Blockade of Interferon Beta, but Not Interferon Alpha, Signaling Controls Persistent Viral Infection

SummaryAlthough type I interferon (IFN-I) is thought to be beneficial against microbial infections, persistent viral infections are characterized by high interferon signatures suggesting that IFN-I signaling may promote disease pathogenesis. During persistent lymphocytic choriomeningitis virus (LCMV) infection, IFNα and IFNβ are highly induced early after infection, and blocking IFN-I receptor (IFNAR) signaling promotes virus clearance. We assessed the specific roles of IFNβ versus IFNα in controlling LCMV infection. While blockade of IFNβ alone does not alter early viral dissemination, it is important in determining lymphoid structure, lymphocyte migration, and anti-viral T cell responses that lead to accelerated virus clearance, approximating what occurs during attenuation of IFNAR signaling. Comparatively, blockade of IFNα was not associated with improved viral control, but with early dissemination of virus. Thus, despite their use of the same receptor, IFNβ and IFNα have unique and distinguishable biologic functions, with IFNβ being mainly responsible for promoting viral persistence

The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Staudinger, M. D., Goyert, H., Suca, J. J., Coleman, K., Welch, L., Llopiz, J. K., Wiley, D., Altman, I., Applegate, A., Auster, P., Baumann, H., Beaty, J., Boelke, D., Kaufman, L., Loring, P., Moxley, J., Paton, S., Powers, K., Richardson, D., Robbins, J., Runge, J., Smith, B., Spiegel, C., & Steinmetz, H. The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management. Fish and Fisheries, 00, (2020): 1-34, doi:10.1111/faf.12445.The American sand lance (Ammodytes americanus, Ammodytidae) and the Northern sand lance (A. dubius, Ammodytidae) are small forage fishes that play an important functional role in the Northwest Atlantic Ocean (NWA). The NWA is a highly dynamic ecosystem currently facing increased risks from climate change, fishing and energy development. We need a better understanding of the biology, population dynamics and ecosystem role of Ammodytes to inform relevant management, climate adaptation and conservation efforts. To meet this need, we synthesized available data on the (a) life history, behaviour and distribution; (b) trophic ecology; (c) threats and vulnerabilities; and (d) ecosystem services role of Ammodytes in the NWA. Overall, 72 regional predators including 45 species of fishes, two squids, 16 seabirds and nine marine mammals were found to consume Ammodytes. Priority research needs identified during this effort include basic information on the patterns and drivers in abundance and distribution of Ammodytes, improved assessments of reproductive biology schedules and investigations of regional sensitivity and resilience to climate change, fishing and habitat disturbance. Food web studies are also needed to evaluate trophic linkages and to assess the consequences of inconsistent zooplankton prey and predator fields on energy flow within the NWA ecosystem. Synthesis results represent the first comprehensive assessment of Ammodytes in the NWA and are intended to inform new research and support regional ecosystem‐based management approaches.This manuscript is the result of follow‐up work stemming from a working group formed at a two‐day multidisciplinary and international workshop held at the Parker River National Wildlife Refuge, Massachusetts in May 2017, which convened 55 experts scientists, natural resource managers and conservation practitioners from 15 state, federal, academic and non‐governmental organizations with interest and expertise in Ammodytes ecology. Support for this effort was provided by USFWS, NOAA Stellwagen Bank National Marine Sanctuary, U.S. Department of the Interior, U.S. Geological Survey, Northeast Climate Adaptation Science Center (Award # G16AC00237), an NSF Graduate Research Fellowship to J.J.S., a CINAR Fellow Award to J.K.L. under Cooperative Agreement NA14OAR4320158, NSF award OCE‐1325451 to J.K.L., NSF award OCE‐1459087 to J.A.R, a Regional Sea Grant award to H.B. (RNE16‐CTHCE‐l), a National Marine Sanctuary Foundation award to P.J.A. (18‐08‐B‐196) and grants from the Mudge Foundation. The contents of this paper are the responsibility of the authors and do not necessarily represent the views of the National Oceanographic and Atmospheric Administration, U.S. Fish and Wildlife Service, New England Fishery Management Council and Mid‐Atlantic Fishery Management Council. This manuscript is submitted for publication with the understanding that the United States Government is authorized to reproduce and distribute reprints for Governmental purposes. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government

TEMPLATES: A Robust Outlier Rejection Method for JWST/NIRSpec Integral Field Spectroscopy

We describe a custom outlier rejection algorithm for JWST/NIRSpec integral field spectroscopy. This method uses a layered sigma clipping approach that adapts clipping thresholds based upon the spatial profile of the science target. We find that this algorithm produces a robust outlier rejection while simultaneously preserving the signal of the science target. Originally developed as a response to unsatisfactory initial performance of the jwst pipeline outlier detection step, this method works either as a standalone solution, or as a supplement to the current pipeline software. Comparing leftover (i.e., not flagged) artifacts with the current pipeline's outlier detection step, we find that our method results in one fifth as many residual artifacts as the jwst pipeline. However, we find a combination of both methods removes nearly all artifacts -- an approach that takes advantage of both our algorithm's robust outlier rejection and the pipeline's use of individual dithers. This combined approach is what the TEMPLATES Early Release Science team has converged upon for our NIRSpec observations. Finally, we publicly release the code and Jupyter notebooks for the custom outlier rejection algorithm.Comment: 10 pages, including 5 figures. Submitted to the Publications of the Astronomical Society of the Pacific (PASP). Code associated with paper released at https://github.com/aibhleog/baryon-swee

SciClone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution

The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy

Bridging Alone: Religious Conservatism, Marital Homogamy, and Voluntary Association Membership

This study characterizes social insularity of religiously conservative American married couples by examining patterns of voluntary associationmembership. Constructing a dataset of 3938 marital dyads from the second wave of the National Survey of Families and Households, the author investigates whether conservative religious homogamy encourages membership in religious voluntary groups and discourages membership in secular voluntary groups. Results indicate that couples’ shared affiliation with conservative denominations, paired with beliefs in biblical authority and inerrancy, increases the likelihood of religious group membership for husbands and wives and reduces the likelihood of secular group membership for wives, but not for husbands. The social insularity of conservative religious groups appears to be reinforced by homogamy—particularly by wives who share faith with husbands

BVRI Light Curves for 29 Type Ia Supernovae

BVRI light curves are presented for 27 Type Ia supernovae discovered during the course of the Calan/Tololo Survey and for two other SNe Ia observed during the same period. Estimates of the maximum light magnitudes in the B, V, and I bands and the initial decline rate parameter m15(B) are also given.Comment: 17 pages, figures and tables are not included (contact first author if needed), to appear in the Astronomical Journa

Spatially Resolved Stellar Populations of 0.3<z<6.00.3<z<6.0 Galaxies in WHL0137-08 and MACS0647+70 Clusters as Revealed by JWST: How do Galaxies Grow and Quench Over Cosmic Time?

We study the spatially resolved stellar populations of 444 galaxies at $0.3<z<6.0$ in two clusters (WHL0137-08 and MACS0647+70) and a blank field, combining imaging data from HST and JWST to perform spatially resolved spectral energy distribution (SED) modeling using pixedfit. The high spatial resolution of the imaging data combined with magnification from gravitational lensing in the cluster fields allows us to resolve some galaxies to sub-kpc scales (for 109 of our galaxies). At redshifts around cosmic noon and higher ($2.5\lesssim z\lesssim 6.0$), we find mass doubling times to be independent of radius, inferred from flat specific star formation rate (sSFR) radial profiles and similarities between the half-mass and half-SFR radii. At lower redshifts ($1.5\lesssim z\lesssim 2.5$), a significant fraction of our star-forming galaxies show evidence for nuclear starbursts, inferred from centrally elevated sSFR, and a much smaller half-SFR radius compared to the half-mass radius. At later epochs, we find more galaxies suppress star formation in their center but are still actively forming stars in the disk. Overall, these trends point toward a picture of inside-out galaxy growth consistent with theoretical models and simulations. We also observe a tight relationship between the central mass surface density and global stellar mass with $\sim 0.38$ dex scatter. Our analysis demonstrates the potential of spatially resolved SED analysis with JWST data. Future analysis with larger samples will be able to further explore the assembly of galaxy mass and the growth of their structuresComment: 31 pages, 18 figures, accepted for publication in ApJ. Some examples and tutorials of spatially resolved SED analysis will be available at https://github.com/aabdurrouf/JWST-HST_resolvedSEDfit

Testing LMC Microlensing Scenarios: The Discrimination Power of the SuperMACHO Microlensing Survey

Characterizing the nature and spatial distribution of the lensing objects that produce the previously measured microlensing optical depth toward the Large Magellanic Cloud (LMC) remains an open problem. We present an appraisal of the ability of the SuperMACHO Project, a next-generation microlensing survey directed toward the LMC, to discriminate between various proposed lensing populations. We consider two scenarios: lensing by a uniform foreground screen of objects and self-lensing by LMC stars. We have carried out extensive simulations, based upon data obtained during the first year of the project, to assess the SuperMACHO survey's ability to discriminate between these two scenarios. We find that the event rate itself shows significant sensitivity to the choice of the LMC luminosity function, limiting the conclusions which can be drawn from the absolute rate. If instead we determine the differential event rate across the LMC, we will decrease the impact of these systematic biases and render our conclusions more robust. With this approach the SuperMACHO Project should be able to distinguish between the two categories of lens populations. This will provide important constraints on the nature of the lensing objects and their contributions to the Galactic dark matter halo.Comment: 40 pages, 9 figures, to appear in ApJ 634 (2005