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  1. Abstract

    Many archaea encode and express histone proteins to compact their genomes. Archaeal and eukaryotic histones share a near-identical fold that permits DNA wrapping through select histone-DNA contacts to generate chromatin-structures that must be traversed by RNA polymerase (RNAP) to generate transcripts. As archaeal histones can spontaneously assemble with a single histone isoform, single-histone chromatin variants provide an idealized platform to detail the impacts of distinct histone-DNA contacts on transcription efficiencies and to detail the role of the conserved cleavage stimulatory factor, Transcription Factor S (TFS), in assisting RNAP through chromatin landscapes. We demonstrate that substitution of histone residues that modify histone-DNA contacts or the three-dimensional chromatin structure result in radically altered transcription elongation rates and pausing patterns. Chromatin-barriers slow and pause RNAP, providing regulatory potential. The modest impacts of TFS on elongation rates through chromatin landscapes is correlated with TFS-dispensability from the archaeonThermococcus kodakarensis. Our results detail the importance of distinct chromatin structures for archaeal gene expression and provide a unique perspective on the evolution of, and regulatory strategies imposed by, eukaryotic chromatin.

     
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  2. We propose a workflow for modeling generalized mid-spatial frequency (MSF) errors in optical imaging systems. This workflow enables the classification of MSF distributions, filtering of bandlimited signatures, propagation of MSF errors to the exit pupil, and performance predictions that differentiate performance impacts due to the MSF distributions. We demonstrate the workflow by modeling the performance impacts of MSF errors for both transmissive and reflective imaging systems with near-diffraction-limited performance.

     
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  3. In this work, we present a methodology for predicting the optical performance impacts of random and structured MSF surface errors using pupil-difference probability distribution (PDPD) moments. In addition, we show that, for random mid-spatial frequency (MSF) surface errors, performance estimates from the PDPD moments converge to performance estimates that assume random statistics. Finally, we apply these methods to several MSF surface errors with different distributions and compare estimated optical performance values to predictions based on earlier methods assuming random error distributions.

     
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  4. Abstract Background

    Pain is a worldwide problem requiring an effective, affordable, non-addictive therapy. Using the edible plant broccoli, a growth protocol was developed to induce a concentrated combinatorial of potential anti-inflammatories in seedlings.

    Methods

    A growth method was utilized to produce a phenylpropanoid-rich broccoli sprout extract, referred to as Original Extract (OE). OE was concentrated and then resuspended for study of the effects on inflammation events. A rabbit disc model of inflammation and degeneration, and, a mouse model of pain behavior were used for in vivo and in vitro tests. To address aspects of mammalian metabolic processing, the OE was treated with the S9 liver microsome fraction derived from mouse, for use in a mouse in vivo study. Analytical chemistry was performed to identify major chemical species. Continuous variables were analyzed with a number of methods including ANOVA, and two-tailedttests, as appropriate.

    Results

    In a rabbit spine (disc) injury model, inflammatory markers were reduced, and levels of regenerative markers were increased as a result of OE treatment, both in vivo and in vitro. In a mouse pain behavioral model, after treatment with S9 liver microsome fraction, the resultant extract significantly reduced early and late pain behavior in response to a pain stimulus. The OE itself reduced pain behavior in the mouse pain model, but did not achieve the level of significance observed for S9-treated extract. Analytical chemistry undertaken on the extract constituents revealed identities of the chemical species in OE, and how S9 liver microsome fraction treatment altered species identities and proportions.

    Conclusions

    In vitro and in vivo results indicate that the OE, and S9-treated OE broccoli extracts are worthwhile materials to develop a non-opiate inflammation and pain-reducing treatment.

     
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  5. In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then re-analyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time. 
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    Free, publicly-accessible full text available December 1, 2024
  6. ABSTRACT

    We present the discoveries of two of AM CVn systems, Gaia14aae and SDSS J080449.49+161624.8, which show X-ray pulsations at their orbital periods, indicative of magnetically collimated accretion. Both also show indications of higher rates of mass transfer relative to the expectations from binary evolution driven purely by gravitational radiation, based on existing optical data for Gaia14aae, which show a hotter white dwarf temperature than expected from standard evolutionary models, and X-ray data for SDSS J080449.49+161624.8 which show a luminosity 10−100 times higher than those for other AM CVn at similar orbital periods. The higher mass transfer rates could be driven by magnetic braking from the disc wind interacting with the magnetosphere of the tidally locked accretor. We discuss implications of this additional angular momentum transport mechanism for evolution and gravitational wave detectability of AM CVn objects.

     
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  7. Abstract

    A 3D microenvironment is known to endorse pancreatic islet development from human induced pluripotent stem cells (iPSCs). However, oxygen supply becomes a limiting factor in a scaffold culture. In this study, oxygen‐releasing biomaterials are fabricated and an oxygenated scaffold culture platform is developed to offer a better oxygen supply during 3D iPSC pancreatic differentiation. It is found that the oxygenation does not alter the scaffold's mechanical properties. The in situ oxygenation improves oxygen tension within the scaffolds. The unique 3D differentiation system enables the generation of islet organoids with enhanced expression of islet signature genes and proteins. Additionally, it is discovered that the oxygenation at the early stage of differentiation has more profound impacts on islet development from iPSCs. More C‐peptide+/MAFA+β and glucagon+/MAFB+α cells formed in the iPSC‐derived islet organoids generated under oxygenated conditions, suggesting enhanced maturation of the organoids. Furthermore, the oxygenated 3D cultures improve islet organoids’ sensitivity to glucose for insulin secretion. It is herein demonstrated that the oxygenated scaffold culture empowers iPSC islet differentiation to generate clinically relevant tissues for diabetes research and treatment.

     
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  8. Abstract Helicopters used for aerial wildlife surveys are expensive, dangerous and time consuming. Drones and thermal infrared cameras can detect wildlife, though the ability to detect individuals is dependent on weather conditions. While we have a good understanding of local weather conditions, we do not have a broad-scale assessment of ambient temperature to plan drone wildlife surveys. Climate change will affect our ability to conduct thermal surveys in the future. Our objective was to determine optimal annual and daily time periods to conduct surveys. We present a case study in Texas, (United States of America [USA]) where we acquired and compared average monthly temperature data from 1990 to 2019, hourly temperature data from 2010 to 2019 and projected monthly temperature data from 2021 to 2040 to identify areas where surveys would detect a commonly studied ungulate (white-tailed deer [ Odocoileus virginianus ]) during sunny or cloudy conditions. Mean temperatures increased when comparing the 1990–2019 to 2010–2019 periods. Mean temperatures above the maximum ambient temperature in which white-tailed deer can be detected increased in 72, 10, 10, and 24 of the 254 Texas counties in June, July, August, and September, respectively. Future climate projections indicate that temperatures above the maximum ambient temperature in which white-tailed deer can be detected will increase in 32, 12, 15, and 47 counties in June, July, August, and September, respectively when comparing 2010–2019 with 2021–2040. This analysis can assist planning, and scheduling thermal drone wildlife surveys across the year and combined with daily data can be efficient to plan drone flights. 
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    Free, publicly-accessible full text available December 1, 2024
  9. Abstract

    Dark matter subhalos with extended profiles and density cores, and globular star clusters of mass 106–108Mthat live near the critical curves in galaxy cluster lenses can potentially be detected through their lensing magnification of stars in background galaxies. In this work, we study the effect such subhalos have on lensed images, and compare to the case of more well-studied microlensing by stars and black holes near critical curves. We find that the cluster density gradient and the extended mass distribution of subhalos are important in determining image properties. Both lead to an asymmetry between the image properties on the positive- and negative-parity sides of the cluster that is more pronounced than in the case of microlensing. For example, on the negative-parity side, subhalos with cores larger than about 50 pc do not generate any images with magnification above ∼100 outside of the immediate vicinity of the cluster critical curve. We discuss these factors using analytical and numerical analysis, and exploit them to identify observable signatures of subhalos: Subhalos create pixel-to-pixel flux variations of ≳0.1 mag on the positive-parity side of clusters. These pixels tend to cluster around (otherwise invisible) subhalos. Unlike in the case of microlensing, signatures of subhalo lensing can be found up to 1″ away from the critical curves of massive clusters.

     
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  10. Applying a coastal-geoarchaeological approach, we synthesize stratigraphic, sedimentological, mollusk-zooarchaeological, and radiometric datasets from recent excavations and sediment coring at Harbor Key (8MA15)—a shell-terraformed Native mound complex within Tampa Bay, on the central peninsular Gulf Coast of Florida. We significantly revise the chronological understanding of the site and place it among the relatively few early civic-ceremonial centers in the region. Analyses of submound contexts revealed that the early first millennium mound center was constructed atop a platform of sand and ex situ cultural shell deposits that were reworked during ancient storm landfalls around 2000 BP. We situate Harbor Key within a seascape-scale stratigraphic and paleoenvironmental framework and show that the shellworks comprise an artificial barrier protecting the leeward estuary basin (and productive inshore wetlands) from high-energy conditions of the open bay and swells from the Gulf of Mexico. The sedimentary and archaeological records attest to the long-term history of morphodynamic interaction between coastal processes and Indigenous shell terraforming in the region and suggest that early first millennium mound building in Tampa Bay was tied to the recognition and reuse of antecedent shellworks and the persistent management of encompassing cultural seascapes. 
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    Free, publicly-accessible full text available September 1, 2024