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Creators/Authors contains: "Johnson, James"

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  1. Chen, Tzong-Yueh (Ed.)
    Salinity gradients act as strong environmental barriers that limit the distribution of aquatic organisms. Changes in gene expression associated with transitions between freshwater and saltwater environments can provide insights into organismal responses to variation in salinity. We used RNA-sequencing (RNA-seq) to investigate genome-wide variation in gene expression between a hypersaline population and a freshwater population of the livebearing fish speciesLimia perugiae(Poeciliidae). Our analyses of gill gene expression revealed potential molecular mechanisms underlying salinity tolerance in this species, including the enrichment of genes involved in ion transport, maintenance of chemical homeostasis, and cell signaling in the hypersaline population. We also found differences in gene expression patterns associated with cell-cycle and protein-folding processes between the hypersaline and freshwaterL.perugiae. Bidirectional freshwater-saltwater transitions have occurred repeatedly during the diversification of fishes, allowing for broad-scale examination of repeatable patterns in evolution. Therefore, we compared transcriptomic variation inL.perugiaewith other teleosts that have made freshwater-saltwater transitions to test for convergence in gene expression. Among the four distantly related population pairs from high- and low-salinity environments that we included in our analysis, we found only ten shared differentially expressed genes, indicating little evidence for convergence. However, we found that differentially expressed genes shared among three or more lineages were functionally enriched for ion transport and immune functioning. Overall, our results—in conjunction with other recent studies—suggest that different genes are involved in salinity transitions across disparate lineages of teleost fishes. 
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    Free, publicly-accessible full text available December 5, 2025
  2. ABSTRACT The scaling of the specific Type Ia supernova (SN Ia) rate with host galaxy stellar mass $$\dot{\text{N}}_\text{Ia} / \text{M}_\star \sim \text{M}_\star ^{-0.3}$$ as measured in ASAS-SN and DES strongly suggests that the number of SNe Ia produced by a stellar population depends inversely on its metallicity. We estimate the strength of the required metallicity dependence by combining the average star formation histories (SFHs) of galaxies as a function of their stellar mass with the mass–metallicity relation (MZR) for galaxies and common parametrizations for the SN Ia delay-time distribution. The differences in SFHs can account for only ∼30 per cent of the increase in the specific SN Ia rate between stellar masses of M⋆ = 1010 and 107.2 M⊙. We find that an additional metallicity dependence of approximately ∼Z−0.5 is required to explain the observed scaling. This scaling matches the metallicity dependence of the close binary fraction observed in APOGEE, suggesting that the enhanced SN Ia rate in low-mass galaxies can be explained by a combination of their more extended SFHs and a higher binary fraction due to their lower metallicities. Due to the shape of the MZR, only galaxies below M⋆ ≈ 3 × 109 M⊙ are significantly affected by the metallicity-dependent SN Ia rates. The $$\dot{\text{N}}_\text{Ia} / \text{M}_\star \sim \text{M}_\star ^{-0.3}$$ scaling becomes shallower with increasing redshift, dropping by factor of ∼2 at 107.2 M⊙ between z = 0 and 1 with our ∼Z−0.5 scaling. With metallicity-independent rates, this decrease is a factor of ∼3. We discuss the implications of metallicity-dependent SN Ia rates for one-zone models of galactic chemical evolution. 
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  3. ABSTRACT We model the stellar abundances and ages of two disrupted dwarf galaxies in the Milky Way stellar halo: Gaia-Sausage Enceladus (GSE) and Wukong/LMS-1. Using a statistically robust likelihood function, we fit one-zone models of galactic chemical evolution with exponential infall histories to both systems, deriving e-folding time-scales of τin = 1.01 ± 0.13 Gyr for GSE and $$\tau _\text{in} = 3.08^{+3.19}_{-1.16}$$ Gyr for Wukong/LMS-1. GSE formed stars for $$\tau _\text{tot} = 5.40^{+0.32}_{-0.31}$$ Gyr, sustaining star formation for ∼1.5–2 Gyr after its first infall into the Milky Way ∼10 Gyr ago. Our fit suggests that star formation lasted for $$\tau _\text{tot} = 3.36^{+0.55}_{-0.47}$$ Gyr in Wukong/LMS-1, though our sample does not contain any age measurements. The differences in evolutionary parameters between the two are qualitatively consistent with trends with stellar mass M⋆ predicted by simulations and semi-analytic models of galaxy formation. Our inferred values of the outflow mass-loading factor reasonably match $$\eta \propto M_\star ^{-1/3}$$ as predicted by galactic wind models. Our fitting method is based only on Poisson sampling from an evolutionary track and requires no binning of the data. We demonstrate its accuracy by testing against mock data, showing that it accurately recovers the input model across a broad range of sample sizes (20 ≤ N ≤ 2000) and measurement uncertainties (0.01 ≤ σ[α/Fe], σ[Fe/H] ≤ 0.5; $$0.02 \le \sigma _{\log _{10}(\text{age})} \le 1$$). Due to the generic nature of our derivation, this likelihood function should be applicable to one-zone models of any parametrization and easily extensible to other astrophysical models which predict tracks in some observed space. 
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  4. Abstract Identifying the migration routes and stopover sites used by declining species is critical for developing targeted conservation actions. Long-distance migratory shorebirds are among the groups of birds declining most rapidly, yet we frequently lack detailed knowledge about the routes and stopover sites they use during their hemisphere-spanning migrations. This is especially true for species that migrate through mid-continental regions in the Western Hemisphere. We therefore used satellite transmitters to track 212 individuals of 6 shorebird species during their southward migrations—Pluvialis dominica (American Golden-Plover), Limosa haemastica (Hudsonian Godwit), Tringa flavipes (Lesser Yellowlegs), and Calidris subruficollis (Buff-breasted Sandpiper), C. melanotos (Pectoral Sandpiper), and Bartramia longicauda (Upland Sandpiper)—as they crossed the Amazon Basin of South America, a region from which reports of shorebird numbers are increasing but remain relatively rare. Our results make clear that the Amazon Basin provides stopover habitat for a large number of shorebirds: more than 74% of individuals tracked crossing the Amazon Basin stopped over in the region for an average of 2–14 days, with some spending the entire nonbreeding season there. All species selected stopover sites along the region’s many rivers and lakes, while within stopover sites each species exhibited distinct habitat preferences. The timing of stopovers within sub-basins of the Amazon Basin also coincided with periods of low water, when the muddy, shallow water habitats preferred by most shorebirds are likely plentiful. Together, our results highlight the need for detailed investigations into shorebird abundance and distribution within the Amazon Basin, threats to shorebirds within particular subbasins, and links between shorebird conservation efforts and those targeting the myriad other species that inhabit this dynamic, hyper-diverse region. 
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    Free, publicly-accessible full text available August 9, 2025
  5. ABSTRACT We derive empirical constraints on the nucleosynthetic yields of nitrogen by incorporating N enrichment into our previously developed and empirically tuned multizone galactic chemical evolution model. We adopt a metallicity-independent (‘primary’) N yield from massive stars and a metallicity-dependent (‘secondary’) N yield from AGB stars. In our model, galactic radial zones do not evolve along the observed [N/O]–[O/H] relation, but first increase in [O/H] at roughly constant [N/O], then move upward in [N/O] via secondary N production. By t ≈ 5 Gyr, the model approaches an equilibrium [N/O]–[O/H] relation, which traces the radial oxygen gradient. Reproducing the [N/O]–[O/H] trend observed in extragalactic systems constrains the ratio of IMF-averaged N yields to the IMF-averaged O yield of core-collapse supernovae. We find good agreement if we adopt $$y_\text{N}^\text{CC}/y_\text{O}^\text{CC}=0.024$$ and $$y_\text{N}^\text{AGB}/y_\text{O}^\text{CC} = 0.062(Z/Z_\odot)$$. For the theoretical AGB yields we consider, simple stellar populations release half their N after only ∼250 Myr. Our model reproduces the [N/O]–[O/H] relation found for Milky Way stars in the APOGEE survey, and it reproduces (though imperfectly) the trends of stellar [N/O] with age and [O/Fe]. The metallicity-dependent yield plays the dominant role in shaping the gas-phase [N/O]–[O/H] relation, but the AGB time-delay is required to match the stellar age and [O/Fe] trends. If we add ∼40 per cent oscillations to the star formation rate, the model reproduces the scatter in the gas phase [N/O]–[O/H] relation observed in external galaxies by MaNGA. We discuss implications of our results for theoretical models of N production by massive stars and AGB stars. 
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  6. Abstract We measure abundances of 12 elements (Na, Mg, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni) in a sample of 86 metal-poor (−2 ≲ [Fe/H] ≲ −1) subgiant stars in the solar neighborhood. Abundances are derived from high-resolution spectra taken with the Potsdam Echelle Polarimetric and Spectroscopic Instrument on the Large Binocular Telescope, modeled using iSpec and MOOG. By carefully quantifying the impact of photon-noise (<0.05 dex for all elements), we robustly measure theintrinsicscatter of abundance ratios. At fixed [Fe/H], the rms intrinsic scatter in [X/Fe] ranges from 0.04 (Cr) to 0.16 dex (Na), with a median of 0.08 dex. Scatter in [X/Mg] is similar, and accounting for [α/Fe] only reduces the overall scatter moderately. We consider several possible origins of the intrinsic scatter with particular attention to fluctuations in the relative enrichment by core-collapse supernovae (CCSN) and Type Ia supernovae and stochastic sampling of the CCSN progenitor mass distribution. The stochastic sampling scenario provides a good quantitative explanation of our data if the effective number of CCSN contributing to the enrichment of a typical sample star isN∼ 50. At the median metallicity of our sample, this interpretation implies that the CCSN ejecta are mixed over a gas mass ∼6 × 104Mbefore forming stars. The scatter of elemental abundance ratios is a powerful diagnostic test for simulations of star formation, feedback, and gas mixing in the early phases of the Galaxy. 
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  7. Abstract We investigate the [X/Mg] abundances of 16 elements for 82,910 Galactic disk stars from GALAH+ DR3. We fit the median trends of low-Ia and high-Ia populations with a two-process model, which describes stellar abundances in terms of a prompt core-collapse and delayed Type-Ia supernova component. For each sample star, we fit the amplitudes of these two components and compute the residual Δ[X/H] abundances from this two-parameter fit. We find rms residuals ≲0.07 dex for well-measured elements and correlated residuals among some elements (such as Ba, Y, and Zn) that indicate common enrichment sources. From a detailed investigation of stars with large residuals, we infer that roughly 40% of the large deviations are physical and 60% are caused by problematic data such as unflagged binarity, poor wavelength solutions, and poor telluric subtraction. As one example of a population with distinctive abundance patterns, we identify 15 stars that have 0.3–0.6 dex enhancements of Na but normal abundances of other elements from O to Ni and positive average residuals of Cu, Zn, Y, and Ba. We measure the median elemental residuals of 14 open clusters, finding systematic ∼0.1–0.4 dex enhancements of O, Ca, K, Y, and Ba and ∼0.2 dex depletion of Cu in young clusters. Finally, we present a restricted three-process model where we add an asymptotic giant branch star (AGB) component to better fit Ba and Y. With the addition of the third process, we identify a population of stars, preferentially young, that have much higher AGB enrichment than expected from their SNIa enrichment. 
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  8. Abstract We report the first direct measurement of the helium isotope ratio, 3 He/ 4 He, outside of the Local Interstellar Cloud, as part of science-verification observations with the upgraded CRyogenic InfraRed Echelle Spectrograph. Our determination of 3 He/ 4 He is based on metastable He i * absorption along the line of sight toward Θ 2 A Ori in the Orion Nebula. We measure a value 3 He/ 4 He = (1.77 ± 0.13) × 10 −4 , which is just ∼40% above the primordial relative abundance of these isotopes, assuming the Standard Model of particle physics and cosmology, ( 3 He/ 4 He) p = (1.257 ± 0.017) × 10 −4 . We calculate a suite of galactic chemical evolution simulations to study the Galactic build up of these isotopes, using the yields from Limongi & Chieffi for stars in the mass range M = 8–100 M ⊙ and Lagarde et al. for M = 0.8–8 M ⊙ . We find that these simulations simultaneously reproduce the Orion and protosolar 3 He/ 4 He values if the calculations are initialized with a primordial ratio 3 He / 4 He p = ( 1.043 ± 0.089 ) × 10 − 4 . Even though the quoted error does not include the model uncertainty, this determination agrees with the Standard Model value to within ∼2 σ . We also use the present-day Galactic abundance of deuterium (D/H), helium (He/H), and 3 He/ 4 He to infer an empirical limit on the primordial 3 He abundance, 3 He / H p ≤ ( 1.09 ± 0.18 ) × 10 − 5 , which also agrees with the Standard Model value. We point out that it is becoming increasingly difficult to explain the discrepant primordial 7 Li/H abundance with nonstandard physics, without breaking the remarkable simultaneous agreement of three primordial element ratios (D/H, 4 He/H, and 3 He/ 4 He) with the Standard Model values. 
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  9. null (Ed.)
    Abstract This work proposes vision-only navigation strategies for an autonomous underwater robot. This approach is a step towards solving the coverage path planning problem in a 3-D environment for surveying underwater structures. Given the challenging conditions of the underwater domain, it is very complicated to obtain accurate state estimates reliably. Consequently, it is a great challenge to extend known path planning or coverage techniques developed for aerial or ground robot controls. In this work, we are investigating a navigation strategy utilizing only vision to assist in covering a complex underwater structure. We propose to use a navigation strategy akin to what a human diver will execute when circumnavigating around a region of interest, in particular when collecting data from a shipwreck. The focus of this article is a step towards enabling the autonomous operation of lightweight robots near underwater wrecks in order to collect data for creating photo-realistic maps and volumetric 3-D models while at the same time avoiding collisions. The proposed method uses convolutional neural networks to learn the control commands based on the visual input. We have demonstrated the feasibility of using a system based only on vision to learn specific strategies of navigation with 80% accuracy on the prediction of control command changes. Experimental results and a detailed overview of the proposed method are discussed. 
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  10. Abstract Sample return capsules (SRCs) entering Earth’s atmosphere at hypervelocity from interplanetary space are a valuable resource for studying meteor phenomena. The 2023 September 24 arrival of the Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer SRC provided an unprecedented chance for geophysical observations of a well-characterized source with known parameters, including timing and trajectory. A collaborative effort involving researchers from 16 institutions executed a carefully planned geophysical observational campaign at strategically chosen locations, deploying over 400 ground-based sensors encompassing infrasound, seismic, distributed acoustic sensing, and Global Positioning System technologies. Additionally, balloons equipped with infrasound sensors were launched to capture signals at higher altitudes. This campaign (the largest of its kind so far) yielded a wealth of invaluable data anticipated to fuel scientific inquiry for years to come. The success of the observational campaign is evidenced by the near-universal detection of signals across instruments, both proximal and distal. This paper presents a comprehensive overview of the collective scientific effort, field deployment, and preliminary findings. The early findings have the potential to inform future space missions and terrestrial campaigns, contributing to our understanding of meteoroid interactions with planetary atmospheres. Furthermore, the data set collected during this campaign will improve entry and propagation models and augment the study of atmospheric dynamics and shock phenomena generated by meteoroids and similar sources. 
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    Free, publicly-accessible full text available September 1, 2025