bluuebunny/crossref_metadata_2025_split huggingface dataset:
Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes)
Authors: Bornbusch Sally L. , Bamford Alexandra , Thacher Piper , Crosier Adrienne , Marinari Paul , Bortner Robyn , Garelle Della , Livieri Travis , Santymire Rachel , Comizzoli Pierre , Maslanka Michael , Maldonado Jesús E. , Koepfli Klaus-Peter , Muletz-Wolz Carly R. , DeCandia Alexandra L. 
Published: February 2024

AbstractReproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry.
Codon language embeddings provide strong signals for use in protein engineering
Authors: Outeiral Carlos , Deane Charlotte M. 
Published: February 2024

AbstractProtein representations from deep language models have yielded state-of-the-art performance across many tasks in computational protein engineering. In recent years, progress has primarily focused on parameter count, with recent models’ capacities surpassing the size of the very datasets they were trained on. Here we propose an alternative direction. We show that large language models trained on codons, instead of amino acid sequences, provide high-quality representations that outperform comparable state-of-the-art models across a variety of tasks. In some tasks, such as species recognition, prediction of protein and transcript abundance or melting point estimation, we show that a language model trained on codons outperforms every other published protein language model, including some that contain over 50 times more parameters. These results indicate that, in addition to commonly studied scale and model complexity, the information content of biological data provides an orthogonal direction to improve the power of machine learning in biology.
Barnacle cement protein as an efficient bioinspired corrosion inhibitor
Authors: Bui My Hanh , Hiew Shu Hui , Salim Teddy , Saw Wan Geok , Webster Richard D. , Grüber Gerhard , Mu Yuguang , Miserez Ali 
Published: February 2024

AbstractTo prevent corrosion damage in aggressive environments such as seawater, metallic surfaces are coated with corrosion inhibitors usually made of organic molecules. Unfortunately, these inhibitors often exhibit environmental toxicity and are hazardous to natural habitats. Thus, developing greener and effective corrosion inhibitors is desirable. Here, we present an alternative green inhibitor, the recombinant protein rMrCP20 derived from the adhesive cement of the barnacle Megabalanus rosa and show that it efficiently protects mild steel against corrosion under high salt conditions mimicking the marine environment. We reveal that these anti-corrosion properties are linked to the protein’s biophysical properties, namely its strong adsorption to surfaces combined with its interaction with Fe ions released by steel substrates, which forms a stable layer that increases the coating’s impedance and delays corrosion. Our findings highlight the synergistic action of rMrCP20 in preventing corrosion and provide molecular-level guidelines to develop alternative green corrosion inhibitor additives.
Multi-scale V-net architecture with deep feature CRF layers for brain extraction
Authors: Park Jong Sung , Fadnavis Shreyas , Garyfallidis Eleftherios 
Published: February 2024

Abstract
Background
Brain extraction is a computational necessity for researchers using brain imaging data. However, the complex structure of the interfaces between the brain, meninges and human skull have not allowed a highly robust solution to emerge. While previous methods have used machine learning with structural and geometric priors in mind, with the development of Deep Learning (DL), there has been an increase in Neural Network based methods. Most proposed DL models focus on improving the training data despite the clear gap between groups in the amount and quality of accessible training data between.

Methods
We propose an architecture we call Efficient V-net with Additional Conditional Random Field Layers (EVAC+). EVAC+ has 3 major characteristics: (1) a smart augmentation strategy that improves training efficiency, (2) a unique way of using a Conditional Random Fields Recurrent Layer that improves accuracy and (3) an additional loss function that fine-tunes the segmentation output. We compare our model to state-of-the-art non-DL and DL methods.

Results
Results show that even with limited training resources, EVAC+ outperforms in most cases, achieving a high and stable Dice Coefficient and Jaccard Index along with a desirable lower Surface (Hausdorff) Distance. More importantly, our approach accurately segmented clinical and pediatric data, despite the fact that the training dataset only contains healthy adults.

Conclusions
Ultimately, our model provides a reliable way of accurately reducing segmentation errors in complex multi-tissue interfacing areas of the brain. We expect our method, which is publicly available and open-source, to be beneficial to a wide range of researchers.
A MnS/MnO-coated S,N-doped carbon anode obtained from a Mn(ii)-coordinated polymer for long-cycle life Li-ion batteries
Authors: Shim Kyubin , Kim Hyun Woo , Park Sungwoo , Seo Kyeong-Deok , Kim Chang-Yeon , Lee Jin Bae , Bae Jong Seong , Kim Hae Jin 
Published: February 2024

A MnS/MnO-decorated S,N-doped carbon electrode was synthesized for advanced LIBs. This shows excellent cycling stability, with the material exhibiting superior performance. In situ XRD and XPS provided a fundamental understanding of the material.
GPR15LG regulates psoriasis-like inflammation by down-regulating inflammatory factors on keratinocytes
Authors: Chen Caifeng , Cai Renhui , Zhou Jun , Zhang Danqun , Chen Li 
Published: February 2024

Abstract
Psoriasis is a common chronic inflammatory skin disease characterized by aberrant proliferation of keratinocytes and infiltration of immune cells. We previously found that GPR15LG protein is highly expressed in psoriasis lesional skin and it positively regulates psoriatic keratinocyte proliferation. Our data also showed that GPR15LG could regulate the activity of NF-κB pathway, which is associated with psoriatic inflammation. In the present study, we demonstrated that Gpr15lg (ortholog of GPR15LG) knockdown attenuated the severity of imiquimod (IMQ)-induced psoriasis-like inflammation in mice. Such an effect was achieved by down-regulating the expression of inflammatory cytokines interleukin (IL)-1α, IL-1β, tumor necrosis factor (TNF)-α and S100A7. Consistently, GPR15LG knockdown in vitro significantly downgraded the expression of inflammatory factors in the cellular model of psoriasis. These results suggested that GPR15LG could be involved in the development of psoriasis by regulating inflammation.
Vestibular Function Monitoring in a Pediatric Cochlear Implant Program
Authors: Doettl Steven M. , Little John P. , Plyler Patrick N. , Davis Connor , Anderson Allison , Little Matthew , Little John G. 
Published: February 2024

Purpose:
The purpose of this project was to retrospectively evaluate a vestibular screening protocol and results in children with cochlear implants (CIs) to provide information for other clinics considering implementing similar programs.

Method:
A retrospective analysis of chart data was completed using descriptive statistics and a repeated measures multivariate analysis of variance design in context with the current state of literature on vestibular monitoring in the pediatric CI population.

Results:
Pre-CI testing was focused on cervical vestibular evoked myogenic potentials (cVEMPs), which is an efficient and obtainable measure in this population. Postimplantation vestibular testing proved challenging with a high no-show/cancellation rate. For patients evaluated both pre- and postimplantation, there was no significant difference across patients noted; however, individual differences were noted.

Conclusions:
Vestibular monitoring of pediatric CI patients is important for the overall health and development of this population. An overall assessment of the program and options for continuation of the program considering this analysis are also provided. cVEMP testing is a good option for vestibular monitoring in pediatric CI patients; however, a multifaceted approach is most likely needed to address the many challenges that exist.
The Mantis Network
Authors: Hoeijmakers H. J. , Kitzmann D. , Morris B. M. , Prinoth B. , Borsato N. W. , Thorsbro B. , Pino L. , Lee E. K. H. , Akın C. , Seidel J. V. , Birkby J. L. , Allart R. , Heng Kevin 
Published: February 2024

Context. Using emission lines from metals, we investigate the three-dimensional distribution of temperature and chemistry in ultra-hot Jupiters.
Aims. Existing observations of WASP-121 b have suggested an underabundance of titanium and titanium oxide in its terminator region. In this study, we aim to determine whether this depletion is global by investigating the dayside emission spectrum.
Methods. We analyzed eight epochs of high-resolution spectra obtained with the ESPRESSO spectrograph, targeting orbital phases when the dayside is in view. We used a cross-correlation method to search for various atoms, TiO, and VO, and compare the results to models. We constrained the velocities and phase function of the emission signal using a Bayesian framework.
Results. We report significant detections of Ca I, V I, Cr I, Mn I, Fe I, Co I, and Ni I, but not Ti or TiO. Models containing titanium are unable to reproduce the data. The detected signals are consistent with the known orbital and systemic velocities and with peak emission originating from the substellar point.
Conclusions. We find that titanium is depleted from regions of the atmosphere where transmission and emission spectroscopy are sensitive. Supported by recent HST observations of the nightside, we interpret this as evidence for the nightside condensation of titanium, which prevents it from being mixed back into the upper layers of the atmosphere elsewhere on the planet. Species with lower condensation temperatures are unaffected, implying that sharp chemical transitions exist between ultra-hot Jupiters that have slight differences in temperature or dynamical properties. As TiO can act as a strong source of stratospheric heating, cold-trapping creates a coupling between the thermal structures on the dayside and nightside, and thus condensation chemistry needs to be included in global circulation models. Observed elemental abundances in hot Jupiters will not reliably be representative of bulk abundances unless nightside condensation is robustly accounted for or the planet is hot enough to avoid nightside cold traps entirely. Secondary eclipse observations by JWST/NIRISS have the potential to confirm an absence of TiO bands at red-optical wavelengths. We also find that the abundance ratios of metal oxides to their atomic metals (e.g., TiO/Ti) depend strongly on the atmospheric C/O ratio, and that planetary rotation may significantly lower the apparent orbital velocity of the emission signal.
Interacting supernovae from wide massive binary systems
Authors: Ercolino A. , Jin H. , Langer N. , Dessart L. 
Published: February 2024

Context. The features in the light curves and spectra of many Type I and Type II supernovae (SNe) can be understood by assuming an interaction of the SN ejecta with circumstellar matter (CSM) surrounding the progenitor star. This suggests that many massive stars may undergo various degrees of envelope stripping shortly before exploding, and may therefore produce a considerable diversity in their pre-explosion CSM properties.
Aims. We explore a generic set of about 100 detailed massive binary evolution models in order to characterize the amount of envelope stripping and the expected CSM configurations.
Methods. Our binary models were computed with the MESA stellar evolution code, considering an initial primary star mass of 12.6 M⊙ and secondaries with initial masses of between ∼12 M⊙ and ∼1.3 M⊙, and focus on initial orbital periods above ∼500 d. We compute these models up to the time of iron core collapse in the primary.
Results. Our models exhibit varying degrees of stripping due to mass transfer, resulting in SN progenitor models ranging from fully stripped helium stars to stars that have not been stripped at all. We find that Roche lobe overflow often leads to incomplete stripping of the mass donor, resulting in a large variety of pre-SN envelope masses. In many of our models, the red supergiant (RSG) donor stars undergo core collapse during Roche lobe overflow, with mass transfer and therefore system mass-loss rates of up to 0.01 M⊙ yr−1 at that time. The corresponding CSM densities are similar to those inferred for Type IIn SNe, such as SN 1998S. In other cases, the mass transfer becomes unstable, leading to a common-envelope phase at such late time that the mass donor explodes before the common envelope is fully ejected or the system has merged. We argue that this may cause significant pre-SN variability, as witnessed for example in SN 2020tlf. Other models suggest a common-envelope ejection just centuries before core collapse, which may lead to the strongest interactions, as observed in superluminous Type IIn SNe, such as SN 1994W and SN 2006gy.
Conclusions. Wide massive binaries exhibit properties that may not only explain the diverse envelope stripping inferred in Type Ib, IIb, IIL, and IIP SNe, but also offer a natural framework to understand a broad range of hydrogen-rich interacting SNe. On the other hand, the flash features observed in many Type IIP SNe, such as SN 2013fs, may indicate that RSG atmospheres are more extended than currently assumed; this could enhance the parameter space for wide binary interaction.
Grain size effects on the infrared spectrum of mineral mixtures with dark components: New laboratory experiments to interpret low-albedo rocky planetary surfaces
Authors: Poggiali G. , Fossi L. , Wargnier A. , Beccarelli J. , Brucato J. R. , Barucci M. A. , Beck P. , Matsuoka M. , Nakamura T. , Merlin F. , Fornasier S. , Pajola M. , Doressoundiram A. , Gautier T. , David G. 
Published: February 2024

Context. A number of bodies in the Solar System are characterized by dark surfaces, from carbonaceous asteroids to the enigmatic surface of Phobos and Deimos. Our understanding of the spectroscopic behavior of low-albedo surfaces remains incomplete. To improve the interpretation of remote sensing data, laboratory studies continue to serve as a pivotal tool for unveiling the physical state and composition of such surfaces.
Aims. Several processes can be simulated in the laboratory, however, the preparation and analysis of a complex mixing of analog material is one of the most fundamental among them, while also being one of the most complex when multiple components are used. In this work, we aim to study how dark material mixed with basaltic material at different grain sizes can affect the spectroscopic features from the near- to mid- infrared (1.25–25 µm).
Methods. Our sample set includes four series of basaltic mix (feldspar and pyroxene) at different grain sizes from <50 µm to 1000 µm, mixed with amorphous carbon at increasing weight percentages ranging from 1% to 50%. We analyzed several features on the spectrum of each mineral mixture. In particular, we investigated the behavior of the: (i) near-infrared slope; (ii) 2.7 µm OH-stretching band; (iii) Christiansen features; and (iv) Reststrahlen band and Transparency feature.
Results. The measurements presented in this work, which take into account a large wavelength range for the first time, point toward a critical effect of dark material, but with a different outcomes for each grain size. Some of the most interesting results involve the slope trend of modification with dark material and the variant behavior of the Reststrahlen band and Transparency feature.
Conclusions. This dataset will offer a key support in the interpretation of data collected on dark surfaces by past and future space missions. This knowledge will be also important in the context of linking analyses of returned samples with remote sensing data collected on planetary surfaces.
Horizontally polarized kink oscillations supported by solar coronal loops in an asymmetric environment
Authors: Shi Mijie , Li Bo , Yuan Shengju 
Published: February 2024

Context. Kink oscillations are ubiquitously observed in solar coronal loops, and understanding them is crucial in the contexts of coronal seismology and atmospheric heating.
Aims. We studied kink modes supported by a straight coronal loop embedded in an asymmetric environment using 3D magnetohydrodynamic simulations.
Methods. We implemented the asymmetric effect by setting different exterior densities below and above the loop interior and initiated the simulation using a kink-like velocity perturbation perpendicular to the loop plane, mimicking the frequently measured horizontally polarized kink modes.
Results. We find that the external velocity fields show fan-blade structures propagating in the azimuthal direction as a result of the successive excitation of higher azimuthal Fourier modes. Resonant absorption and phase-mixing can still occur despite an asymmetric environment, leading to the development of small-scale structures at loop boundaries. These small-scale structures nonetheless develop asymmetrically at the upper and lower boundaries due to the different gradients of the Alfvén speed.
Conclusions. These findings enrich our understanding of kink modes in coronal loops embedded within an asymmetric environment, providing insights that will be helpful for future high-resolution observations.
Bayesian test of Brans–Dicke theories with planetary ephemerides: Investigating the strong equivalence principle
Authors: Mariani V. , Minazzoli O. , Fienga A. , Laskar J. , Gastineau M. 
Published: February 2024

Aims. We are testing the Brans–Dicke class of scalar tensor theories with planetary ephemerides.
Methods. In this work, we apply our recently proposed Bayesian methodology to the Brans–Dicke case, with an emphasis on the issue of the strong equivalence principle (SEP).
Results. We use an MCMC approach coupled to full, consistent planetary ephemeris construction (from point-mass body integration to observational fit) and compare the posterior distributions obtained with and without the introduction of potential violations of the SEP.
Conclusions. We observe a shift in the confidence levels of the posteriors obtained. We interpret this shift as marginal evidence that the effect of violation of the SEP can no longer be assumed to be negligible in planetary ephemerides with the current data. We also notably report that the constraint on the Brans–Dicke parameter with planetary ephemerides is getting closer to the figure reported from the Cassini spacecraft alone, and also to the constraints from pulsars. We anticipate that data from future spacecraft missions, such as BepiColombo, will significantly enhance the constraints based on planetary ephemerides.
European VLBI Network observations of the peculiar radio source 4C 35.06 overlapping with a compact group of nine galaxies
Authors: Veres P. M. , Gabányi K. É. , Frey S. , Paragi Z. , An T. , Bagchi J. , Bogdán Á. , Biju K. G. , Kun E. , Jacob J. , Adebahr B. 
Published: February 2024

Context. According to the hierarchical structure formation model, brightest cluster galaxies (BCGs) evolve into the most luminous and massive galaxies in the Universe through multiple merger events. The peculiar radio source 4C 35.06 is located at the core of the galaxy cluster Abell 407, overlapping with a compact group of nine galaxies. Low-frequency radio observations have revealed a helical, steep-spectrum, kiloparsec-scale jet structure and inner lobes with less steep spectra, compatible with a recurring active galactic nucleus (AGN) activity scenario. However, the host galaxy of the AGN responsible for the detected radio emission remained unclear.
Aims. We aim to identify the host of 4C 35.06 by studying the object at high angular resolution and thereby confirm the recurrent AGN activity scenario.
Methods. To reveal the host of the radio source, we carried out very long baseline interferometry (VLBI) observations with the European VLBI Network of the nine galaxies in the group at 1.7 and 4.9 GHz.
Results. We detected compact radio emission from an AGN located between the two inner lobes at both observing frequencies. In addition, we detected another galaxy at 1.7 GHz, whose position appears more consistent with the principal jet axis and is located closer to the low-frequency radio peak of 4C 35.06. The presence of another radio-loud AGN in the nonet sheds new light on the BCG formation and provides an alternative scenario in which not just one but two AGNs are responsible for the complex large-scale radio structure.