bluuebunny/crossref_metadata_2025_split huggingface dataset:
K Locus Effects in Gray Wolves: Experimental Assessment of TLR3 Signaling and the Gene Expression Response to Canine Distemper Virus
Authors: Johnston Rachel A , Rheinwald James G , vonHoldt Bridgett M , Stahler Daniel R , Lowry William , Tung Jenny , Wayne Robert K 
Published: May 2021

AbstractIn North American gray wolves, black coat color is dominantly inherited via a 3 base pair coding deletion in the canine beta defensin 3 (CBD103) gene. This 3 base pair deletion, called the KB allele, was introduced through hybridization with dogs and subsequently underwent a selective sweep that increased its frequency in wild wolves. Despite apparent positive selection, KBB wolves have lower fitness than wolves with the KyB genotype, even though the 2 genotypes show no observable differences in black coat color. Thus, the KB allele is thought to have pleiotropic effects on as-yet unknown phenotypes. Given the role of skin-expressed CBD103 in innate immunity, we hypothesized that the KB allele influences the keratinocyte gene expression response to TLR3 pathway stimulation and/or infection by canine distemper virus (CDV). To test this hypothesis, we developed a panel of primary epidermal keratinocyte cell cultures from 24 wild North American gray wolves of both Kyy and KyB genotypes. In addition, we generated an immortalized Kyy line and used CRISPR/Cas9 editing to produce a KyB line on the same genetic background. We assessed the transcriptome-wide responses of wolf keratinocytes to the TLR3 agonist polyinosinic:polycytidylic acid (polyI:C), and to live CDV. K locus genotype did not predict the transcriptional response to either challenge, suggesting that variation in the gene expression response does not explain pleiotropic effects of the KB allele on fitness. This study supports the feasibility of using cell culture methods to investigate the phenotypic effects of naturally occurring genetic variation in wild mammals.
Detection of Genetic Variability in Borrelia miyamotoi (Spirochaetales: Spirochaetaceae) Between and Within the Eastern and Western United States
Authors: Hojgaard Andrias , Osikowicz Lynn M , Maes Sarah , Eisen Lars , Eisen Rebecca J 
Published: May 2021

Abstract
Borrelia miyamotoi is a hard tick-associated relapsing fever spirochete that is geographically widespread in Ixodes spp. (Acari: Ixodidae) ticks, but typically occurs at low prevalence. Genetic variability has been described among strains derived from Asia, Europe, and North America, and among tick species that carry the infection, but little variability has been described within foci or tick species. Capitalizing on access to B. miyamotoi nucleic acid extracted from host-seeking Ixodes scapularis Say or Ixodes pacificus Cooley & Kohls from 16 states, we explored genetic variability based on sequence analysis of four amplicons described herein. Consistent with previous studies, we detected significant genetic differences between strains derived from I. scapularis (eastern United States) and I. pacificus (western United States) and identified two distinct sequences in the western United States (Am-West-1 and Am-West-2). Unique to this study, we identified two distinct sequences in the eastern United States (Am-East-1 and Am-East-2). Based on the 161 samples we analyzed, Am-East-1 was the only type represented in 50 B. miyamotoi-infected ticks collected from the Northeast (Vermont, Maine, New York, Connecticut, and Rhode Island), whereas ticks collected from the North-Central and Mid-Atlantic states harbored B. miyamotoi comprised of both Am-East-1 and Am-East-2. Further studies are needed to better characterize the phylogeography of B. miyamotoi and to discern if there are biologically meaningful differences among sequence types. To facilitate further exploration, we developed a polymerase chain reaction (PCR) assay designed to differentiate Am-East-1, Am-East-2, and Am-West sequence types without having to sequence the amplicon.
Study on the dissolution of β-precipitates in the Zr–1Nb alloy under the influence of Ne ion irradiation
Authors: Goel Lokesh , Mir Anamul H , Naveen Kumar N , Satyam Parlapalli V , Hinks Jonathan A , Donelly Stephen E , Tewari Raghvendra 
Published: May 2021

Abstract
The stability of β-precipitates in the Zr–1Nb alloy has been studied under Ne ion irradiation of energy 250 keV by insitu transmission electron microscope as a function of irradiation dose. The irradiation was carried out up to ∼136 dpa at 573 K. Microstructural investigations have shown that up to ∼38 dpa, precipitates showed an increase in size, and for irradiation doses &gt;38 dpa, the size of the precipitates was noticed to reduce. Post-irradiation energy-dispersive spectrometry of the specimens revealed the Nb concentration throughout the matrix to be ∼0.8–1.5%. Three-dimensional atom probe tomography was also carried out for irradiated specimens to look for the presence of any nanoclusters. However, Nb clustering was not observed in the specimens. It is proposed that the dissolution of the precipitates may be facilitated by an increase in the solubility limit of Nb in Zr caused by irradiation. The solubility limit may increase by the introduction of defects generated by irradiation and by the destabilization of the β-phase. This may result in back-diffusion of Nb atoms to the matrix by radiation-enhanced diffusion to lower the strain produced by the defects, resulting in the dissolution of the precipitates.
Introducing SYSPROP—A Software Tool to Identify Small but Economically Viable Timber Parcels in the Pacific Northwest
Authors: Helderop Edward , Grubesic Tony H , Edson Clayton N 
Published: May 2021

AbstractThe past several decades have seen a steady decline in timber harvest rates from many parts of the United States, particularly the Pacific Northwest. Although various factors fuel this decline, one of the principal drivers is increasing rates of parcelization of the landscape. Increasingly parcelized forested landscapes tend to be more challenging to log—both because urbanization rates are somewhat correlated with parcelization but also due to the additional administrative overhead in securing logging rights in increasingly smaller parcels. The purpose of this note is to introduce SYSPROP, a tool to aid in the automatic identification of economically viable parcels for logging. We conclude with a case study of a small logging company operating in Washington State that used this tool to identify several promising parcels.
The transcription factor KNAT2/6b mediates changes in plant architecture in response to drought via down-regulating GA20ox1 in Populus alba × P. glandulosa
Authors: Song Xueqin , Zhao Yanqiu , Wang Jinnan , Lu Meng-Zhu 
Published: May 2021

Abstract
Plant architecture is genetically controlled, but is influenced by environmental factors. Plants have evolved adaptive mechanisms that allow changes in their architecture under stress, in which phytohormones play a central role. However, the gene regulators that connect growth and stress signals are rarely reported. Here, we report that a class I KNOX gene, PagKNAT2/6b, can directly inhibit the synthesis of gibberellin (GA), altering plant architecture and improving drought resistance in Populus. Expression of PagKNAT2/6b was significantly induced under drought conditions, and transgenic poplars overexpressing PagKNAT2/6b exhibited shorter internode length and smaller leaf size with short or even absent petioles. Interestingly, these transgenic plants showed improved drought resistance under both short- and long-term drought stress. Histological observations indicated that decreased internode length and leaf size were mainly caused by the inhibition of cell elongation and expansion. GA content was reduced, and the GA20-oxidase gene PagGA20ox1 was down-regulated in overexpressing plants. Expression of PagGA20ox1 was negatively related to that of PagKNAT2/6b under drought stress. ChIP and transient transcription activity assays revealed that PagGA20ox1 was directly targeted by PagKNAT2/6b. Therefore, this study provides evidence that PagKNAT2/6b mediates stress signals and changes in plant architecture via GA signaling by down-regulating PagGA20ox1.
Plant thermotropism: an underexplored thermal engagement and avoidance strategy
Authors: van Zanten Martijn , Ai Haiyue , Quint Marcel 
Published: May 2021

AbstractVarious strategies evolved in plants to adjust the position of organs relative to the prevailing temperature condition, which allows optimal plant growth and performance. Such responses are classically separated into nastic and tropic responses. During plant thermotropic responses, organs move towards (engage) or away from (avoid) a directional temperature cue. Despite thermotropism being a classic botanical concept, the underlying ecological function and molecular and biophysical mechanisms remain poorly understood to this day. This is in contrast to the relatively well-studied thermonastic movements (hyponasty) of, for example, rosette leaves. In this review, we provide an update on the current knowledge on plant thermotropisms and propose directions for future research and application.
Constraining the ratio of median pixel optical depth profile around z ∼ 4 quasars using the longitudinal proximity effect
Authors: Jalan Priyanka , Chand Hum , Srianand Raghunathan 
Published: May 2021

ABSTRACT
We present a detailed study of the longitudinal proximity effect using a sample of 85 quasars spanning an emission redshift range of 3.5 ≤ zem ≤ 4.5 and Lyman continuum luminosity (L912) ranging from 1.06 × 1031 to 2.24 × 1032 erg s−1 Hz−1. We use the high-quality spectra of these quasars obtained at a spectral resolution of R ∼ 5100 and S/N ∼ 30 using X-SHOOTER spectrograph mounted on the Very Large Telescope (VLT). In our analysis, we compared the transmitted flux and pixel optical depth of the Ly α absorption originating from the vicinity of quasars to those from the general intergalactic medium (IGM) by using a redshift-matched control sample. The longitudinal proximity effect is found up to r ≤ 12 Mpc (proper) from quasars. By appropriately scaling up the pixel optical depth in the vicinity of quasars to account for the excess ionization by quasars, we constrain the ratio of median H i optical depth in the vicinity of the quasar to that of the IGM (Rτ(r)). The Rτ(r) is found to be significantly higher than unity up to 6 Mpc from the quasar with a typical radial profile of the form Rτ(r) = 1 + A × exp(− r/r0) with A = 9.16 ± 0.68 and r0 = 1.27 ± 0.08 Mpc. The integrated value of the scaled pixel optical depth over the radial bin of 0–6 Mpc is found to be higher by a factor of 2.55 ± 0.17 than the corresponding integrated value of the median pixel optical depth of the IGM. We also found Rτ(r) to be luminosity dependent.
Modelling of atmospheric optical turbulence with the Weather Research and Forecasting model at the Ali observatory, Tibet
Authors: Qian Xuan , Yao Yongqiang , Zou Lei , Wang Hongshuai , Yin Jia , Li Yao 
Published: May 2021

ABSTRACT
In this study, we make use of a meso-scale numerical model to obtain the parameters of atmospheric optical turbulence at the Ali observatory above the Tibetan Plateau. These parameters are essential for ground-based optical observations and some adaptive optics techniques. We present the characterization of the vertical distributions of atmospheric optical turbulence Cn2 and the main integral parameters, such as coherence time τ0, isoplanatic angle θ0 and seeing ε0 derived from Cn2. Meanwhile, the measurement of Cn2 obtained with a radiosonde instrument is used to quantify the model performance on reconstructing the optical turbulence above the site. This shows a high level of agreement and provides a reliable tool for astronomical site testing. The results presented in this paper demonstrate the good behaviour of the atmospheric optical turbulence condition at Ali, particularly during the summer half of the year. We find yearly median values of seeing ε0 = 0.47 arcsec, isoplanatic angle θ0 = 4.35 arcsec and atmospheric coherence time τ0 = 5.52 ms in 2016, and we also provide independent confirmation of the potential of the Ali site in adaptive optics. Moreover, it has been proven that meso-scale models can provide reliable estimations of atmospheric optical turbulence conditions above an astronomical site on the Tibetan Plateau.
Magneto-hydrodynamic simulations of young supernova remnants and their energy-conversion phase
Authors: Petruk O , Kuzyo T , Orlando S , Pohl M , Brose R 
Published: May 2021

ABSTRACT
Supernova remnants (SNRs) can be rich sources of information on the parent SN (supernova) explosion. Thus, investigating the transition from the phase of SN to that of SNR can be crucial to link these two phases of evolution. Here, we aim to study the early development of SNR in more detail, paying the major attention to the transition from the early expansion stage to the Sedov stage and the role played by magnetic field in this transition. To this end, spherical magnetohydrodynamic simulations of SNRs have been performed to study the evolution of magnetic field in young SNRs and explore a sequence of the SNR evolutionary stages in the pre-radiative epoch. Remnants of three supernova types are considered, namely, SNIa, SNIc, and SNIIP, that covers a wide space of parameters relevant for SNRs. Changes in global characteristics and development of spatial distributions are analysed. It is shown that the radial component of magnetic field rapidly drops downstream of the forward shock. Therefore, the radially aligned polarization patterns observed in few young SNRs cannot be reproduced in the 1D MHD simulations. The period SNR takes for the transition from the earliest ejecta-driven phase to the Sedov phase is long enough, with its distinctive physical features, headed by the energy conversion from mostly kinetic one to a fixed ratio between the thermal and kinetic components. This transition worth to be distinguished as a phase in SNR evolutionary scheme. The updated sequence of stages in SNR evolution could be the free expansion (of gas) – energy conversion – Sedov–Taylor – post-adiabatic – radiative.
Cosmic rays and non-thermal emission in simulated galaxies – II. γ-ray maps, spectra, and the far-infrared–γ-ray relation
Authors: Werhahn Maria , Pfrommer Christoph , Girichidis Philipp , Winner Georg 
Published: May 2021

ABSTRACT
The γ-ray emission of star-forming (SF) galaxies is attributed to hadronic interactions of cosmic ray (CR) protons with the interstellar gas and contributions from CR electrons via bremsstrahlung and inverse Compton (IC) scattering. The relative importance of these processes in different galaxy types is still unclear. We model these processes in three-dimensional magnetohydrodynamical (MHD) simulations of the formation of isolated galactic discs using the moving-mesh code arepo, including dynamically coupled CR protons and adopting different CR transport models. We calculate steady-state CR spectra and also account for the emergence of secondary electrons and positrons. This allows us to produce detailed γ-ray maps, luminosities, and spectra of our simulated galaxies at different evolutionary stages. Our simulations with anisotropic CR diffusion and a low CR injection efficiency at supernovae (SNe; $\zeta_\mathrm{SN}=0.05$) can successfully reproduce the observed far-infrared (FIR)–γ-ray relation. Starburst galaxies are close to the calorimetric limit, where CR protons lose most of their energy due to hadronic interactions and hence, their γ-ray emission is dominated by neutral pion decay. However, in low SF galaxies, the increasing diffusive losses soften the CR proton spectra due to energy-dependent diffusion, and likewise steepen the pionic γ-ray spectra. In turn, IC emission hardens the total spectra and can contribute up to ∼40 per cent of the total luminosity in low SF galaxies. Furthermore, in order to match the observed γ-ray spectra of starburst galaxies, we require a weaker energy dependence of the CR diffusion coefficient, $D\propto E^{0.3}$, in comparison to Milky Way-like galaxies.
Modelling synchrotron and synchrotron self-Compton emission of gamma-ray burst afterglows from radio to very-high energies
Authors: Joshi Jagdish C , Razzaque Soebur 
Published: May 2021

ABSTRACT
Synchrotron radiation from a decelerating blastwave is a widely accepted model of radio to X-ray afterglow emission from gamma-ray bursts (GRBs). GeV gamma-ray emission detected by the Fermi Large Area Telescope (LAT) and the duration of which extends beyond the prompt gamma-ray emission phase is also compatible with broad features of afterglow emission. We revisit the synchrotron self-Compton (SSC) emission model from a decelerating blastwave to fit multiwavelength data from three bright GRBs, namely GRB 190114C, GRB 130427A, and GRB 090510. We constrain the afterglow model parameters using the simultaneous fit of the spectral energy distributions at different times and light curves at different frequencies for these bursts. We find that a constant density interstellar medium is favoured for the short GRB 090510, while a wind-type environment is favoured for the long GRB 130427A and GRB 190114C. The sub-TeV component in GRB 190114C detected by MAGIC is the SSC emission in our modelling. Furthermore, we find that the SSC emission in the Thomson regime is adequate to fit the spectra and light curves of GRB 190114C. For the other two GRBs, lacking sub-TeV detection, the SSC emissions are also modelled in the Thomson regime. For the model parameters we have used, the γγ attenuation in the blastwave is negligible in the sub-TeV range compared to the redshift-dependent γγ attenuation in the extragalactic background light.
Apsidal asymmetric-alignment of Jupiter Trojans
Authors: Li Jian , Lei Hanlun , Xia Zhihong J 
Published: May 2021

ABSTRACT
The most distant Kuiper belt objects exhibit the clustering in their orbits, and this anomalous architecture could be caused by Planet 9 with large eccentricity and high inclination. We then suppose that the orbital clustering of minor planets may be observed somewhere else in the Solar system. In this paper, we consider the over 7000 Jupiter Trojans from the Minor Planet Center, and find that they are clustered in the longitude of perihelion ϖ, around the locations ϖJ + 60○ and ϖJ − 60○ (ϖJ is the longitude of perihelion of Jupiter) for the L4 and L5 swarms, respectively. Then we build a Hamiltonian system to describe the associated dynamical aspects for the co-orbital motion. The phase space displays the existence of the apsidally aligned islands of libration centred on Δϖ = ϖ − ϖJ ≈ ±60○, for the Trojan-like orbits with eccentricities e &lt; 0.1. Through a detailed analysis, we have shown that the observed Jupiter Trojans with proper eccentricities ep &lt; 0.1 spend most of their time in the range of |Δϖ| = 0°–120○, while the more eccentric ones with ep &gt; 0.1 are too few to affect the orbital clustering within this Δϖ range for the entire Trojan population. Our numerical results further prove that, even starting from a uniform Δϖ distribution, the apsidal alignment of simulated Trojans similar to the observation can appear on the order of the age of the Solar system. We conclude that the apsidal asymmetric-alignment of Jupiter Trojans is robust, and this new finding can be helpful to design the survey strategy in the future.
Hierarchical black hole mergers in young, globular and nuclear star clusters: the effect of metallicity, spin and cluster properties
Authors: Mapelli Michela , Dall’Amico Marco , Bouffanais Yann , Giacobbo Nicola , Arca Sedda Manuel , Artale M Celeste , Ballone Alessandro , Di Carlo Ugo N , Iorio Giuliano , Santoliquido Filippo , Torniamenti Stefano 
Published: May 2021

ABSTRACTWe explore hierarchical black hole (BH) mergers in nuclear star clusters (NSCs), globular clusters (GCs) and young star clusters (YSCs), accounting for both original and dynamically assembled binary BHs (BBHs). We find that the median mass of both first- and nth-generation dynamical mergers is larger in GCs and YSCs with respect to NSCs because the lighter BHs are ejected by supernova kicks from the lower mass clusters. Also, first- and nth-generation BH masses are strongly affected by the metallicity of the progenitor stars: the median mass of the primary BH of a nth-generation merger is ∼24–38 M⊙ (∼9–15 M⊙) in metal-poor (metal-rich) NSCs. The maximum BH mass mainly depends on the escape velocity: BHs with mass up to several thousand M⊙ form in NSCs, while YSCs and GCs host BHs with mass up to several hundred M⊙. Furthermore, we calculate the fraction of mergers with at least one component in the pair-instability mass gap (fPI) and in the intermediate-mass BH regime (fIMBH). In the fiducial model for dynamical BBHs with metallicity Z = 0.002, we find fPI ≈ 0.05, 0.02 and 0.007 (fIMBH ≈ 0.01, 0.002 and 0.001) in NSCs, GCs and YSCs, respectively. Both fPI and fIMBH drop by at least one order of magnitude at solar metallicity. Finally, we investigate the formation of GW190521 by assuming that it is either a nearly equal-mass BBH or an intermediate-mass ratio inspiral.
Resource Uptake and the Evolution of Moderately Efficient Enzymes
Authors: Labourel Florian , Rajon Etienne 
Published: May 2021

Abstract
Enzymes speed up reactions that would otherwise be too slow to sustain the metabolism of selfreplicators. Yet, most enzymes seem only moderately efficient, exhibiting kinetic parameters orders of magnitude lower than their expected physically achievable maxima and spanning over surprisingly large ranges of values. Here, we question how these parameters evolve using a mechanistic model where enzyme efficiency is a key component of individual competition for resources. We show that kinetic parameters are under strong directional selection only up to a point, above which enzymes appear to evolve under near-neutrality, thereby confirming the qualitative observation of other modeling approaches. While the existence of a large fitness plateau could potentially explain the extensive variation in enzyme features reported, we show using a population genetics model that such a widespread distribution is an unlikely outcome of evolution on a common landscape, as mutation–selection–drift balance occupy a narrow area even when very moderate biases towards lower efficiency are considered. Instead, differences in the evolutionary context encountered by each enzyme should be involved, such that each evolves on an individual, unique landscape. Our results point to drift and effective population size playing an important role, along with the kinetics of nutrient transporters, the tolerance to high concentrations of intermediate metabolites, and the reversibility of reactions. Enzyme concentration also shapes selection on kinetic parameters, but we show that the joint evolution of concentration and efficiency does not yield extensive variance in evolutionary outcomes when documented costs to protein expression are applied.