First radial velocity results from the MINiature Exoplanet Radial Velocity Array (MINERVA)

The MINiature Exoplanet Radial Velocity Array (MINERVA) is a dedicated observatory of four 0.7m robotic telescopes fiber-fed to a KiwiSpec spectrograph. The MINERVA mission is to discover super-Earths in the habitable zones of nearby stars. This can be accomplished with MINERVA's unique combination of high precision and high cadence over long time periods. In this work, we detail changes to the MINERVA facility that have occurred since our previous paper. We then describe MINERVA's robotic control software, the process by which we perform 1D spectral extraction, and our forward modeling Doppler pipeline. In the process of improving our forward modeling procedure, we found that our spectrograph's intrinsic instrumental profile is stable for at least nine months. Because of that, we characterized our instrumental profile with a time-independent, cubic spline function based on the profile in the cross dispersion direction, with which we achieved a radial velocity precision similar to using a conventional "sum-of-Gaussians" instrumental profile: 1.8 m s$^{-1}$ over 1.5 months on the RV standard star HD 122064. Therefore, we conclude that the instrumental profile need not be perfectly accurate as long as it is stable. In addition, we observed 51 Peg and our results are consistent with the literature, confirming our spectrograph and Doppler pipeline are producing accurate and precise radial velocities.Comment: 22 pages, 9 figures, submitted to PASP, Peer-Reviewed and Accepte

Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines

In higher eukaryotes, replication program specification in different cell types remains to be fully understood. We show for seven human cell lines that about half of the genome is divided in domains that display a characteristic U-shaped replication timing profile with early initiation zones at borders and late replication at centers. Significant overlap is observed between U-domains of different cell lines and also with germline replication domains exhibiting a N-shaped nucleotide compositional skew. From the demonstration that the average fork polarity is directly reflected by both the compositional skew and the derivative of the replication timing profile, we argue that the fact that this derivative displays a N-shape in U-domains sustains the existence of large-scale gradients of replication fork polarity in somatic and germline cells. Analysis of chromatin interaction (Hi-C) and chromatin marker data reveals that U-domains correspond to high-order chromatin structural units. We discuss possible models for replication origin activation within U/N-domains. The compartmentalization of the genome into replication U/N-domains provides new insights on the organization of the replication program in the human genome

Role of the Kelvin-Helmholtz instability in the evolution of magnetized relativistic sheared plasma flows

We explore, via analytical and numerical methods, the Kelvin-Helmholtz (KH) instability in relativistic magnetized plasmas, with applications to astrophysical jets. We solve the single-fluid relativistic magnetohydrodynamic (RMHD) equations in conservative form using a scheme which is fourth order in space and time. To recover the primitive RMHD variables, we use a highly accurate, rapidly convergent algorithm which improves upon such schemes as the Newton-Raphson method. Although the exact RMHD equations are marginally stable, numerical discretization renders them unstable. We include numerical viscosity to restore numerical stability. In relativistic flows, diffusion can lead to a mathematical anomaly associated with frame transformations. However, in our KH studies, we remain in the rest frame of the system, and therefore do not encounter this anomaly. We use a two-dimensional slab geometry with periodic boundary conditions in both directions. The initial unperturbed velocity peaks along the central axis and vanishes asymptotically at the transverse boundaries. Remaining unperturbed quantities are uniform, with a flow-aligned unperturbed magnetic field. The early evolution in the nonlinear regime corresponds to the formation of counter-rotating vortices, connected by filaments, which persist in the absence of a magnetic field. A magnetic field inhibits the vortices through a series of stages, namely, field amplification, vortex disruption, turbulent breakdown, and an approach to a flow-aligned equilibrium configuration. Similar stages have been discussed in MHD literature. We examine how and to what extent these stages manifest in RMHD for a set of representative field strengths. To characterize field strength, we define a relativistic extension of the Alfvénic Mach number M(A). We observe close complementarity between flow and magnetic field behavior. Weaker fields exhibit more vortex rotation, magnetic reconnection, jet broadening, and intermediate turbulence. Sufficiently strong fields (M(A)<6) completely suppress vortex formation. Maximum jet deceleration, and viscous dissipation, occur for intermediate vortex-disruptive fields, while electromagnetic energy is maximized for the strongest fields which allow vortex formation. Highly relativistic flows destabilize the system, supporting modes with near-maximum growth at smaller wavelengths than the shear width of the velocity. This helps to explain early numerical breakdown of highly relativistic simulations using numerical viscosity, a long-standing problem. While magnetic fields generally stabilize the system, we have identified many features of the complex and turbulent reorganization that occur for sufficiently weak fields in RMHD flows, and have described the transition from disruptive to stabilizing fields at M(A)≈6. Our results are qualitatively similar to observations of numerous jets, including M87, whose knots may exhibit vortex-like behavior. Furthermore, in both the linear and nonlinear analyses, we have successfully unified the HD, MHD, RHD, and RMHD regimes

A Novel Human Cytomegalovirus Locus Modulates Cell Type-Specific Outcomes of Infection

Clinical strains of HCMV encode 20 putative ORFs within a region of the genome termed ULb′ that are postulated to encode functions related to persistence or immune evasion. We have previously identified ULb′-encoded pUL138 as necessary, but not sufficient, for HCMV latency in CD34+ hematopoietic progenitor cells (HPCs) infected in vitro. pUL138 is encoded on polycistronic transcripts that also encode 3 additional proteins, pUL133, pUL135, and pUL136, collectively comprising the UL133-UL138 locus. This work represents the first characterization of these proteins and identifies a role for this locus in infection. Similar to pUL138, pUL133, pUL135, and pUL136 are integral membrane proteins that partially co-localized with pUL138 in the Golgi during productive infection in fibroblasts. As expected of ULb′ sequences, the UL133-UL138 locus was dispensable for replication in cultured fibroblasts. In CD34+ HPCs, this locus suppressed viral replication in HPCs, an activity attributable to both pUL133 and pUL138. Strikingly, the UL133-UL138 locus was required for efficient replication in endothelial cells. The association of this locus with three context-dependent phenotypes suggests an exciting role for the UL133-UL138 locus in modulating the outcome of viral infection in different contexts of infection. Differential profiles of protein expression from the UL133-UL138 locus correlated with the cell-type dependent phenotypes associated with this locus. We extended our in vitro findings to analyze viral replication and dissemination in a NOD-scid IL2Rγcnull-humanized mouse model. The UL133-UL138NULL virus exhibited an increased capacity for replication and/or dissemination following stem cell mobilization relative to the wild-type virus, suggesting an important role in viral persistence and spread in the host. As pUL133, pUL135, pUL136, and pUL138 are conserved in virus strains infecting higher order primates, but not lower order mammals, the functions encoded likely represent host-specific viral adaptations

DDT, epigenetic harm, and transgenerational environmental justice

Although the environmentally harmful effects of widespread dichlorodiphenyltrichloroethane (DDT) use became well-known following Rachel Carson’s Silent Spring (1962), its human health effects have more recently become clearer. A ban on the use of DDT has been in place for over 30 years, but recently DDT has been used for malaria control in areas such as Africa. Recent work shows that DDT has transgenerational effects in progeny and generations never directly exposed to DDT. These effects have health implications for individuals who are not able to have any voice in the decision to use the pesticide. The transgenerational effects of DDT are considered in light of some widely accepted ethical principles. We argue that this reframes the decision to use DDT, requiring us to incorporate new considerations, and new kinds of decision making, into the deliberative process that determines its ongoing use. Ethical considerations for intergenerational environmental justice are presented that include concern and respect for autonomy, nonmaleficence, and justice. Here, we offer a characterization of the kinds of ethical considerations that must be taken into account in any satisfactory decisions to use DDT

Impact of Optimized Breastfeeding on the Costs of Necrotizing Enterocolitis in Extremely Low Birthweight Infants

To estimate risk of NEC for ELBW infants as a function of preterm formula and maternal milk (MM) intake and calculate the impact of suboptimal feeding on NEC incidence and costs