate that both NeTT and mNeRF distinctly improve pose estimation within our framework. By defining a successful pose estimate to be a 3D angle error of less than 3 deg, we find that NeTT and mNeRF can achieve similar results, both with overall success rates more than 93%. However, the computational cost of NeTT is significantly lower than mNeRF in both training and pose estimation. Furthermore, we show that a NeTT trained for a single subject can generalize to synthesize high-fidelity DRRs and ensure robust pose estimations for all other subjects. Therefore, we suggest that NeTT is an attractive option for robust pose estimation using fluoroscopic projections

Ozone depletion events observed in the high latitude surface layer during the TOPSE aircraft program

During the Tropospheric Ozone Production about the Spring Equinox (TOPSE) aircraft program, ozone depletion events (ODEs) in the high latitude surface layer were investigated using lidar and in situ instruments. Flight legs of 100 km or longer distance were flown 32 times at 30 m altitude over a variety of regions north of 58° between early February and late May 2000. ODEs were found on each flight over the Arctic Ocean but their occurrence was rare at more southern latitudes. However, large area events with depletion to over 2 km altitude in one case were found as far south as Baffin Bay and Hudson Bay and as late as 22 May. There is good evidence that these more southern events did not form in situ but were the result of export of ozone-depleted air from the surface layer of the Arctic Ocean. Surprisingly, relatively intact transport of ODEs occurred over distances of 900–2000 km and in some cases over rough terrain. Accumulation of constituents in the frozen surface over the dark winter period cannot be a strong prerequisite of ozone depletion since latitudes south of the Arctic Ocean would also experience a long dark period. Some process unique to the Arctic Ocean surface or its coastal regions remains unidentified for the release of ozone-depleting halogens. There was no correspondence between coarse surface features such as solid ice/snow, open leads, or polynyas with the occurrence of or intensity of ozone depletion over the Arctic or subarctic regions. Depletion events also occurred in the absence of long-range transport of relatively fresh “pollution” within the high latitude surface layer, at least in spring 2000. Direct measurements of halogen radicals were not made. However, the flights do provide detailed information on the vertical structure of the surface layer and, during the constant 30 m altitude legs, measurements of a variety of constituents including hydroxyl and peroxy radicals. A summary of the behavior of these constituents is made. The measurements were consistent with a source of formaldehyde from the snow/ice surface. Median NOx in the surface layer was 15 pptv or less, suggesting that surface emissions were substantially converted to reservoir constituents by 30 m altitude and that ozone production rates were small (0.15–1.5 ppbv/d) at this altitude. Peroxyacetylnitrate (PAN) was by far the major constituent of NOy in the surface layer independent of the ozone mixing ratio

A Cluster Randomized Trial of Routine HIV-1 Viral Load Monitoring in Zambia: Study Design, Implementation, and Baseline Cohort Characteristics

The benefit of routine HIV-1 viral load (VL) monitoring of patients on antiretroviral therapy (ART) in resource-constrained settings is uncertain because of the high costs associated with the test and the limited treatment options. We designed a cluster randomized controlled trial to compare the use of routine VL testing at ART-initiation and at 3, 6, 12, and 18 months, versus our local standard of care (which uses immunological and clinical criteria to diagnose treatment failure, with discretionary VL testing when the two do not agree).Dedicated study personnel were integrated into public-sector ART clinics. We collected participant information in a dedicated research database. Twelve ART clinics in Lusaka, Zambia constituted the units of randomization. Study clinics were stratified into pairs according to matching criteria (historical mortality rate, size, and duration of operation) to limit the effect of clustering, and independently randomized to the intervention and control arms. The study was powered to detect a 36% reduction in mortality at 18 months.From December 2006 to May 2008, we completed enrollment of 1973 participants. Measured baseline characteristics did not differ significantly between the study arms. Enrollment was staggered by clinic pair and truncated at two matched sites.A large clinical trial of routing VL monitoring was successfully implemented in a dynamic and rapidly growing national ART program. Close collaboration with local health authorities and adequate reserve staff were critical to success. Randomized controlled trials such as this will likely prove valuable in determining long-term outcomes in resource-constrained settings.Clinicaltrials.gov NCT00929604