bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of sire plane of nutrition and targeted body weight gain on ewe lamb growth, glucose metabolism, and ovarian reserve
Authors: Bochantin-Winders Kerri A , Slavick Kathryn R , Jurgens Isabella M , Hurlbert Jennifer L , Menezes Ana Clara B , Kirsch James D , Borowicz Pawel P , Schauer Christopher S , Dahlen Carl R 
Published: October 2024

Abstract
Rambouillet rams were managed on either a positive (POS; gain 12% body weight [BW]; n = 8), maintenance (MAINT; maintain BW; n = 8), or negative (NEG; lose 12% BW; n = 8) plane of nutrition before breeding. Rams were bred to ewes (n = 10 per ram) that were managed similarly throughout gestation, and lambs were fed a common diet postnatally. Two ewe lambs (7.6 ± 0.02 mo of age, BW = 47.1 ± 1.17 kg) from each sire were selected and within-pair, randomly assigned to be managed for a moderate (MOD, 0.11 kg/d; n = 23) or accelerated (ACC, 0.20 kg/d; n = 22) rate of gain for 56 d. Ewe lamb BW was recorded on a weekly basis and blood was collected on days 0, 28, and 56 for analysis of insulin-like growth factor 1 (IGF-1), triiodothyronine (T3), thyroxine (T4), glucose, blood urea nitrogen (BUN), and non-esterified fatty acids (NEFA). Intravenous glucose tolerance tests (IVGTT) were conducted from days −7 to −4 and days 57 to 64. A unilateral ovariectomy was performed and ovarian follicles were staged and counted macro and microscopically. Sire treatment × day and ewe treatment × day interactions were present for BW (P ≤ 0.05), where POS had slower growth than MAINT and NEG, and tended (P = 0.10) to have reduced average daily gain (ADG) when managed at an accelerated rate of gain. By design, ACC had greater BW and ADG than MOD (P &lt; 0.05). Concentrations of IGF-1 and T4 were greater in ACC than MOD (P ≤ 0.05), and NEG tended to have greater concentrations of IGF-1 than POS and MAINT (P = 0.08). At the first IVGTT, the concentration of insulin was influenced by a sire treatment × time interaction (P ≤ 0.05), suggesting impaired secretion in NEG-sires ewes, but no differences in area under the curve (AUC) for glucose, insulin, or their ratio (P ≥ 0.11). No interactive effects of sire and ewe treatment (P ≥ 0.52) were observed at the second IVGTT, but insulin and insulin:glucose ratio were influenced by sire treatment × time (P ≤ 0.02), as NEG had greater insulin concentration at 60 min than MAINT (P = 0.03) and greater AUC than POS and MAINT (P ≤ 0.04). No differences in ovary size, weight, or total counts of macro and microscopic follicles were observed (P ≥ 0.23). Ewes-fed ACC had a greater number of small surface follicles (P = 0.02), whereas MOD tended to have a greater number of large surface follicles and tertiary follicles (P &lt; 0.06). These findings suggest that the paternal plane of nutrition influences female offspring physiology, particularly at varying growth rates.
Reference genome for the endangered, genetically subdivided, northern tidewater goby, Eucyclogobius newberryi
Authors: Jacobs David K , Kinziger Andrew , Abrecht Mira , McCraney W Tyler , Hà Benjamin A , Spies Brenton T , Heath-Heckman Elizabeth , Marimuhtu Mohan P A , Nguyen Oanh , Fairbairn Colin W , Seligmann William E , Escalona Merly , Miller Courtney , Shaffer H Bradley 
Published: October 2024

Abstract
The federally endangered sister species, Eucyclogobius newberryi (northern tidewater goby, NTG) and E. kristinae (southern tidewater goby) comprise the California endemic genus Eucyclogobius, which historically occurred in all coastal California counties. Isolated lagoons that only intermittently connect to the sea are their primary habitat. Reproduction occurs during lagoon closure, minimizing marine dispersal and generating the most genetically subdivided vertebrate genus on the California coast. We present a new genome assembly for E. newberryi using HiFi long reads and Hi-C chromatin-proximity sequencing. The 980 Mb E. newberryi reference genome has an N50 of 34 Mb with 22 well-described scaffolds comprising 88% of the genome and a complete BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 96.7%. This genome will facilitate studies addressing selection, drift, and metapopulation genetics in subdivided populations, as well as the persistence of the critically endangered E. kristinae, where reintroduction will be an essential element of conservation actions for recovery. It also provides tools critical to the recovery of the genetically distinct management units in the NTG, as well as broader ecological and evolutionary studies of gobies, the most speciose family of fishes in the world.
Past and current climate as a driver in shaping the distribution of the Longitarsus candidulus species group (Coleoptera: Chrysomelidae)
Authors: Biondi Maurizio , D’Alessandro Paola , Salvi Daniele , Berrilli Emanuele , Iannella Mattia 
Published: October 2024

Abstract
Longitarsus candidulus (Foudras) is a thermophilic flea beetle species widely distributed in the Mediterranean Basin and associated with Daphne gnidium L. and Thymelaea hirsuta (L.). Longitarsus laureolae Biondi and Longitarsus leonardii Doguet, phylogenetically closely related to L. candidulus, show together a peculiar and rare disjunct distribution along the central-southern Apennines and the Cantabrian-Pyrenean mountain system, respectively. Both are associated with Daphne laureola L. in mesophilic habitats. We used “ecological niche modeling” to infer the Pleistocene dynamics in the distribution of the three flea beetle species and their host plants. We interpreted their current distributions, paying particular attention to the presumed time of species divergence as inferred from recent studies. The differentiation of L. laureolae and L. leonardii from L. candidulus likely represents a response to the marked climatic changes during the Late Pliocene. Such a split was likely associated with a trophic niche shift of the laureolae/leonardii ancestor towards the typically mesophilic host plant D. laureola. The subsequent split between L. laureolae and L. leonardii, possibly due at first to the niche competition, was then boosted by an allopatric divergence during the Middle Pleistocene, likely caused by a large area of low environmental suitability for both species, mainly located between the northern Apennines and the south-western Alps.
Between Worlds: Ontological Security among Syrian Refugees in Germany and Turkey
Authors: Secen Sefa 
Published: October 2024

Abstract
Sometimes physical security may come at the cost of ontological security for refugees. They may struggle to develop stable narratives of identity and fail to situate themselves within their new social environments. States often prioritize addressing refugees’ physical security needs to facilitate their integration, but largely overlook the importance of identity security. This study argues that ontological security is crucial to integration processes, and refugees reestablish it by engaging in various forms of identity backlash, lowering their interest in the politics of the host country, and heightening their desire to return home. In other words, identity backlash, political disinterest, and an intensified desire to return home function as ontological security-seeking mechanisms and anxiety responses. The study contributes to ontological security theory (OST) by introducing a novel and nuanced framework that defines a set of indicators for the emotional and narrative-oriented aspects of ontological security among refugees. It takes a micro-level approach examining ontological security at the individual level for Syrian refugees in Turkey and Germany. The specific findings of this study are threefold. First, I find a significantly lower level of narrative-oriented security among Syrian refugees in Turkey than in Germany. Second, the results indicate that narrative-oriented ontological security among Syrian refugees is strongly associated with identity backlash, low political interest, and a willingness to return to the home country. Third, the results show that physical security and ontological security are not always correlated. Overall, this study demonstrates how OST can provide insights into the complex interplay between perceptions of security, identity backlash, political integration, and willingness to return among refugee communities.
Efficient statistical inference methods for assessing changes in species’ populations using citizen science data
Authors: Dennis Emily B , Diana Alex , Matechou Eleni , Morgan Byron J T 
Published: October 2024

Abstract
The global decline of biodiversity, driven by habitat degradation and climate breakdown, is a significant concern. Accurate measures of change are crucial to provide reliable evidence of species’ population changes. Meanwhile citizen science data have witnessed a remarkable expansion in both quantity and sources and serve as the foundation for assessing species’ status. The growing data reservoir presents opportunities for novel and improved inference but often comes with computational costs: computational efficiency is paramount, especially as regular analysis updates are necessary. Building upon recent research, we present illustrations of computationally efficient methods for fitting new models, applied to three major citizen science data sets for butterflies. We extend a method for modelling abundance changes of seasonal organisms, firstly to accommodate multiple years of count data efficiently, and secondly for application to counts from a snapshot mass-participation survey. We also present a variational inference approach for fitting occupancy models efficiently to opportunistic citizen science data. The continuous growth of citizen science data offers unprecedented opportunities to enhance our understanding of how species respond to anthropogenic pressures. Efficient techniques in fitting new models are vital for accurately assessing species’ status, supporting policy-making, setting measurable targets, and enabling effective conservation efforts.
Synchrotron self-Compton in a radiative-adiabatic fireball scenario: modelling the multiwavelength observations in some Fermi/LAT bursts
Authors: Fraija Nissim , Veres P , Betancourt Kamenetskaia B , Galvan-Gamez A , Dainotti M G , Dichiara Simone , Becerra R L 
Published: October 2024

ABSTRACT
Energetic GeV photons expected from the closest and the most energetic Gamma-ray bursts (GRBs) provide a unique opportunity to study the very-high-energy emission as well as the possible correlations with lower energy bands in realistic GRB afterglow models. In the standard GRB afterglow model, the relativistic homogeneous shock is usually considered to be fully adiabatic, however, it could be partially radiative. Based on the external forward-shock scenario in both stellar wind and constant-density medium, we present a radiative-adiabatic analytical model of the synchrotron self-Compton (SSC) and synchrotron processes considering an electron energy distribution with a power-law index of $1\lt p\lt 2$ and $2\le p$. We show that the SSC scenario plays a relevant role in the radiative parameter $\epsilon$, leading to a prolonged evolution during the slow cooling regime. In a particular case, we derive the Fermi/LAT light curves together with the photons with energies $\ge 100$ MeV in a sample of nine bursts from the second Fermi/LAT GRB catalogue that exhibited temporal and spectral indices with $\gtrsim 1.5$ and $\approx 2$, respectively. These events can hardly be described with closure relations of the standard synchrotron afterglow model, and also exhibit energetic photons above the synchrotron limit. We have modelled the multiwavelength observations of our sample to constrain the microphysical parameters, the circumburst density, the bulk Lorentz factor, and the mechanism responsible for explaining the energetic GeV photons.
Constraints on the early luminosity history of the Sun: applications to the Faint Young Sun problem
Authors: Basinger Connor , Pinsonneault Marc , Bastelberger Sandra T , Gaudi B Scott , Domagal-Goldman Shawn D 
Published: October 2024

ABSTRACT
Stellar evolution theory predicts that the Sun was fainter in the past, which can pose difficulties for understanding Earth’s climate history. One proposed solution to this Faint Young Sun (FYS) problem is a more luminous Sun in the past. In this paper, we address the robustness of the solar luminosity history using the yrec code to compute solar models including rotation, magnetized winds, and the associated mass-loss. We present detailed solar models, including their evolutionary history, which are in excellent agreement with solar observables. Consistent with prior standard models, we infer a high solar metal content. We provide predicted X-ray luminosities and rotation histories for usage in climate reconstructions and activity studies. We find that the Sun’s luminosity deviates from the standard solar model trajectory by at most 0.5 per cent during the Archean (corresponding to a radiative forcing of 0.849 W m$^{-2}$). The total mass-loss experienced by solar models is modest because of strong feedback between mass and angular momentum loss. We find a maximum mass-loss of $1.35 \times 10^{-3} \,{\rm M}_\odot$ since birth, at or below the level predicted by empirical estimates. The associated maximum luminosity increase falls well short of the level necessary to solve the FYS problem. We present compilations of paleotemperature and CO$_2$ reconstructions. One-dimensional ‘inverse’ climate models demonstrate a mismatch between the solar constant needed to reach high temperatures (e.g. 60–80 $^{\circ }$C) and the narrow range of plausible solar luminosities determined in this study. Maintaining a temperate Earth, however, is plausible given these conditions.
General relativistic self-gravitating equilibrium discs around rotating neutron stars
Authors: Kim Yoonsoo , Kim Jinho , Kim Hee Il , Lee Hyung Mok 
Published: October 2024

ABSTRACT
In modelling a relativistic disc around a compact object, the self-gravity of the disc is often neglected while it needs to be incorporated for more accurate descriptions in several circumstances. Extending the Komatsu–Eriguchi–Hachisu self-consistent field method, we present numerical models of a rapidly rotating neutron star with a self-gravitating disc in stationary equilibrium. In particular, our approach allows us to obtain numerical solutions involving a massive disc with the rest mass $\mathcal {O}(10^{-1})-\mathcal {O}(10^0)\, \mathrm{ M}_\odot$ closely attached to a rotating neutron star, given that the disc is mainly supported by the relativistic electron degeneracy pressure. We also assess the impact of self-gravity on the internal structure of the disc and the neutron star. These axisymmetric, stationary solutions can be employed for simulations involving the neutron star–disc system in the context of high-energy transients and gravitational-wave emissions.
Evaluating the variance of individual halo properties in constrained cosmological simulations
Authors: Stiskalek Richard , Desmond Harry , Devriendt Julien , Slyz Adrianne 
Published: October 2024

ABSTRACT
Constrained cosmological simulations play an important role in modelling the local Universe, enabling investigation of the dark matter content of local structures and their formation. We introduce an internal method for quantifying the extent to which the variance of individual halo properties is suppressed by the constraints imposed on the initial conditions. We apply it to the Constrained Simulations in BORG (CSiBORG) suite of 101 high-resolution realizations across the posterior probability distribution of initial conditions from the Bayesian Origin Reconstruction from Galaxies (BORG) algorithm. The method is based on the overlap of the initial Lagrangian patch of a halo in one simulation with those in another, measuring the degree to which the haloes’ particles are initially coincident. This addresses the extent to which the imposed large-scale structure constraints reduce the variance of individual halo properties. We find consistent reconstructions of $M\gtrsim 10^{14}~\mathrm{M}_\odot \, h^{-1}$ haloes, indicating that the constraints from the BORG algorithm are sufficient to pin down the masses, positions, and peculiar velocities of clusters to high precision, though we do not assess how well they reproduce observations of the local Universe. The effect of the constraints tapers off towards lower mass, and the halo spins and concentrations are largely unconstrained at all masses. We document the advantages of evaluating halo consistency in the initial conditions and describe how the method may be used to quantify our knowledge of the halo field given galaxy survey data analysed through the lens of probabilistic inference machines such as BORG.
Most extremely low mass white dwarfs with non-degenerate companions are inner binaries of hierarchical triples
Authors: Lagos-Vilches Felipe , Hernandez Mercedes , Schreiber Matthias R , Parsons Steven G , Gänsicke Boris T 
Published: October 2024

ABSTRACT
Extremely low-mass white dwarfs (ELM WDs) with non-degenerate companions are believed to originate from solar-type main-sequence binaries undergoing stable Roche lobe overflow mass transfer when the ELM WD progenitor is at (or just past) the termination of the main-sequence. This implies that the orbital period of the binary at the onset of the first mass transfer phase must have been $\lesssim 3-5$ d. This prediction in turn suggests that most of these binaries should have tertiary companions since $\approx 90$ per cent of solar-type main-sequence binaries in that period range are inner binaries of hierarchical triples. Until recently, only precursors of this type of binaries have been observed in the form of EL CVn binaries, which are also known for having tertiary companions. Here, we present high-angular-resolution images of TYC 6992-827-1, an ELM WD with a sub-giant (SG) companion, confirming the presence of a tertiary companion. Furthermore, we show that TYC 6992-827-1, along with its sibling TYC 8394-1331-1 (whose triple companion was detected via radial velocity variations), are in fact descendants of EL CVn binaries. Both TYC 6992-827-1 and TYC 8394-1331-1 will evolve through a common envelope phase, which depending on the ejection efficiency of the envelope, might lead to a single WD or a tight double WD binary, which would likely merge into a WD within a few Gyr due to gravitational wave emission. The former triple configuration will be reduced to a wide binary composed of a WD (the merger product) and the current tertiary companion.
a-sloth reveals the nature of the first stars
Authors: Hartwig Tilman , Lipatova Veronika , Glover Simon C O , Klessen Ralf S 
Published: October 2024

ABSTRACT
The first generation of stars (Pop III) are too dim to be observed directly and probably too short-lived to have survived for local observations. Hence, we rely on simulations and indirect observations to constrain the nature of the first stars. In this study, we calibrate the semi-analytical model a-sloth (Ancient Stars and Local Observables by Tracing Haloes), designed for simulating star formation in the early Universe, using a likelihood function based on nine independent observables. These observables span Milky Way-specific and cosmologically representative variables, ensuring a comprehensive calibration process. This calibration methodology ensures that a-sloth provides a robust representation of the early Universe’s star formation processes, aligning simulated values with observed benchmarks across a diverse set of parameters. The outcome of this calibration process is best-fitting values and their uncertainties for 11 important parameters that describe star formation in the early Universe, such as the shape of the initial mass function (IMF) of Pop III stars or escape fractions of ionizing photons. Our best-fitting model has a Pop III IMF with a steeper slope, dN/d$M \propto M^{-1.77}$, than the log-flat models often proposed in the literature, and also relatively high minimum and maximum masses, $M_{\rm min} = 13.6~\, \mathrm{M}_\odot$ and $M_{\rm max} = 197~\, \mathrm{M}_\odot$. However, we emphasize that the IMF-generating parameters are poorly constrained and, e.g. the IMF slope could vary from log-flat to Salpeter. We also provide data products, such as delay time distribution, bubble size distributions for ionizing and metal-enriched bubbles at high redshift, and correlation plots between all 11 input parameters. Our study contributes to understanding the formation of early stars through a-sloth, providing valuable insights into the nature of Pop III stars and the intricate processes involved in the early Universe’s star formation.
Indication of rapid magnetic field decay in X-ray dim isolated neutron star RX J0720.4−3125
Authors: Igoshev Andrei P , Popov Sergei B 
Published: October 2024

ABSTRACT
Magnetic field evolution of neutron stars is a long-standing debate. The rate of magnetic field decay for isolated, non-accreting neutron stars can be quantified by measuring the negative second derivative of the spin period. Alternatively, this rate can be estimated by observing an excess of thermal emission with respect to the standard cooling without additional heating mechanisms involved. One of the nearby cooling isolated neutron stars – RX J0720.4−3125, – offers a unique opportunity to probe the field decay as for this source there are independent measurements of the surface X-ray luminosity, the second spin period derivative, and magnetic field. We demonstrate that the evolution rate of the spin period derivative is in correspondence with the rate of dissipation of magnetic energy of the dipolar field if a significant part of the released energy is emitted in X-rays. The instantaneous time-scale for the magnetic field decay is ${\sim} 10^4$ yr.
DDBJ update in 2024: the DDBJ Group Cloud service for sharing pre-publication data
Authors: Kodama Yuichi , Ara Takeshi , Fukuda Asami , Tokimatsu Toshiaki , Mashima Jun , Kosuge Takehide , Tanizawa Yasuhiro , Tanjo Tomoya , Ogasawara Osamu , Fujisawa Takatomo , Nakamura Yasukazu , Arita Masanori 
Published: October 2024

Abstract
The Bioinformation and DNA Data Bank of Japan Center (DDBJ Center, https://www.ddbj.nig.ac.jp) provides public databases that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), the DDBJ Center accepts and distributes nucleotide sequence data ranging from raw reads to assembled and annotated sequences with the National Center for Biotechnology Information and the European Bioinformatics Institute. Besides INSDC databases, the DDBJ Center provides databases for functional genomics (Genomic Expression Archive), metabolomics (MetaboBank), human genetic variations (TogoVar-repository) and human genetic and phenotypic data (Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics supercomputer, which is also a platform for the DDBJ Group Cloud (DGC) services for sharing and analysis of pre-publication data among research groups. This paper reports recent updates on the databases and the services of the DDBJ Center, highlighting the DGC service.